Starting phenix.real_space_refine on Wed Aug 27 01:25:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2u_43759/08_2025/8w2u_43759_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2u_43759/08_2025/8w2u_43759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w2u_43759/08_2025/8w2u_43759_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2u_43759/08_2025/8w2u_43759_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w2u_43759/08_2025/8w2u_43759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2u_43759/08_2025/8w2u_43759.map" } resolution = 2.46 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= 0.013 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: 5 Type Number sf(0) Gaussians Zn 20 6.06 5 S 260 5.16 5 C 28400 2.51 5 N 8160 2.21 5 O 7980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 161 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: 44820 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1632 SG CYS A1081 132.745 97.600 12.879 1.00 96.61 S ATOM 1692 SG CYS A1089 130.547 99.924 10.625 1.00 96.61 S ATOM 1718 SG CYS A1092 129.580 96.700 11.019 1.00103.27 S ATOM 3872 SG CYS B1081 127.735 44.620 26.787 1.00 89.75 S ATOM 3932 SG CYS B1089 128.578 47.494 24.398 1.00 93.27 S ATOM 3958 SG CYS B1092 124.918 46.490 25.013 1.00 93.88 S ATOM 6112 SG CYS C1081 83.220 16.401 39.714 1.00 80.55 S ATOM 6172 SG CYS C1089 86.230 17.462 37.978 1.00 85.16 S ATOM 6198 SG CYS C1092 83.102 19.547 37.691 1.00 86.35 S ATOM 8352 SG CYS D1081 33.711 34.155 53.980 1.00 82.72 S ATOM 8412 SG CYS D1089 36.607 32.825 51.599 1.00 84.44 S ATOM 10592 SG CYS E1081 17.957 85.077 67.484 1.00 76.76 S ATOM 10652 SG CYS E1089 18.190 81.896 65.416 1.00 74.66 S ATOM 10678 SG CYS E1092 21.249 84.271 65.760 1.00 77.36 S ATOM 12832 SG CYS F1081 48.060 128.830 81.219 1.00 65.06 S ATOM 12892 SG CYS F1089 45.889 126.447 79.136 1.00 70.33 S ATOM 12918 SG CYS F1092 49.533 125.682 79.585 1.00 66.86 S ATOM 15072 SG CYS G1081 100.732 131.288 94.901 1.00 69.37 S ATOM 15132 SG CYS G1089 97.544 131.666 92.819 1.00 62.24 S ATOM 15158 SG CYS G1092 98.256 128.428 94.537 1.00 74.33 S ATOM 17312 SG CYS H1081 134.712 90.949 108.405 1.00 76.04 S ATOM 17372 SG CYS H1089 133.119 93.641 106.260 1.00 72.94 S ATOM 17398 SG CYS H1092 131.338 90.255 106.809 1.00 71.64 S ATOM 19552 SG CYS I1081 123.370 38.589 122.135 1.00 80.31 S ATOM 19612 SG CYS I1089 124.736 41.210 120.088 1.00 76.41 S ATOM 19638 SG CYS I1092 121.171 40.704 120.242 1.00 81.94 S ATOM 21792 SG CYS J1081 76.004 15.759 135.530 1.00 81.70 S ATOM 21852 SG CYS J1089 79.175 16.742 133.621 1.00 84.35 S ATOM 21878 SG CYS J1092 76.272 19.244 133.901 1.00 85.87 S ATOM 24032 SG CYS L1081 136.060 83.319 173.841 1.00 81.93 S ATOM 24092 SG CYS L1089 135.568 80.308 176.048 1.00 74.97 S ATOM 24118 SG CYS L1092 132.656 82.806 175.529 1.00 84.87 S ATOM 26272 SG CYS M1081 106.520 128.075 160.426 1.00 67.70 S ATOM 26332 SG CYS M1089 108.867 125.871 162.146 1.00 72.39 S ATOM 26358 SG CYS M1092 105.702 124.659 161.500 1.00 73.67 S ATOM 28512 SG CYS N1081 54.495 131.643 146.533 1.00 64.32 S ATOM 28572 SG CYS N1089 57.507 132.131 148.617 1.00 67.31 S ATOM 28598 SG CYS N1092 55.891 128.801 148.546 1.00 76.21 S ATOM 30752 SG CYS O1081 19.539 92.128 132.800 1.00 71.48 S ATOM 30812 SG CYS O1089 21.032 94.795 135.043 1.00 79.20 S ATOM 30838 SG CYS O1092 22.719 91.450 134.497 1.00 71.01 S ATOM 32992 SG CYS P1081 29.428 39.810 118.980 1.00 67.38 S ATOM 33052 SG CYS P1089 28.074 42.764 120.913 1.00 65.11 S ATOM 33078 SG CYS P1092 31.661 41.967 120.868 1.00 67.73 S ATOM 35232 SG CYS Q1081 76.449 15.867 105.523 1.00 77.86 S ATOM 35292 SG CYS Q1089 73.572 16.603 107.441 1.00 66.57 S ATOM 35318 SG CYS Q1092 76.215 18.945 107.426 1.00 66.39 S ATOM 37472 SG CYS R1081 123.894 38.851 92.055 1.00 80.57 S ATOM 37532 SG CYS R1089 121.795 36.803 94.178 1.00 77.11 S ATOM 37558 SG CYS R1092 120.753 40.110 93.295 1.00 79.51 S ATOM 39712 SG CYS S1081 134.758 90.703 78.269 1.00 88.12 S ATOM 39772 SG CYS S1089 134.773 87.588 80.376 1.00 84.54 S ATOM 39798 SG CYS S1092 131.582 89.625 80.009 1.00 89.03 S ATOM 41952 SG CYS T1081 100.078 131.276 64.762 1.00 91.38 S ATOM 42012 SG CYS T1089 102.863 129.844 66.715 1.00 90.76 S ATOM 42038 SG CYS T1092 99.490 128.191 66.752 1.00 86.98 S ATOM 44192 SG CYS U1081 47.944 128.714 51.009 1.00 94.19 S ATOM 44252 SG CYS U1089 51.080 129.170 53.206 1.00 95.00 S ATOM 44278 SG CYS U1092 49.648 125.682 52.582 1.00 96.80 S Time building chain proxies: 10.67, per 1000 atoms: 0.24 Number of scatterers: 44820 At special positions: 0 Unit cell: (155.288, 154.462, 186.676, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 20 29.99 S 260 16.00 O 7980 8.00 N 8160 7.00 C 28400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 1.7 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" ND1 HIS A1084 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1092 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1089 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1081 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" ND1 HIS B1084 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1081 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1089 " pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C1084 " pdb="ZN ZN C1201 " - pdb=" SG CYS C1081 " pdb="ZN ZN C1201 " - pdb=" SG CYS C1092 " pdb="ZN ZN C1201 " - pdb=" SG CYS C1089 " pdb=" ZN D1201 " pdb="ZN ZN D1201 " - pdb=" SG CYS D1081 " pdb="ZN ZN D1201 " - pdb=" SG CYS D1089 " pdb="ZN ZN D1201 " - pdb=" ND1 HIS D1084 " pdb=" ZN E1201 " pdb="ZN ZN E1201 " - pdb=" ND1 HIS E1084 " pdb="ZN ZN E1201 " - pdb=" SG CYS E1081 " pdb="ZN ZN E1201 " - pdb=" SG CYS E1092 " pdb="ZN ZN E1201 " - pdb=" SG CYS E1089 " pdb=" ZN F1201 " pdb="ZN ZN F1201 " - pdb=" ND1 HIS F1084 " pdb="ZN ZN F1201 " - pdb=" SG CYS F1092 " pdb="ZN ZN F1201 " - pdb=" SG CYS F1089 " pdb="ZN ZN F1201 " - pdb=" SG CYS F1081 " pdb=" ZN G1201 " pdb="ZN ZN G1201 " - pdb=" ND1 HIS G1084 " pdb="ZN ZN G1201 " - pdb=" SG CYS G1089 " pdb="ZN ZN G1201 " - pdb=" SG CYS G1081 " pdb="ZN ZN G1201 " - pdb=" SG CYS G1092 " pdb=" ZN H1201 " pdb="ZN ZN H1201 " - pdb=" ND1 HIS H1084 " pdb="ZN ZN H1201 " - pdb=" SG CYS H1081 " pdb="ZN ZN H1201 " - pdb=" SG CYS H1092 " pdb="ZN ZN H1201 " - pdb=" SG CYS H1089 " pdb=" ZN I1201 " pdb="ZN ZN I1201 " - pdb=" SG CYS I1092 " pdb="ZN ZN I1201 " - pdb=" SG CYS I1089 " pdb="ZN ZN I1201 " - pdb=" SG CYS I1081 " pdb="ZN ZN I1201 " - pdb=" ND1 HIS I1084 " pdb=" ZN J1201 " pdb="ZN ZN J1201 " - pdb=" ND1 HIS J1084 " pdb="ZN ZN J1201 " - pdb=" SG CYS J1081 " pdb="ZN ZN J1201 " - pdb=" SG CYS J1089 " pdb="ZN ZN J1201 " - pdb=" SG CYS J1092 " pdb=" ZN L1201 " pdb="ZN ZN L1201 " - pdb=" ND1 HIS L1084 " pdb="ZN ZN L1201 " - pdb=" SG CYS L1081 " pdb="ZN ZN L1201 " - pdb=" SG CYS L1089 " pdb="ZN ZN L1201 " - pdb=" SG CYS L1092 " pdb=" ZN M1201 " pdb="ZN ZN M1201 " - pdb=" ND1 HIS M1084 " pdb="ZN ZN M1201 " - pdb=" SG CYS M1092 " pdb="ZN ZN M1201 " - pdb=" SG CYS M1081 " pdb="ZN ZN M1201 " - pdb=" SG CYS M1089 " pdb=" ZN N1201 " pdb="ZN ZN N1201 " - pdb=" ND1 HIS N1084 " pdb="ZN ZN N1201 " - pdb=" SG CYS N1081 " pdb="ZN ZN N1201 " - pdb=" SG CYS N1092 " pdb="ZN ZN N1201 " - pdb=" SG CYS N1089 " pdb=" ZN O1201 " pdb="ZN ZN O1201 " - pdb=" ND1 HIS O1084 " pdb="ZN ZN O1201 " - pdb=" SG CYS O1092 " pdb="ZN ZN O1201 " - pdb=" SG CYS O1081 " pdb="ZN ZN O1201 " - pdb=" SG CYS O1089 " pdb=" ZN P1201 " pdb="ZN ZN P1201 " - pdb=" SG CYS P1089 " pdb="ZN ZN P1201 " - pdb=" SG CYS P1092 " pdb="ZN ZN P1201 " - pdb=" SG CYS P1081 " pdb="ZN ZN P1201 " - pdb=" NE2 HIS P1084 " pdb=" ZN Q1201 " pdb="ZN ZN Q1201 " - pdb=" SG CYS Q1092 " pdb="ZN ZN Q1201 " - pdb=" SG CYS Q1089 " pdb="ZN ZN Q1201 " - pdb=" SG CYS Q1081 " pdb="ZN ZN Q1201 " - pdb=" ND1 HIS Q1084 " pdb=" ZN R1201 " pdb="ZN ZN R1201 " - pdb=" ND1 HIS R1084 " pdb="ZN ZN R1201 " - pdb=" SG CYS R1092 " pdb="ZN ZN R1201 " - pdb=" SG CYS R1081 " pdb="ZN ZN R1201 " - pdb=" SG CYS R1089 " pdb=" ZN S1201 " pdb="ZN ZN S1201 " - pdb=" ND1 HIS S1084 " pdb="ZN ZN S1201 " - pdb=" SG CYS S1081 " pdb="ZN ZN S1201 " - pdb=" SG CYS S1092 " pdb="ZN ZN S1201 " - pdb=" SG CYS S1089 " pdb=" ZN T1201 " pdb="ZN ZN T1201 " - pdb=" ND1 HIS T1084 " pdb="ZN ZN T1201 " - pdb=" SG CYS T1081 " pdb="ZN ZN T1201 " - pdb=" SG CYS T1092 " pdb="ZN ZN T1201 " - pdb=" SG CYS T1089 " pdb=" ZN U1201 " pdb="ZN ZN U1201 " - pdb=" ND1 HIS U1084 " pdb="ZN ZN U1201 " - pdb=" SG CYS U1092 " pdb="ZN ZN U1201 " - pdb=" SG CYS U1089 " pdb="ZN ZN U1201 " - pdb=" SG CYS U1081 " Number of angles added : 57 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: 312 helices and 40 sheets defined 44.4% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 876 through 885 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 Processing helix chain 'A' and resid 1002 through 1020 Processing helix chain 'A' and resid 1035 through 1043 removed outlier: 3.883A pdb=" N HIS A1041 " --> pdb=" O ASN A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 3.868A pdb=" N HIS A1048 " --> pdb=" O ASP A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1070 removed outlier: 3.610A 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: 3.508A pdb=" N LEU B 885 " --> pdb=" O PHE B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 889 No H-bonds generated for 'chain 'B' and resid 887 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 916 Processing helix chain 'B' and resid 919 through 935 removed outlier: 3.513A pdb=" N ARG B 923 " --> pdb=" O ALA B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 940 Processing helix chain 'B' and resid 941 through 946 removed outlier: 3.503A pdb=" N THR B 945 " --> pdb=" O ASN B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 974 Processing helix chain 'B' and resid 1002 through 1020 Processing helix chain 'B' and resid 1035 through 1043 removed outlier: 3.812A pdb=" N HIS B1041 " --> pdb=" O ASN B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1049 Processing helix chain 'B' and resid 1064 through 1069 removed outlier: 3.539A pdb=" N SER B1068 " --> pdb=" O ASN B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1072 No H-bonds generated for 'chain 'B' and resid 1070 through 1072' 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 removed outlier: 3.519A pdb=" N LEU C 885 " --> pdb=" O PHE C 881 " (cutoff:3.500A) 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 898 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: 3.527A pdb=" N THR C 975 " --> pdb=" O GLU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1020 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 1069 Processing helix chain 'C' and resid 1070 through 1072 No H-bonds generated for 'chain 'C' and resid 1070 through 1072' 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: 3.544A 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 removed outlier: 3.642A pdb=" N HIS D1041 " --> pdb=" O ASN D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1049 Processing helix chain 'D' and resid 1064 through 1069 Processing helix chain 'D' and resid 1070 through 1072 No H-bonds generated for 'chain 'D' and resid 1070 through 1072' 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 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 916 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 974 Processing helix chain 'E' and resid 1002 through 1019 Processing helix chain 'E' and resid 1035 through 1043 removed outlier: 3.564A pdb=" N HIS E1041 " --> pdb=" O ASN E1037 " (cutoff:3.500A) Processing helix chain 'E' and resid 1045 through 1049 Processing helix chain 'E' and resid 1064 through 1070 removed outlier: 3.542A pdb=" N SER E1068 " --> pdb=" O ASN E1064 " (cutoff:3.500A) 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 886 Processing helix chain 'F' and resid 887 through 889 No H-bonds generated for 'chain 'F' and resid 887 through 889' Processing helix chain 'F' and resid 890 through 898 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 946 Processing helix chain 'F' and resid 962 through 975 removed outlier: 3.554A pdb=" N THR F 975 " --> pdb=" O GLU F 971 " (cutoff:3.500A) Processing helix chain 'F' and resid 1002 through 1019 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 1069 removed outlier: 3.562A pdb=" N SER F1068 " --> pdb=" O ASN F1064 " (cutoff:3.500A) Processing helix chain 'F' and resid 1070 through 1072 No H-bonds generated for 'chain 'F' and resid 1070 through 1072' 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 removed outlier: 3.607A pdb=" N LEU G 885 " --> pdb=" O PHE G 881 " (cutoff:3.500A) 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: 3.599A pdb=" N THR G 975 " --> pdb=" O GLU G 971 " (cutoff:3.500A) Processing helix chain 'G' and resid 1002 through 1020 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 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 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 946 Processing helix chain 'H' and resid 962 through 974 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 removed outlier: 3.582A pdb=" N GLN H1070 " --> pdb=" O SER H1066 " (cutoff:3.500A) 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 Processing helix chain 'I' and resid 887 through 889 No H-bonds generated for 'chain 'I' and resid 887 through 889' Processing helix chain 'I' and resid 890 through 898 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 removed outlier: 3.506A pdb=" N ARG I 923 " --> pdb=" O ALA I 919 " (cutoff:3.500A) Processing helix chain 'I' and resid 937 through 940 Processing helix chain 'I' and resid 941 through 947 Processing helix chain 'I' and resid 962 through 975 removed outlier: 3.625A pdb=" N THR I 975 " --> pdb=" O GLU I 971 " (cutoff:3.500A) Processing helix chain 'I' and resid 1003 through 1020 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 1069 Processing helix chain 'I' and resid 1070 through 1072 No H-bonds generated for 'chain 'I' and resid 1070 through 1072' 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 886 removed outlier: 3.523A pdb=" N LEU J 885 " --> pdb=" O PHE J 881 " (cutoff:3.500A) Processing helix chain 'J' and resid 887 through 889 No H-bonds generated for 'chain 'J' and resid 887 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 946 Processing helix chain 'J' and resid 962 through 975 removed outlier: 3.531A pdb=" N THR J 975 " --> pdb=" O GLU J 971 " (cutoff:3.500A) Processing helix chain 'J' and resid 1002 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: 3.608A 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 916 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: 3.516A pdb=" N THR L 945 " --> pdb=" O ASN L 941 " (cutoff:3.500A) Processing helix chain 'L' and resid 962 through 975 removed outlier: 3.695A pdb=" N THR L 975 " --> pdb=" O GLU L 971 " (cutoff:3.500A) Processing helix chain 'L' and resid 1002 through 1019 removed outlier: 3.556A pdb=" N GLU L1019 " --> pdb=" O GLU L1015 " (cutoff:3.500A) Processing helix chain 'L' and resid 1020 through 1023 Processing helix chain 'L' and resid 1035 through 1043 removed outlier: 3.576A pdb=" N HIS L1041 " --> pdb=" O ASN L1037 " (cutoff:3.500A) Processing helix chain 'L' and resid 1045 through 1049 Processing helix chain 'L' and resid 1064 through 1069 Processing helix chain 'L' and resid 1070 through 1072 No H-bonds generated for 'chain 'L' and resid 1070 through 1072' 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 886 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 898 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 946 removed outlier: 3.562A pdb=" N THR M 945 " --> pdb=" O ASN M 941 " (cutoff:3.500A) Processing helix chain 'M' and resid 962 through 975 removed outlier: 3.560A pdb=" N THR M 975 " --> pdb=" O GLU M 971 " (cutoff:3.500A) Processing helix chain 'M' and resid 1002 through 1020 Processing helix chain 'M' and resid 1035 through 1043 removed outlier: 3.856A pdb=" N HIS M1041 " --> pdb=" O ASN M1037 " (cutoff:3.500A) Processing helix chain 'M' and resid 1045 through 1049 Processing helix chain 'M' and resid 1064 through 1069 removed outlier: 3.554A pdb=" N SER M1068 " --> pdb=" O ASN M1064 " (cutoff:3.500A) Processing helix chain 'M' and resid 1070 through 1072 No H-bonds generated for 'chain 'M' and resid 1070 through 1072' Processing helix chain 'M' and resid 1074 through 1078 removed outlier: 3.662A pdb=" N GLY M1078 " --> pdb=" O ILE M1075 " (cutoff:3.500A) 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 removed outlier: 3.531A pdb=" N LEU N 885 " --> pdb=" O PHE N 881 " (cutoff:3.500A) 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: 3.633A pdb=" N THR N 975 " --> pdb=" O GLU N 971 " (cutoff:3.500A) Processing helix chain 'N' and resid 1002 through 1019 removed outlier: 3.659A 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: 3.568A pdb=" N GLN N1070 " --> pdb=" O SER N1066 " (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 916 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 removed outlier: 3.565A pdb=" N THR O 945 " --> pdb=" O ASN O 941 " (cutoff:3.500A) Processing helix chain 'O' and resid 962 through 975 removed outlier: 3.573A pdb=" N THR O 975 " --> pdb=" O GLU O 971 " (cutoff:3.500A) Processing helix chain 'O' and resid 1002 through 1019 removed outlier: 3.691A pdb=" N GLU O1019 " --> pdb=" O GLU O1015 " (cutoff:3.500A) 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 removed outlier: 3.539A pdb=" N SER O1068 " --> pdb=" O ASN O1064 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN O1070 " --> pdb=" O SER O1066 " (cutoff:3.500A) 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 removed outlier: 3.535A pdb=" N LEU P 885 " --> pdb=" O PHE P 881 " (cutoff:3.500A) 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 898 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 removed outlier: 3.503A pdb=" N ARG P 923 " --> pdb=" O ALA P 919 " (cutoff:3.500A) Processing helix chain 'P' and resid 937 through 940 Processing helix chain 'P' and resid 941 through 946 Processing helix chain 'P' and resid 962 through 975 removed outlier: 3.660A pdb=" N THR P 975 " --> pdb=" O GLU P 971 " (cutoff:3.500A) Processing helix chain 'P' and resid 1003 through 1019 Processing helix chain 'P' and resid 1035 through 1043 removed outlier: 3.858A pdb=" N HIS P1041 " --> pdb=" O ASN P1037 " (cutoff:3.500A) Processing helix chain 'P' and resid 1045 through 1049 Processing helix chain 'P' and resid 1064 through 1069 removed outlier: 3.509A pdb=" N SER P1068 " --> pdb=" O ASN P1064 " (cutoff:3.500A) Processing helix chain 'P' and resid 1070 through 1072 No H-bonds generated for 'chain 'P' and resid 1070 through 1072' 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 886 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 898 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 Processing helix chain 'Q' and resid 1003 through 1019 Processing helix chain 'Q' and resid 1035 through 1043 removed outlier: 3.889A pdb=" N HIS Q1041 " --> pdb=" O ASN Q1037 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1045 through 1049 Processing helix chain 'Q' and resid 1064 through 1069 Processing helix chain 'Q' and resid 1070 through 1072 No H-bonds generated for 'chain 'Q' and resid 1070 through 1072' 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 removed outlier: 3.545A pdb=" N PHE R 894 " --> pdb=" O LEU R 890 " (cutoff:3.500A) Processing helix chain 'R' and resid 900 through 905 Processing helix chain 'R' and resid 908 through 916 Processing helix chain 'R' and resid 919 through 937 removed outlier: 3.773A pdb=" N GLN R 937 " --> pdb=" O LEU R 933 " (cutoff:3.500A) Processing helix chain 'R' and resid 938 through 940 No H-bonds generated for 'chain 'R' and resid 938 through 940' Processing helix chain 'R' and resid 941 through 946 Processing helix chain 'R' and resid 962 through 975 Processing helix chain 'R' and resid 1002 through 1019 removed outlier: 3.606A pdb=" N GLU R1019 " --> pdb=" O GLU R1015 " (cutoff:3.500A) Processing helix chain 'R' and resid 1035 through 1043 removed outlier: 3.628A pdb=" N HIS R1041 " --> pdb=" O ASN R1037 " (cutoff:3.500A) Processing helix chain 'R' and resid 1045 through 1049 Processing helix chain 'R' and resid 1064 through 1070 removed outlier: 3.709A pdb=" N GLN R1070 " --> pdb=" O SER R1066 " (cutoff:3.500A) 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 removed outlier: 3.534A pdb=" N THR S 945 " --> pdb=" O ASN S 941 " (cutoff:3.500A) Processing helix chain 'S' and resid 962 through 975 removed outlier: 3.592A pdb=" N THR S 975 " --> pdb=" O GLU S 971 " (cutoff:3.500A) Processing helix chain 'S' and resid 1003 through 1019 removed outlier: 3.550A pdb=" N GLU S1019 " --> pdb=" O GLU S1015 " (cutoff:3.500A) 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 1069 Processing helix chain 'S' and resid 1070 through 1072 No H-bonds generated for 'chain 'S' and resid 1070 through 1072' 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 898 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 946 Processing helix chain 'T' and resid 962 through 975 Processing helix chain 'T' and resid 1003 through 1019 Processing helix chain 'T' and resid 1035 through 1043 removed outlier: 3.808A pdb=" N HIS T1041 " --> pdb=" O ASN T1037 " (cutoff:3.500A) Processing helix chain 'T' and resid 1045 through 1049 Processing helix chain 'T' and resid 1064 through 1070 removed outlier: 3.758A pdb=" N SER T1068 " --> pdb=" O ASN T1064 " (cutoff:3.500A) 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 885 removed outlier: 3.508A pdb=" N LEU U 885 " --> pdb=" O PHE U 881 " (cutoff:3.500A) 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 974 Processing helix chain 'U' and resid 1002 through 1019 Processing helix chain 'U' and resid 1035 through 1043 removed outlier: 4.231A pdb=" N HIS U1041 " --> pdb=" O ASN U1037 " (cutoff:3.500A) Processing helix chain 'U' and resid 1045 through 1049 Processing helix chain 'U' and resid 1064 through 1070 removed outlier: 3.743A pdb=" N GLN U1070 " --> pdb=" O SER U1066 " (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: 5.296A pdb=" N TYR A 992 " --> pdb=" O MET A1158 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N MET A1158 " --> pdb=" O TYR A 992 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE A 994 " --> pdb=" O GLN A1156 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLN A1156 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLU A1150 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA A1147 " --> pdb=" O THR A1102 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR A1102 " --> pdb=" O ALA A1147 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG A1100 " --> pdb=" O PRO A1149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1059 through 1061 Processing sheet with id=AA3, first strand: chain 'B' and resid 954 through 957 removed outlier: 3.569A pdb=" N ARG B 991 " --> pdb=" O MET B1158 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR B1154 " --> pdb=" O LEU B 995 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 997 " --> pdb=" O LEU B1152 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B1152 " --> pdb=" O ILE B 997 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS B 999 " --> pdb=" O GLU B1150 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLU B1150 " --> pdb=" O LYS B 999 " (cutoff:3.500A) removed outlier: 9.480A pdb=" N CYS B1001 " --> pdb=" O TYR B1148 " (cutoff:3.500A) removed outlier: 12.221A pdb=" N TYR B1148 " --> pdb=" O CYS B1001 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA B1147 " --> pdb=" O THR B1102 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR B1102 " --> pdb=" O ALA B1147 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG B1100 " --> pdb=" O PRO B1149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1050 through 1053 removed outlier: 3.974A pdb=" N GLY B1058 " --> pdb=" O TYR B1050 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY B1056 " --> pdb=" O GLY B1052 " (cutoff:3.500A) removed outlier: 6.086A 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: 5.545A pdb=" N TYR C 992 " --> pdb=" O MET C1158 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N MET C1158 " --> pdb=" O TYR C 992 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE C 994 " --> pdb=" O GLN C1156 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN C1156 " --> pdb=" O ILE C 994 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU C1150 " --> pdb=" O VAL C1000 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA C1147 " --> pdb=" O THR C1102 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR C1102 " --> pdb=" O ALA C1147 " (cutoff:3.500A) removed outlier: 6.673A 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: 6.159A 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: 6.161A pdb=" N TYR D 992 " --> pdb=" O MET D1158 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N MET D1158 " --> pdb=" O TYR D 992 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE D 994 " --> pdb=" O GLN D1156 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN D1156 " --> pdb=" O ILE D 994 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLU D1150 " --> pdb=" O VAL D1000 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA D1147 " --> pdb=" O THR D1102 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR D1102 " --> pdb=" O ALA D1147 " (cutoff:3.500A) removed outlier: 6.710A 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: 5.671A pdb=" N ILE D1051 " --> pdb=" O GLY D1058 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY D1058 " --> pdb=" O ILE D1051 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D1053 " --> pdb=" O GLY D1056 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE D1107 " --> pdb=" O THR D1126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 954 through 957 removed outlier: 5.391A pdb=" N ILE E 994 " --> pdb=" O GLN E1156 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN E1156 " --> pdb=" O ILE E 994 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLU E1150 " --> pdb=" O VAL E1000 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA E1147 " --> pdb=" O THR E1102 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR E1102 " --> pdb=" O ALA E1147 " (cutoff:3.500A) removed outlier: 6.461A 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: 6.066A 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: 5.172A pdb=" N ILE F 994 " --> pdb=" O GLN F1156 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN F1156 " --> pdb=" O ILE F 994 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU F1150 " --> pdb=" O VAL F1000 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA F1147 " --> pdb=" O THR F1102 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR F1102 " --> pdb=" O ALA F1147 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG F1100 " --> pdb=" O PRO F1149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 1059 through 1062 removed outlier: 6.119A 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: 4.208A pdb=" N ARG G 991 " --> pdb=" O MET G1158 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR G1154 " --> pdb=" O LEU G 995 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE G 997 " --> pdb=" O LEU G1152 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU G1152 " --> pdb=" O ILE G 997 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS G 999 " --> pdb=" O GLU G1150 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLU G1150 " --> pdb=" O LYS G 999 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N CYS G1001 " --> pdb=" O TYR G1148 " (cutoff:3.500A) removed outlier: 12.459A pdb=" N TYR G1148 " --> pdb=" O CYS G1001 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA G1147 " --> pdb=" O THR G1102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR G1102 " --> pdb=" O ALA G1147 " (cutoff:3.500A) removed outlier: 6.715A 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: 5.453A pdb=" N ILE G1051 " --> pdb=" O GLY G1058 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY G1058 " --> pdb=" O ILE G1051 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY G1053 " --> pdb=" O GLY G1056 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 954 through 957 removed outlier: 6.288A pdb=" N TYR H 992 " --> pdb=" O MET H1158 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET H1158 " --> pdb=" O TYR H 992 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE H 994 " --> pdb=" O GLN H1156 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLN H1156 " --> pdb=" O ILE H 994 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLU H1150 " --> pdb=" O VAL H1000 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA H1147 " --> pdb=" O THR H1102 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR H1102 " --> pdb=" O ALA H1147 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG H1100 " --> pdb=" O PRO H1149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 1059 through 1061 Processing sheet with id=AB8, first strand: chain 'I' and resid 953 through 957 removed outlier: 3.858A pdb=" N ARG I 991 " --> pdb=" O MET I1158 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR I1154 " --> pdb=" O LEU I 995 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE I 997 " --> pdb=" O LEU I1152 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU I1152 " --> pdb=" O ILE I 997 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS I 999 " --> pdb=" O GLU I1150 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLU I1150 " --> pdb=" O LYS I 999 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N CYS I1001 " --> pdb=" O TYR I1148 " (cutoff:3.500A) removed outlier: 12.436A pdb=" N TYR I1148 " --> pdb=" O CYS I1001 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA I1147 " --> pdb=" O THR I1102 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR I1102 " --> pdb=" O ALA I1147 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG I1100 " --> pdb=" O PRO I1149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 1050 through 1053 removed outlier: 4.149A pdb=" N GLY I1058 " --> pdb=" O TYR I1050 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY I1052 " --> pdb=" O GLY I1056 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY I1056 " --> pdb=" O GLY I1052 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 954 through 957 removed outlier: 5.539A pdb=" N TYR J 992 " --> pdb=" O MET J1158 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N MET J1158 " --> pdb=" O TYR J 992 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE J 994 " --> pdb=" O GLN J1156 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN J1156 " --> pdb=" O ILE J 994 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU J1150 " --> pdb=" O VAL J1000 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA J1147 " --> pdb=" O THR J1102 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR J1102 " --> pdb=" O ALA J1147 " (cutoff:3.500A) removed outlier: 6.689A 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 removed outlier: 6.142A pdb=" N PHE J1107 " --> pdb=" O THR J1126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 954 through 957 removed outlier: 6.063A pdb=" N TYR L 992 " --> pdb=" O MET L1158 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N MET L1158 " --> pdb=" O TYR L 992 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE L 994 " --> pdb=" O GLN L1156 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLN L1156 " --> pdb=" O ILE L 994 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU L1150 " --> pdb=" O VAL L1000 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA L1147 " --> pdb=" O THR L1102 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR L1102 " --> pdb=" O ALA L1147 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG L1100 " --> pdb=" O PRO L1149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 1050 through 1053 removed outlier: 3.877A pdb=" N GLY L1058 " --> pdb=" O TYR L1050 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLY L1052 " --> pdb=" O GLY L1056 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY L1056 " --> pdb=" O GLY L1052 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE L1107 " --> pdb=" O THR L1126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 954 through 957 removed outlier: 5.141A pdb=" N ILE M 994 " --> pdb=" O GLN M1156 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN M1156 " --> pdb=" O ILE M 994 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU M1150 " --> pdb=" O VAL M1000 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA M1147 " --> pdb=" O THR M1102 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR M1102 " --> pdb=" O ALA M1147 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG M1100 " --> pdb=" O PRO M1149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 1059 through 1062 removed outlier: 6.232A 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: 4.184A pdb=" N ARG N 991 " --> pdb=" O MET N1158 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR N1154 " --> pdb=" O LEU N 995 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE N 997 " --> pdb=" O LEU N1152 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU N1152 " --> pdb=" O ILE N 997 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS N 999 " --> pdb=" O GLU N1150 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N GLU N1150 " --> pdb=" O LYS N 999 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N CYS N1001 " --> pdb=" O TYR N1148 " (cutoff:3.500A) removed outlier: 12.413A pdb=" N TYR N1148 " --> pdb=" O CYS N1001 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALA N1147 " --> pdb=" O THR N1102 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR N1102 " --> pdb=" O ALA N1147 " (cutoff:3.500A) removed outlier: 6.531A 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: 6.117A 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: 5.321A pdb=" N ILE O 994 " --> pdb=" O GLN O1156 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN O1156 " --> pdb=" O ILE O 994 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU O1150 " --> pdb=" O VAL O1000 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA O1147 " --> pdb=" O THR O1102 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N THR O1102 " --> pdb=" O ALA O1147 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG O1100 " --> pdb=" O PRO O1149 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 1059 through 1062 removed outlier: 6.110A pdb=" N PHE O1107 " --> pdb=" O THR O1126 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 953 through 957 removed outlier: 6.905A pdb=" N THR P1154 " --> pdb=" O LEU P 995 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE P 997 " --> pdb=" O LEU P1152 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU P1152 " --> pdb=" O ILE P 997 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS P 999 " --> pdb=" O GLU P1150 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLU P1150 " --> pdb=" O LYS P 999 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N CYS P1001 " --> pdb=" O TYR P1148 " (cutoff:3.500A) removed outlier: 12.409A pdb=" N TYR P1148 " --> pdb=" O CYS P1001 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE P1098 " --> pdb=" O GLU P1150 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU P1152 " --> pdb=" O LEU P1096 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU P1096 " --> pdb=" O LEU P1152 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR P1154 " --> pdb=" O ARG P1094 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG P1094 " --> pdb=" O THR P1154 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 1050 through 1053 removed outlier: 4.040A pdb=" N GLY P1058 " --> pdb=" O TYR P1050 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY P1052 " --> pdb=" O GLY P1056 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLY P1056 " --> pdb=" O GLY P1052 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE P1107 " --> pdb=" O THR P1126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 953 through 957 removed outlier: 5.208A pdb=" N ILE Q 994 " --> pdb=" O GLN Q1156 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN Q1156 " --> pdb=" O ILE Q 994 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU Q1150 " --> pdb=" O VAL Q1000 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N ASN Q1002 " --> pdb=" O TYR Q1148 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N TYR Q1148 " --> pdb=" O ASN Q1002 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA Q1147 " --> pdb=" O THR Q1102 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR Q1102 " --> pdb=" O ALA Q1147 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG Q1100 " --> pdb=" O PRO Q1149 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 1059 through 1062 Processing sheet with id=AD6, first strand: chain 'R' and resid 954 through 957 removed outlier: 5.195A pdb=" N ILE R 994 " --> pdb=" O GLN R1156 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN R1156 " --> pdb=" O ILE R 994 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU R1150 " --> pdb=" O VAL R1000 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA R1147 " --> pdb=" O THR R1102 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR R1102 " --> pdb=" O ALA R1147 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG R1100 " --> pdb=" O PRO R1149 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 1059 through 1062 removed outlier: 6.100A pdb=" N PHE R1107 " --> pdb=" O THR R1126 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 953 through 957 removed outlier: 5.485A pdb=" N TYR S 992 " --> pdb=" O MET S1158 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N MET S1158 " --> pdb=" O TYR S 992 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE S 994 " --> pdb=" O GLN S1156 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN S1156 " --> pdb=" O ILE S 994 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU S1150 " --> pdb=" O VAL S1000 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N ASN S1002 " --> pdb=" O TYR S1148 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N TYR S1148 " --> pdb=" O ASN S1002 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA S1147 " --> pdb=" O THR S1102 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR S1102 " --> pdb=" O ALA S1147 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG S1100 " --> pdb=" O PRO S1149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 1059 through 1062 removed outlier: 6.151A 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: 5.227A pdb=" N TYR T 992 " --> pdb=" O MET T1158 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N MET T1158 " --> pdb=" O TYR T 992 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE T 994 " --> pdb=" O GLN T1156 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN T1156 " --> pdb=" O ILE T 994 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLU T1150 " --> pdb=" O VAL T1000 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N ASN T1002 " --> pdb=" O TYR T1148 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N TYR T1148 " --> pdb=" O ASN T1002 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA T1147 " --> pdb=" O THR T1102 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR T1102 " --> pdb=" O ALA T1147 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG T1100 " --> pdb=" O PRO T1149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 1059 through 1062 removed outlier: 5.970A 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: 3.516A pdb=" N ARG U 991 " --> pdb=" O MET U1158 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR U1154 " --> pdb=" O LEU U 995 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE U 997 " --> pdb=" O LEU U1152 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU U1152 " --> pdb=" O ILE U 997 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS U 999 " --> pdb=" O GLU U1150 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLU U1150 " --> pdb=" O LYS U 999 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N CYS U1001 " --> pdb=" O TYR U1148 " (cutoff:3.500A) removed outlier: 12.241A pdb=" N TYR U1148 " --> pdb=" O CYS U1001 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA U1147 " --> pdb=" O THR U1102 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR U1102 " --> pdb=" O ALA U1147 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG U1100 " --> pdb=" O PRO U1149 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 1059 through 1062 1917 hydrogen bonds defined for protein. 5232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.98 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14996 1.34 - 1.46: 11168 1.46 - 1.59: 19276 1.59 - 1.71: 0 1.71 - 1.83: 420 Bond restraints: 45860 Sorted by residual: bond pdb=" C GLN C1156 " pdb=" N ILE C1157 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.97e-02 2.58e+03 2.44e+00 bond pdb=" CB ARG I1100 " pdb=" CG ARG I1100 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CB GLU N1015 " pdb=" CG GLU N1015 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CB GLN G1146 " pdb=" CG GLN G1146 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" CB ARG P1100 " pdb=" CG ARG P1100 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.66e+00 ... (remaining 45855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 58985 1.32 - 2.64: 2392 2.64 - 3.95: 324 3.95 - 5.27: 32 5.27 - 6.59: 7 Bond angle restraints: 61740 Sorted by residual: angle pdb=" CA PRO E1149 " pdb=" C PRO E1149 " pdb=" N GLU E1150 " ideal model delta sigma weight residual 116.09 119.08 -2.99 9.20e-01 1.18e+00 1.06e+01 angle pdb=" N ASN R1022 " pdb=" CA ASN R1022 " pdb=" CB ASN R1022 " ideal model delta sigma weight residual 113.65 108.90 4.75 1.47e+00 4.63e-01 1.04e+01 angle pdb=" CA PRO P1149 " pdb=" C PRO P1149 " pdb=" N GLU P1150 " ideal model delta sigma weight residual 116.09 118.84 -2.75 9.20e-01 1.18e+00 8.95e+00 angle pdb=" N ASN M 947 " pdb=" CA ASN M 947 " pdb=" CB ASN M 947 " ideal model delta sigma weight residual 113.65 109.40 4.25 1.47e+00 4.63e-01 8.37e+00 angle pdb=" N ASN F 947 " pdb=" CA ASN F 947 " pdb=" CB ASN F 947 " ideal model delta sigma weight residual 113.65 109.42 4.23 1.47e+00 4.63e-01 8.26e+00 ... (remaining 61735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 24250 17.90 - 35.80: 1955 35.80 - 53.69: 619 53.69 - 71.59: 126 71.59 - 89.49: 50 Dihedral angle restraints: 27000 sinusoidal: 10860 harmonic: 16140 Sorted by residual: dihedral pdb=" CA GLU P1018 " pdb=" C GLU P1018 " pdb=" N GLU P1019 " pdb=" CA GLU P1019 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA PHE O1098 " pdb=" C PHE O1098 " pdb=" N CYS O1099 " pdb=" CA CYS O1099 " ideal model delta harmonic sigma weight residual 180.00 -155.23 -24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA PHE E1098 " pdb=" C PHE E1098 " pdb=" N CYS E1099 " pdb=" CA CYS E1099 " ideal model delta harmonic sigma weight residual 180.00 -155.53 -24.47 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 26997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3449 0.030 - 0.061: 2101 0.061 - 0.091: 586 0.091 - 0.121: 247 0.121 - 0.152: 77 Chirality restraints: 6460 Sorted by residual: chirality pdb=" CA GLN G1146 " pdb=" N GLN G1146 " pdb=" C GLN G1146 " pdb=" CB GLN G1146 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA VAL G1000 " pdb=" N VAL G1000 " pdb=" C VAL G1000 " pdb=" CB VAL G1000 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE H1059 " pdb=" N ILE H1059 " pdb=" C ILE H1059 " pdb=" CB ILE H1059 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 6457 not shown) Planarity restraints: 8040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 947 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.06e+00 pdb=" C ASN H 947 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN H 947 " -0.016 2.00e-02 2.50e+03 pdb=" N THR H 948 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 991 " -0.159 9.50e-02 1.11e+02 7.19e-02 4.19e+00 pdb=" NE ARG A 991 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 991 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 991 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 991 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER P1033 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO P1034 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO P1034 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO P1034 " -0.027 5.00e-02 4.00e+02 ... (remaining 8037 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 143 2.51 - 3.11: 32501 3.11 - 3.71: 65943 3.71 - 4.30: 105625 4.30 - 4.90: 171723 Nonbonded interactions: 375935 Sorted by model distance: nonbonded pdb=" OE2 GLU R 964 " pdb=" OH TYR R1151 " model vdw 1.914 3.040 nonbonded pdb=" OG1 THR U 900 " pdb=" OD1 ASP U 902 " model vdw 1.959 3.040 nonbonded pdb=" OG1 THR E 900 " pdb=" OD1 ASP E 902 " model vdw 2.043 3.040 nonbonded pdb=" O ILE T 988 " pdb=" OH TYR T1090 " model vdw 2.055 3.040 nonbonded pdb=" OE2 GLU H 964 " pdb=" OH TYR H1151 " model vdw 2.056 3.040 ... (remaining 375930 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: 4.710 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 48.970 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.190 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:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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 : 0.007 0.821 45939 Z= 0.253 Angle : 0.637 17.133 61797 Z= 0.354 Chirality : 0.044 0.152 6460 Planarity : 0.004 0.072 8040 Dihedral : 15.329 89.490 16800 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.98 % Allowed : 11.48 % Favored : 87.54 % 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: 0.10 (0.11), residues: 1980 sheet: -0.22 (0.13), residues: 1220 loop : -0.61 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG T1027 TYR 0.017 0.002 TYR S1142 PHE 0.022 0.002 PHE T1098 TRP 0.011 0.002 TRP T1006 HIS 0.018 0.001 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00547 (45860) covalent geometry : angle 0.60511 (61740) hydrogen bonds : bond 0.16806 ( 1917) hydrogen bonds : angle 6.21185 ( 5232) metal coordination : bond 0.11219 ( 79) metal coordination : angle 6.57816 ( 57) *********************** 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 805 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 760 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 897 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7575 (mm-30) REVERT: B 928 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8106 (mmtm) REVERT: C 913 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8077 (tmtt) REVERT: C 969 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: C 1027 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7511 (mmm160) REVERT: I 1150 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: O 963 LYS cc_start: 0.8442 (pttt) cc_final: 0.7758 (tptt) REVERT: Q 1113 MET cc_start: 0.6733 (mtp) cc_final: 0.6467 (mmp) REVERT: R 969 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: S 1003 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8327 (tmtm) REVERT: S 1113 MET cc_start: 0.8206 (tpp) cc_final: 0.7733 (tpp) REVERT: T 913 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8427 (tmtt) REVERT: T 1115 MET cc_start: 0.7369 (mtm) cc_final: 0.6629 (mtt) REVERT: U 1109 GLN cc_start: 0.7214 (tt0) cc_final: 0.6490 (tt0) outliers start: 45 outliers final: 14 residues processed: 790 average time/residue: 0.7160 time to fit residues: 684.5634 Evaluate side-chains 753 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 731 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain C residue 913 LYS Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1027 ARG Chi-restraints excluded: chain E residue 975 THR Chi-restraints excluded: chain I residue 877 SER Chi-restraints excluded: chain I residue 974 SER Chi-restraints excluded: chain I residue 1150 GLU Chi-restraints excluded: chain J residue 913 LYS Chi-restraints excluded: chain L residue 975 THR Chi-restraints excluded: chain N residue 1014 LYS Chi-restraints excluded: chain O residue 1014 LYS Chi-restraints excluded: chain P residue 877 SER Chi-restraints excluded: chain Q residue 1067 LYS Chi-restraints excluded: chain R residue 969 GLU Chi-restraints excluded: chain S residue 1003 LYS Chi-restraints excluded: chain S residue 1154 THR Chi-restraints excluded: chain T residue 913 LYS Chi-restraints excluded: chain U residue 953 THR 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: 8.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 0.8980 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 941 ASN B1069 ASN C 947 ASN ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 937 GLN D 966 GLN D1070 GLN E 889 HIS E 941 ASN E 947 ASN E 993 ASN F1022 ASN F1109 GLN G1048 HIS ** H1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1048 HIS J 947 ASN L 947 ASN N 947 ASN ** P1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q1109 GLN R 937 GLN R 941 ASN R 973 GLN R1022 ASN S 937 GLN S1156 GLN T 880 GLN T 947 ASN T1146 GLN U 898 GLN U 924 HIS U 947 ASN U1156 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120065 restraints weight = 42861.736| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.31 r_work: 0.3255 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 45939 Z= 0.141 Angle : 0.521 11.594 61797 Z= 0.287 Chirality : 0.043 0.136 6460 Planarity : 0.004 0.085 8040 Dihedral : 5.682 83.635 6337 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.17 % Allowed : 11.48 % Favored : 86.35 % 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: 0.06 (0.11), residues: 5640 helix: 0.53 (0.12), residues: 2040 sheet: 0.09 (0.13), residues: 1200 loop : -0.27 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O1087 TYR 0.019 0.002 TYR B1090 PHE 0.016 0.001 PHE O 881 TRP 0.007 0.001 TRP T1006 HIS 0.012 0.001 HIS M1084 Details of bonding type rmsd covalent geometry : bond 0.00310 (45860) covalent geometry : angle 0.50566 (61740) hydrogen bonds : bond 0.05136 ( 1917) hydrogen bonds : angle 4.83929 ( 5232) metal coordination : bond 0.03932 ( 79) metal coordination : angle 4.10823 ( 57) *********************** 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 903 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 803 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 998 GLN cc_start: 0.8278 (mt0) cc_final: 0.8003 (mt0) REVERT: A 1115 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6846 (ttm) REVERT: A 1154 THR cc_start: 0.7984 (m) cc_final: 0.7766 (m) REVERT: B 1113 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6914 (tpt) REVERT: C 969 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: C 1028 MET cc_start: 0.9057 (mmt) cc_final: 0.8490 (mmt) REVERT: C 1109 GLN cc_start: 0.7951 (tp40) cc_final: 0.7696 (tp40) REVERT: D 1072 VAL cc_start: 0.7670 (m) cc_final: 0.7280 (t) REVERT: E 1093 HIS cc_start: 0.7773 (m170) cc_final: 0.7438 (m170) REVERT: F 891 MET cc_start: 0.8576 (mmm) cc_final: 0.8228 (tpt) REVERT: F 972 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7356 (tpt) REVERT: G 1113 MET cc_start: 0.8308 (ptm) cc_final: 0.7913 (ptm) REVERT: H 902 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8423 (p0) REVERT: H 963 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7951 (ttpt) REVERT: J 972 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7052 (tpt) REVERT: L 1004 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7766 (mtpp) REVERT: L 1138 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6803 (tp30) REVERT: M 1004 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7854 (mppt) REVERT: M 1067 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8410 (ttmm) REVERT: O 963 LYS cc_start: 0.8375 (pttt) cc_final: 0.7348 (tptt) REVERT: O 1087 ARG cc_start: 0.5948 (mtm-85) cc_final: 0.5586 (mtm-85) REVERT: P 910 LYS cc_start: 0.8371 (ttpp) cc_final: 0.8146 (ttpt) REVERT: P 963 LYS cc_start: 0.7596 (tttm) cc_final: 0.7233 (tptm) REVERT: P 1018 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7010 (mt-10) REVERT: Q 941 ASN cc_start: 0.8356 (m-40) cc_final: 0.8139 (m-40) REVERT: Q 1113 MET cc_start: 0.7107 (mtp) cc_final: 0.6498 (mmp) REVERT: R 876 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.6366 (t80) REVERT: R 902 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7933 (p0) REVERT: R 1004 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7833 (ttpm) REVERT: R 1022 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8257 (t0) REVERT: S 990 ASN cc_start: 0.7472 (t0) cc_final: 0.6713 (p0) REVERT: S 1113 MET cc_start: 0.8201 (tpp) cc_final: 0.7604 (tpp) REVERT: T 1115 MET cc_start: 0.6890 (mtm) cc_final: 0.5940 (mtt) REVERT: U 1087 ARG cc_start: 0.6997 (mtm-85) cc_final: 0.5956 (mtm-85) REVERT: U 1109 GLN cc_start: 0.7257 (tt0) cc_final: 0.6204 (tt0) REVERT: U 1113 MET cc_start: 0.7646 (tpp) cc_final: 0.7349 (tpp) outliers start: 100 outliers final: 29 residues processed: 832 average time/residue: 0.7119 time to fit residues: 717.7720 Evaluate side-chains 779 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 735 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 902 ASP Chi-restraints excluded: chain F residue 947 ASN Chi-restraints excluded: chain F residue 972 MET Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 957 ASP Chi-restraints excluded: chain H residue 1004 LYS Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1111 SER Chi-restraints excluded: chain I residue 1113 MET Chi-restraints excluded: chain I residue 1150 GLU Chi-restraints excluded: chain J residue 963 LYS Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain L residue 1004 LYS Chi-restraints excluded: chain L residue 1138 GLU Chi-restraints excluded: chain M residue 947 ASN Chi-restraints excluded: chain M residue 1004 LYS Chi-restraints excluded: chain M residue 1067 LYS Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 988 ILE Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain O residue 902 ASP Chi-restraints excluded: chain O residue 1014 LYS Chi-restraints excluded: chain P residue 957 ASP Chi-restraints excluded: chain P residue 1018 GLU Chi-restraints excluded: chain P residue 1098 PHE Chi-restraints excluded: chain P residue 1115 MET Chi-restraints excluded: chain R residue 876 PHE Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 1004 LYS Chi-restraints excluded: chain R residue 1022 ASN Chi-restraints excluded: chain R residue 1033 SER Chi-restraints excluded: chain S residue 1018 GLU Chi-restraints excluded: chain S residue 1106 SER Chi-restraints excluded: chain U residue 931 GLU Chi-restraints excluded: chain U residue 959 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 139 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 356 optimal weight: 0.0020 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 211 optimal weight: 8.9990 chunk 291 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 469 optimal weight: 10.0000 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 GLN A 973 GLN A1109 GLN B1064 ASN C 947 ASN ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 937 GLN D 966 GLN E 884 ASN E 941 ASN E 947 ASN E 993 ASN F1109 GLN H1037 ASN ** H1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 947 ASN M1064 ASN ** P1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 937 GLN R 973 GLN R1109 GLN S 937 GLN S1069 ASN T 947 ASN U 947 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.166067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118839 restraints weight = 42824.105| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.33 r_work: 0.3241 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 45939 Z= 0.162 Angle : 0.508 7.455 61797 Z= 0.281 Chirality : 0.044 0.138 6460 Planarity : 0.004 0.048 8040 Dihedral : 5.186 81.242 6293 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.70 % Allowed : 12.59 % Favored : 84.72 % 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: 0.09 (0.11), residues: 5640 helix: 0.67 (0.12), residues: 2040 sheet: -0.05 (0.13), residues: 1240 loop : -0.26 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T1027 TYR 0.023 0.002 TYR A1155 PHE 0.015 0.001 PHE D 881 TRP 0.007 0.002 TRP D1006 HIS 0.010 0.001 HIS C1084 Details of bonding type rmsd covalent geometry : bond 0.00375 (45860) covalent geometry : angle 0.50004 (61740) hydrogen bonds : bond 0.05016 ( 1917) hydrogen bonds : angle 4.62731 ( 5232) metal coordination : bond 0.03046 ( 79) metal coordination : angle 3.08149 ( 57) *********************** 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 909 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 785 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 998 GLN cc_start: 0.8381 (mt0) cc_final: 0.8094 (mt0) REVERT: A 1109 GLN cc_start: 0.7528 (tp40) cc_final: 0.6703 (tp-100) REVERT: B 928 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7989 (mmtm) REVERT: B 1113 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6772 (tpt) REVERT: C 947 ASN cc_start: 0.7724 (m-40) cc_final: 0.7423 (m110) REVERT: D 896 ARG cc_start: 0.8619 (tpt170) cc_final: 0.8373 (tpt170) REVERT: D 943 TYR cc_start: 0.8091 (t80) cc_final: 0.7883 (t80) REVERT: D 972 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8058 (ttt) REVERT: D 1067 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8017 (tttp) REVERT: D 1072 VAL cc_start: 0.7683 (m) cc_final: 0.7292 (t) REVERT: E 977 ARG cc_start: 0.7644 (mpt180) cc_final: 0.7391 (mpt180) REVERT: F 972 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7284 (tpt) REVERT: H 883 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8308 (ttp-170) REVERT: H 902 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8420 (p0) REVERT: H 947 ASN cc_start: 0.7740 (t0) cc_final: 0.7450 (t0) REVERT: H 963 LYS cc_start: 0.8224 (ttpp) cc_final: 0.8008 (ttpt) REVERT: I 931 GLU cc_start: 0.8386 (tp30) cc_final: 0.7673 (mp0) REVERT: I 947 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7623 (m110) REVERT: J 892 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7840 (p0) REVERT: J 972 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.6913 (tpt) REVERT: J 1007 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8284 (mt-10) REVERT: L 1004 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7852 (mtpp) REVERT: L 1054 MET cc_start: 0.8126 (ttm) cc_final: 0.7810 (ttt) REVERT: L 1138 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6832 (tp30) REVERT: M 896 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7476 (mtp180) REVERT: M 1004 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7984 (mppt) REVERT: M 1067 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8472 (ttmm) REVERT: O 963 LYS cc_start: 0.8438 (pttt) cc_final: 0.7453 (tptt) REVERT: O 991 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7761 (ttt90) REVERT: O 1087 ARG cc_start: 0.6062 (mtm-85) cc_final: 0.5732 (mtm-85) REVERT: P 910 LYS cc_start: 0.8434 (ttpp) cc_final: 0.8218 (ttpt) REVERT: P 977 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7652 (tpp-160) REVERT: P 1018 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: Q 931 GLU cc_start: 0.7874 (tt0) cc_final: 0.7446 (tt0) REVERT: Q 1007 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8639 (mt-10) REVERT: Q 1113 MET cc_start: 0.7151 (mtp) cc_final: 0.6545 (mmp) REVERT: R 876 PHE cc_start: 0.6781 (OUTLIER) cc_final: 0.6520 (t80) REVERT: R 902 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7958 (p0) REVERT: R 1004 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7963 (ttpm) REVERT: R 1022 ASN cc_start: 0.8577 (t0) cc_final: 0.8266 (t0) REVERT: R 1138 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: R 1145 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8260 (pm20) REVERT: S 911 GLU cc_start: 0.8597 (mp0) cc_final: 0.8253 (mp0) REVERT: S 964 GLU cc_start: 0.8159 (tt0) cc_final: 0.7804 (tt0) REVERT: S 967 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8086 (p) REVERT: S 990 ASN cc_start: 0.7534 (t0) cc_final: 0.6845 (p0) REVERT: S 1113 MET cc_start: 0.8151 (tpp) cc_final: 0.7607 (tpp) REVERT: T 1109 GLN cc_start: 0.7240 (mt0) cc_final: 0.6785 (tt0) REVERT: T 1115 MET cc_start: 0.6828 (mtm) cc_final: 0.5893 (mtt) REVERT: U 888 GLU cc_start: 0.7787 (tp30) cc_final: 0.7115 (mm-30) REVERT: U 1068 SER cc_start: 0.7935 (m) cc_final: 0.7611 (p) REVERT: U 1109 GLN cc_start: 0.7418 (tt0) cc_final: 0.6473 (tt0) REVERT: U 1113 MET cc_start: 0.7669 (tpp) cc_final: 0.7363 (tpp) outliers start: 124 outliers final: 44 residues processed: 834 average time/residue: 0.8471 time to fit residues: 851.1197 Evaluate side-chains 820 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 753 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1067 LYS Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain F residue 902 ASP Chi-restraints excluded: chain F residue 947 ASN Chi-restraints excluded: chain F residue 957 ASP Chi-restraints excluded: chain F residue 972 MET Chi-restraints excluded: chain F residue 1113 MET Chi-restraints excluded: chain F residue 1118 SER 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 1143 ARG Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 910 LYS Chi-restraints excluded: chain H residue 957 ASP Chi-restraints excluded: chain H residue 1004 LYS Chi-restraints excluded: chain H residue 1109 GLN Chi-restraints excluded: chain I residue 947 ASN Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1111 SER Chi-restraints excluded: chain I residue 1113 MET Chi-restraints excluded: chain I residue 1150 GLU Chi-restraints excluded: chain J residue 892 ASP Chi-restraints excluded: chain J residue 913 LYS Chi-restraints excluded: chain J residue 963 LYS Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1007 GLU Chi-restraints excluded: chain L residue 931 GLU Chi-restraints excluded: chain L residue 1004 LYS Chi-restraints excluded: chain L residue 1138 GLU Chi-restraints excluded: chain M residue 947 ASN Chi-restraints excluded: chain M residue 1004 LYS Chi-restraints excluded: chain M residue 1067 LYS Chi-restraints excluded: chain M residue 1113 MET Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 988 ILE Chi-restraints excluded: chain N residue 1017 SER Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain O residue 902 ASP Chi-restraints excluded: chain O residue 1014 LYS Chi-restraints excluded: chain P residue 957 ASP Chi-restraints excluded: chain P residue 977 ARG Chi-restraints excluded: chain P residue 1018 GLU Chi-restraints excluded: chain P residue 1098 PHE Chi-restraints excluded: chain P residue 1115 MET Chi-restraints excluded: chain Q residue 1007 GLU Chi-restraints excluded: chain R residue 876 PHE Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 944 LEU Chi-restraints excluded: chain R residue 1004 LYS Chi-restraints excluded: chain R residue 1033 SER Chi-restraints excluded: chain R residue 1138 GLU Chi-restraints excluded: chain R residue 1145 GLU Chi-restraints excluded: chain S residue 967 SER Chi-restraints excluded: chain S residue 1106 SER Chi-restraints excluded: chain T residue 1157 ILE Chi-restraints excluded: chain U residue 953 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 533 optimal weight: 9.9990 chunk 548 optimal weight: 0.6980 chunk 402 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 523 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 327 optimal weight: 6.9990 chunk 315 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 GLN B1037 ASN B1069 ASN ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 937 GLN D 966 GLN E 947 ASN E 993 ASN E1022 ASN ** F1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1037 ASN ** H1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 966 GLN J 947 ASN J1093 HIS L 884 ASN O1064 ASN P1084 HIS Q 990 ASN Q1064 ASN R 937 GLN R 973 GLN S 937 GLN S1069 ASN T 880 GLN T 937 GLN T 947 ASN T 966 GLN T1093 HIS U 947 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114951 restraints weight = 43193.239| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.31 r_work: 0.3172 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.834 45939 Z= 0.242 Angle : 0.571 12.870 61797 Z= 0.313 Chirality : 0.046 0.150 6460 Planarity : 0.004 0.048 8040 Dihedral : 5.318 80.550 6290 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.37 % Allowed : 13.11 % Favored : 83.52 % 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: -0.13 (0.11), residues: 5640 helix: 0.50 (0.11), residues: 2040 sheet: -0.26 (0.14), residues: 1280 loop : -0.33 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 977 TYR 0.021 0.002 TYR B1090 PHE 0.017 0.002 PHE C 965 TRP 0.008 0.002 TRP M1006 HIS 0.012 0.001 HIS M1084 Details of bonding type rmsd covalent geometry : bond 0.00553 (45860) covalent geometry : angle 0.55759 (61740) hydrogen bonds : bond 0.05746 ( 1917) hydrogen bonds : angle 4.76872 ( 5232) metal coordination : bond 0.09926 ( 79) metal coordination : angle 4.04715 ( 57) *********************** 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 939 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 784 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 998 GLN cc_start: 0.8424 (mt0) cc_final: 0.8085 (mt0) REVERT: B 928 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7980 (mmtm) REVERT: B 1113 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6751 (tpt) REVERT: C 947 ASN cc_start: 0.7765 (m-40) cc_final: 0.7362 (m110) REVERT: C 1113 MET cc_start: 0.7926 (ptm) cc_final: 0.7571 (ptp) REVERT: C 1138 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7207 (mt-10) REVERT: D 947 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7287 (m-40) REVERT: D 972 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8140 (ttt) REVERT: D 1072 VAL cc_start: 0.7663 (m) cc_final: 0.7254 (t) REVERT: E 932 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7403 (mtp180) REVERT: E 977 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7320 (mpt180) REVERT: E 1004 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7766 (ttmm) REVERT: F 972 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7202 (tpt) REVERT: H 883 ARG cc_start: 0.8667 (ttp-110) cc_final: 0.8366 (ttp-170) REVERT: H 902 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8491 (p0) REVERT: H 947 ASN cc_start: 0.7827 (t0) cc_final: 0.7507 (t0) REVERT: H 963 LYS cc_start: 0.8181 (ttpp) cc_final: 0.7960 (ttpt) REVERT: H 1113 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7594 (ptm) REVERT: I 931 GLU cc_start: 0.8385 (tp30) cc_final: 0.7638 (mp0) REVERT: I 947 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7609 (m110) REVERT: I 1143 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8354 (mtp-110) REVERT: J 972 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.6987 (tpt) REVERT: L 884 ASN cc_start: 0.8559 (m-40) cc_final: 0.8358 (m110) REVERT: L 1004 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7919 (mtpp) REVERT: L 1054 MET cc_start: 0.8154 (ttm) cc_final: 0.7834 (ttt) REVERT: L 1138 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6910 (tp30) REVERT: M 1004 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8010 (mppt) REVERT: M 1067 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8462 (ttmm) REVERT: M 1113 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7736 (ttp) REVERT: N 1087 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7233 (mtm-85) REVERT: O 963 LYS cc_start: 0.8399 (pttt) cc_final: 0.7391 (tptt) REVERT: O 991 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7821 (ttt90) REVERT: O 1063 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: O 1087 ARG cc_start: 0.6195 (mtm-85) cc_final: 0.5775 (mtm-85) REVERT: P 910 LYS cc_start: 0.8425 (ttpp) cc_final: 0.8214 (ttpt) REVERT: P 977 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7685 (tpp-160) REVERT: P 1018 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: Q 931 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: Q 1007 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8609 (mt-10) REVERT: Q 1113 MET cc_start: 0.7156 (mtp) cc_final: 0.6520 (tpp) REVERT: R 876 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6693 (t80) REVERT: R 1004 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8013 (ttpm) REVERT: R 1022 ASN cc_start: 0.8692 (t0) cc_final: 0.8190 (t0) REVERT: R 1138 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: R 1145 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: S 964 GLU cc_start: 0.8213 (tt0) cc_final: 0.7831 (tt0) REVERT: S 967 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8102 (p) REVERT: S 990 ASN cc_start: 0.7579 (t0) cc_final: 0.7010 (p0) REVERT: S 1004 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7848 (mtpp) REVERT: S 1028 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8430 (mmt) REVERT: S 1113 MET cc_start: 0.8056 (tpp) cc_final: 0.7105 (ttp) REVERT: T 1087 ARG cc_start: 0.6264 (mtm-85) cc_final: 0.5998 (mtm-85) REVERT: T 1109 GLN cc_start: 0.7203 (mt0) cc_final: 0.6605 (tt0) REVERT: T 1113 MET cc_start: 0.7827 (mmm) cc_final: 0.7192 (mmm) REVERT: T 1115 MET cc_start: 0.7017 (mtm) cc_final: 0.6146 (mtt) REVERT: U 888 GLU cc_start: 0.7928 (tp30) cc_final: 0.7255 (mm-30) REVERT: U 964 GLU cc_start: 0.7769 (tt0) cc_final: 0.7416 (tt0) REVERT: U 1068 SER cc_start: 0.7852 (m) cc_final: 0.7592 (p) REVERT: U 1109 GLN cc_start: 0.7542 (tt0) cc_final: 0.6535 (tt0) REVERT: U 1113 MET cc_start: 0.7725 (tpp) cc_final: 0.7420 (tpp) outliers start: 155 outliers final: 67 residues processed: 846 average time/residue: 0.8494 time to fit residues: 868.2884 Evaluate side-chains 853 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 755 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain E residue 932 ARG Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 977 ARG Chi-restraints excluded: chain E residue 1004 LYS Chi-restraints excluded: chain E residue 1037 ASN Chi-restraints excluded: chain F residue 902 ASP Chi-restraints excluded: chain F residue 947 ASN Chi-restraints excluded: chain F residue 957 ASP Chi-restraints excluded: chain F residue 972 MET Chi-restraints excluded: chain F residue 1036 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1113 MET Chi-restraints excluded: chain F residue 1118 SER 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 1143 ARG Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 910 LYS Chi-restraints excluded: chain H residue 957 ASP Chi-restraints excluded: chain H residue 977 ARG Chi-restraints excluded: chain H residue 1004 LYS Chi-restraints excluded: chain H residue 1102 THR Chi-restraints excluded: chain H residue 1108 LEU Chi-restraints excluded: chain H residue 1113 MET Chi-restraints excluded: chain H residue 1126 THR Chi-restraints excluded: chain I residue 947 ASN Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1111 SER Chi-restraints excluded: chain I residue 1113 MET Chi-restraints excluded: chain I residue 1143 ARG Chi-restraints excluded: chain I residue 1150 GLU Chi-restraints excluded: chain J residue 913 LYS Chi-restraints excluded: chain J residue 963 LYS Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1108 LEU Chi-restraints excluded: chain L residue 931 GLU Chi-restraints excluded: chain L residue 1004 LYS Chi-restraints excluded: chain L residue 1018 GLU Chi-restraints excluded: chain L residue 1138 GLU Chi-restraints excluded: chain M residue 1004 LYS Chi-restraints excluded: chain M residue 1067 LYS Chi-restraints excluded: chain M residue 1113 MET Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 988 ILE Chi-restraints excluded: chain N residue 1017 SER Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain N residue 1102 THR Chi-restraints excluded: chain O residue 902 ASP Chi-restraints excluded: chain O residue 934 ILE Chi-restraints excluded: chain O residue 991 ARG Chi-restraints excluded: chain O residue 1014 LYS Chi-restraints excluded: chain O residue 1063 GLU Chi-restraints excluded: chain P residue 957 ASP Chi-restraints excluded: chain P residue 969 GLU Chi-restraints excluded: chain P residue 977 ARG Chi-restraints excluded: chain P residue 1018 GLU Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain P residue 1098 PHE Chi-restraints excluded: chain P residue 1115 MET Chi-restraints excluded: chain Q residue 931 GLU Chi-restraints excluded: chain Q residue 1007 GLU Chi-restraints excluded: chain R residue 876 PHE Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 944 LEU Chi-restraints excluded: chain R residue 1004 LYS Chi-restraints excluded: chain R residue 1033 SER Chi-restraints excluded: chain R residue 1138 GLU Chi-restraints excluded: chain R residue 1145 GLU Chi-restraints excluded: chain S residue 967 SER Chi-restraints excluded: chain S residue 1004 LYS Chi-restraints excluded: chain S residue 1028 MET Chi-restraints excluded: chain S residue 1106 SER Chi-restraints excluded: chain S residue 1108 LEU Chi-restraints excluded: chain S residue 1150 GLU Chi-restraints excluded: chain T residue 882 VAL Chi-restraints excluded: chain T residue 1118 SER Chi-restraints excluded: chain T residue 1150 GLU Chi-restraints excluded: chain T residue 1157 ILE Chi-restraints excluded: chain U residue 953 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 21 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 chunk 375 optimal weight: 2.9990 chunk 539 optimal weight: 0.0870 chunk 535 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 459 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 553 optimal weight: 4.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 GLN B 941 ASN B1069 ASN ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1109 GLN D 937 GLN D 966 GLN E 941 ASN E 947 ASN E 993 ASN E1022 ASN F1093 HIS ** F1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1146 GLN H1037 ASN H1048 HIS ** H1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 941 ASN J 889 HIS J 947 ASN L1064 ASN R 937 GLN R 973 GLN R1109 GLN S 937 GLN S 941 ASN S1048 HIS S1069 ASN T 880 GLN T 937 GLN T 947 ASN T 966 GLN T 993 ASN T1093 HIS U 947 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116316 restraints weight = 43170.030| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.35 r_work: 0.3192 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 45939 Z= 0.164 Angle : 0.521 14.640 61797 Z= 0.280 Chirality : 0.043 0.138 6460 Planarity : 0.004 0.045 8040 Dihedral : 5.087 80.078 6290 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.17 % Allowed : 13.87 % Favored : 82.96 % 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: 0.03 (0.11), residues: 5640 helix: 0.69 (0.12), residues: 2040 sheet: -0.07 (0.14), residues: 1240 loop : -0.39 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T1027 TYR 0.018 0.002 TYR U1090 PHE 0.014 0.001 PHE D 881 TRP 0.007 0.001 TRP D1006 HIS 0.019 0.001 HIS P1084 Details of bonding type rmsd covalent geometry : bond 0.00378 (45860) covalent geometry : angle 0.49635 (61740) hydrogen bonds : bond 0.04838 ( 1917) hydrogen bonds : angle 4.58563 ( 5232) metal coordination : bond 0.04353 ( 79) metal coordination : angle 5.21708 ( 57) *********************** 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 937 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 791 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 998 GLN cc_start: 0.8397 (mt0) cc_final: 0.8035 (mt0) REVERT: A 1109 GLN cc_start: 0.7515 (tp-100) cc_final: 0.7282 (tt0) REVERT: B 928 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7874 (mmtm) REVERT: B 1113 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6725 (tpt) REVERT: C 947 ASN cc_start: 0.7618 (m-40) cc_final: 0.7178 (m110) REVERT: C 1138 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7090 (mt-10) REVERT: D 896 ARG cc_start: 0.8555 (tpt170) cc_final: 0.8350 (tpt170) REVERT: D 947 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7247 (m-40) REVERT: D 972 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8030 (ttt) REVERT: D 1067 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7912 (tttp) REVERT: D 1072 VAL cc_start: 0.7547 (m) cc_final: 0.7154 (t) REVERT: D 1087 ARG cc_start: 0.7620 (mtm-85) cc_final: 0.7328 (mtm-85) REVERT: E 977 ARG cc_start: 0.7602 (mpt180) cc_final: 0.7317 (mpt180) REVERT: F 972 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7169 (tpt) REVERT: H 883 ARG cc_start: 0.8603 (ttp-170) cc_final: 0.8280 (ttp-170) REVERT: H 902 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8464 (p0) REVERT: H 947 ASN cc_start: 0.7767 (t0) cc_final: 0.7318 (m-40) REVERT: H 963 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7935 (ttpt) REVERT: H 1113 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7648 (ptm) REVERT: I 1143 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8070 (mtt180) REVERT: J 972 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.6966 (tpt) REVERT: L 1004 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7872 (mtpp) REVERT: L 1037 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8334 (t0) REVERT: L 1054 MET cc_start: 0.8129 (ttm) cc_final: 0.7795 (ttt) REVERT: L 1138 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6842 (tp30) REVERT: M 1004 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7912 (mppt) REVERT: M 1067 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8407 (ttmm) REVERT: O 878 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8346 (tp) REVERT: O 963 LYS cc_start: 0.8365 (pttt) cc_final: 0.7342 (tptt) REVERT: O 1063 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: O 1087 ARG cc_start: 0.6220 (mtm-85) cc_final: 0.5774 (mtm-85) REVERT: P 910 LYS cc_start: 0.8374 (ttpp) cc_final: 0.8152 (ttpt) REVERT: P 977 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7660 (tpp-160) REVERT: P 1018 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: P 1079 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7956 (p) REVERT: Q 931 GLU cc_start: 0.7807 (tt0) cc_final: 0.7384 (tt0) REVERT: Q 1007 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8552 (mt-10) REVERT: Q 1113 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6510 (tpp) REVERT: R 876 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6630 (t80) REVERT: R 966 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.5890 (mt0) REVERT: R 1004 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7874 (ttpm) REVERT: R 1022 ASN cc_start: 0.8714 (t0) cc_final: 0.8092 (t0) REVERT: R 1113 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7133 (pmm) REVERT: R 1138 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7417 (tp30) REVERT: R 1145 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: S 967 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8063 (p) REVERT: S 990 ASN cc_start: 0.7623 (t0) cc_final: 0.7104 (p0) REVERT: S 1028 MET cc_start: 0.8633 (mmm) cc_final: 0.8421 (mmt) REVERT: S 1113 MET cc_start: 0.8001 (tpp) cc_final: 0.7123 (ttp) REVERT: S 1138 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: T 991 ARG cc_start: 0.6870 (mtp85) cc_final: 0.6649 (mtp-110) REVERT: T 1109 GLN cc_start: 0.7224 (mt0) cc_final: 0.6561 (tt0) REVERT: T 1113 MET cc_start: 0.7797 (mmm) cc_final: 0.7179 (mmm) REVERT: T 1115 MET cc_start: 0.6980 (mtm) cc_final: 0.6034 (mtt) REVERT: U 888 GLU cc_start: 0.7921 (tp30) cc_final: 0.7239 (mm-30) REVERT: U 964 GLU cc_start: 0.7755 (tt0) cc_final: 0.7382 (tt0) REVERT: U 1004 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7328 (UNCLASSIFIED) REVERT: U 1109 GLN cc_start: 0.7489 (tt0) cc_final: 0.6472 (tt0) REVERT: U 1113 MET cc_start: 0.7733 (tpp) cc_final: 0.7462 (tpp) REVERT: U 1148 TYR cc_start: 0.8516 (t80) cc_final: 0.8223 (t80) outliers start: 146 outliers final: 67 residues processed: 853 average time/residue: 0.8251 time to fit residues: 851.1099 Evaluate side-chains 872 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 774 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1067 LYS Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain E residue 957 ASP Chi-restraints excluded: chain F residue 902 ASP Chi-restraints excluded: chain F residue 947 ASN Chi-restraints excluded: chain F residue 957 ASP Chi-restraints excluded: chain F residue 972 MET Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 1004 LYS Chi-restraints excluded: chain F residue 1106 SER Chi-restraints excluded: chain F residue 1113 MET Chi-restraints excluded: chain F residue 1118 SER Chi-restraints excluded: chain F residue 1126 THR Chi-restraints excluded: chain F residue 1143 ARG Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 910 LYS Chi-restraints excluded: chain H residue 957 ASP Chi-restraints excluded: chain H residue 977 ARG Chi-restraints excluded: chain H residue 1004 LYS Chi-restraints excluded: chain H residue 1108 LEU Chi-restraints excluded: chain H residue 1109 GLN Chi-restraints excluded: chain H residue 1113 MET Chi-restraints excluded: chain H residue 1126 THR Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1143 ARG Chi-restraints excluded: chain I residue 1150 GLU Chi-restraints excluded: chain J residue 913 LYS Chi-restraints excluded: chain J residue 963 LYS Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1036 VAL Chi-restraints excluded: chain L residue 931 GLU Chi-restraints excluded: chain L residue 1004 LYS Chi-restraints excluded: chain L residue 1037 ASN Chi-restraints excluded: chain L residue 1138 GLU Chi-restraints excluded: chain M residue 947 ASN Chi-restraints excluded: chain M residue 1004 LYS Chi-restraints excluded: chain M residue 1067 LYS Chi-restraints excluded: chain M residue 1092 CYS Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain M residue 1118 SER Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 988 ILE Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain O residue 878 ILE Chi-restraints excluded: chain O residue 902 ASP Chi-restraints excluded: chain O residue 1017 SER Chi-restraints excluded: chain O residue 1063 GLU Chi-restraints excluded: chain P residue 957 ASP Chi-restraints excluded: chain P residue 977 ARG Chi-restraints excluded: chain P residue 1018 GLU Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain P residue 1079 THR Chi-restraints excluded: chain P residue 1091 ILE Chi-restraints excluded: chain P residue 1098 PHE Chi-restraints excluded: chain P residue 1115 MET Chi-restraints excluded: chain Q residue 990 ASN Chi-restraints excluded: chain Q residue 1007 GLU Chi-restraints excluded: chain Q residue 1113 MET Chi-restraints excluded: chain R residue 876 PHE Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 944 LEU Chi-restraints excluded: chain R residue 966 GLN Chi-restraints excluded: chain R residue 1004 LYS Chi-restraints excluded: chain R residue 1033 SER Chi-restraints excluded: chain R residue 1113 MET Chi-restraints excluded: chain R residue 1138 GLU Chi-restraints excluded: chain R residue 1145 GLU Chi-restraints excluded: chain R residue 1158 MET Chi-restraints excluded: chain S residue 967 SER Chi-restraints excluded: chain S residue 1018 GLU Chi-restraints excluded: chain S residue 1036 VAL Chi-restraints excluded: chain S residue 1106 SER Chi-restraints excluded: chain S residue 1108 LEU Chi-restraints excluded: chain S residue 1138 GLU Chi-restraints excluded: chain S residue 1150 GLU Chi-restraints excluded: chain T residue 882 VAL Chi-restraints excluded: chain T residue 1118 SER Chi-restraints excluded: chain T residue 1157 ILE Chi-restraints excluded: chain T residue 1158 MET Chi-restraints excluded: chain U residue 953 THR Chi-restraints excluded: chain U residue 959 SER Chi-restraints excluded: chain U residue 1004 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 523 optimal weight: 9.9990 chunk 385 optimal weight: 6.9990 chunk 490 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 235 optimal weight: 0.2980 chunk 182 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 GLN A 973 GLN B 941 ASN ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1109 GLN D 937 GLN D 966 GLN E 947 ASN E 993 ASN E1022 ASN F1093 HIS ** F1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1146 GLN ** H1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 947 ASN J 947 ASN L 884 ASN P 937 GLN R 937 GLN R 973 GLN S 937 GLN S1069 ASN T 880 GLN T 937 GLN T 947 ASN T 966 GLN T 993 ASN T1093 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.163139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116373 restraints weight = 43428.756| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.10 r_work: 0.3194 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 45939 Z= 0.181 Angle : 0.534 16.663 61797 Z= 0.286 Chirality : 0.044 0.155 6460 Planarity : 0.004 0.044 8040 Dihedral : 5.069 78.704 6286 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.39 % Allowed : 14.39 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.03 (0.11), residues: 5640 helix: 0.71 (0.12), residues: 2040 sheet: -0.44 (0.13), residues: 1360 loop : -0.23 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T1027 TYR 0.021 0.002 TYR B1090 PHE 0.021 0.001 PHE U1107 TRP 0.007 0.002 TRP M1006 HIS 0.021 0.001 HIS M1084 Details of bonding type rmsd covalent geometry : bond 0.00416 (45860) covalent geometry : angle 0.50615 (61740) hydrogen bonds : bond 0.05007 ( 1917) hydrogen bonds : angle 4.59098 ( 5232) metal coordination : bond 0.05457 ( 79) metal coordination : angle 5.58041 ( 57) *********************** 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 942 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 786 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 977 ARG cc_start: 0.6086 (mmt-90) cc_final: 0.5884 (mmt-90) REVERT: A 998 GLN cc_start: 0.8440 (mt0) cc_final: 0.8050 (mt0) REVERT: B 928 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7957 (mmtm) REVERT: B 1113 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6861 (tpp) REVERT: C 947 ASN cc_start: 0.7660 (m-40) cc_final: 0.7233 (m110) REVERT: D 947 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7281 (m-40) REVERT: D 972 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8023 (ttt) REVERT: D 1067 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7996 (tttp) REVERT: D 1072 VAL cc_start: 0.7604 (m) cc_final: 0.7205 (t) REVERT: D 1087 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7427 (mtm-85) REVERT: D 1113 MET cc_start: 0.7956 (ptm) cc_final: 0.7656 (ptt) REVERT: E 977 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7354 (mpt180) REVERT: F 972 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7232 (tpt) REVERT: H 883 ARG cc_start: 0.8624 (ttp-170) cc_final: 0.8335 (ttp-170) REVERT: H 902 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8479 (p0) REVERT: H 947 ASN cc_start: 0.7749 (t0) cc_final: 0.7317 (m-40) REVERT: H 963 LYS cc_start: 0.8214 (ttpp) cc_final: 0.8012 (ttpt) REVERT: H 1113 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7629 (ptm) REVERT: I 1143 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8107 (mtt180) REVERT: J 972 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.6982 (tpt) REVERT: L 1004 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7905 (mtpp) REVERT: L 1054 MET cc_start: 0.8150 (ttm) cc_final: 0.7843 (ttt) REVERT: L 1138 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6907 (tp30) REVERT: M 1004 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7952 (mppt) REVERT: M 1067 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8444 (ttmm) REVERT: N 1087 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7233 (mtm-85) REVERT: O 963 LYS cc_start: 0.8388 (pttt) cc_final: 0.7397 (tptt) REVERT: O 1063 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: O 1087 ARG cc_start: 0.6282 (mtm-85) cc_final: 0.5849 (mtm-85) REVERT: P 910 LYS cc_start: 0.8416 (ttpp) cc_final: 0.8205 (ttpt) REVERT: P 932 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7958 (mtp180) REVERT: P 977 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7636 (tpp-160) REVERT: P 1018 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: P 1138 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: Q 931 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: Q 1007 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8578 (mt-10) REVERT: Q 1113 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6529 (tpp) REVERT: R 876 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6717 (t80) REVERT: R 966 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.5915 (mt0) REVERT: R 1004 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7933 (ttpm) REVERT: R 1022 ASN cc_start: 0.8766 (t0) cc_final: 0.8145 (t0) REVERT: R 1138 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7484 (tp30) REVERT: R 1145 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: S 964 GLU cc_start: 0.8148 (tt0) cc_final: 0.7834 (tt0) REVERT: S 967 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8125 (p) REVERT: S 990 ASN cc_start: 0.7628 (t0) cc_final: 0.7163 (p0) REVERT: S 1004 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7795 (mtpp) REVERT: S 1028 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8394 (mmt) REVERT: S 1113 MET cc_start: 0.7984 (tpp) cc_final: 0.7227 (ttp) REVERT: T 991 ARG cc_start: 0.6889 (mtp85) cc_final: 0.6677 (mtp-110) REVERT: T 1109 GLN cc_start: 0.7227 (mt0) cc_final: 0.6512 (tt0) REVERT: T 1113 MET cc_start: 0.7788 (mmm) cc_final: 0.7122 (mmm) REVERT: T 1115 MET cc_start: 0.7107 (mtm) cc_final: 0.6212 (mtt) REVERT: U 888 GLU cc_start: 0.7925 (tp30) cc_final: 0.7270 (mm-30) REVERT: U 964 GLU cc_start: 0.7812 (tt0) cc_final: 0.7414 (tt0) REVERT: U 1004 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7323 (UNCLASSIFIED) REVERT: U 1109 GLN cc_start: 0.7515 (tt0) cc_final: 0.6542 (tt0) REVERT: U 1113 MET cc_start: 0.7769 (tpp) cc_final: 0.7498 (tpp) outliers start: 156 outliers final: 81 residues processed: 853 average time/residue: 0.5606 time to fit residues: 580.0243 Evaluate side-chains 873 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 760 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 1098 PHE Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1067 LYS Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain E residue 957 ASP Chi-restraints excluded: chain E residue 977 ARG Chi-restraints excluded: chain F residue 902 ASP Chi-restraints excluded: chain F residue 947 ASN Chi-restraints excluded: chain F residue 957 ASP Chi-restraints excluded: chain F residue 972 MET Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 1036 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1106 SER Chi-restraints excluded: chain F residue 1113 MET Chi-restraints excluded: chain F residue 1118 SER Chi-restraints excluded: chain F residue 1126 THR Chi-restraints excluded: chain F residue 1143 ARG Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain G residue 1143 ARG Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 910 LYS Chi-restraints excluded: chain H residue 957 ASP Chi-restraints excluded: chain H residue 977 ARG Chi-restraints excluded: chain H residue 1004 LYS Chi-restraints excluded: chain H residue 1108 LEU Chi-restraints excluded: chain H residue 1109 GLN Chi-restraints excluded: chain H residue 1113 MET Chi-restraints excluded: chain H residue 1126 THR Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1111 SER Chi-restraints excluded: chain I residue 1143 ARG Chi-restraints excluded: chain I residue 1150 GLU Chi-restraints excluded: chain J residue 913 LYS Chi-restraints excluded: chain J residue 963 LYS Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1036 VAL Chi-restraints excluded: chain L residue 931 GLU Chi-restraints excluded: chain L residue 1004 LYS Chi-restraints excluded: chain L residue 1108 LEU Chi-restraints excluded: chain L residue 1138 GLU Chi-restraints excluded: chain M residue 947 ASN Chi-restraints excluded: chain M residue 1004 LYS Chi-restraints excluded: chain M residue 1067 LYS Chi-restraints excluded: chain M residue 1092 CYS Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain M residue 1118 SER Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 988 ILE Chi-restraints excluded: chain N residue 1017 SER Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain N residue 1158 MET Chi-restraints excluded: chain O residue 902 ASP Chi-restraints excluded: chain O residue 1014 LYS Chi-restraints excluded: chain O residue 1017 SER Chi-restraints excluded: chain O residue 1063 GLU Chi-restraints excluded: chain P residue 932 ARG Chi-restraints excluded: chain P residue 957 ASP Chi-restraints excluded: chain P residue 977 ARG Chi-restraints excluded: chain P residue 1018 GLU Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain P residue 1098 PHE Chi-restraints excluded: chain P residue 1115 MET Chi-restraints excluded: chain P residue 1138 GLU Chi-restraints excluded: chain Q residue 931 GLU Chi-restraints excluded: chain Q residue 990 ASN Chi-restraints excluded: chain Q residue 1007 GLU Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1113 MET Chi-restraints excluded: chain R residue 876 PHE Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 944 LEU Chi-restraints excluded: chain R residue 966 GLN Chi-restraints excluded: chain R residue 1004 LYS Chi-restraints excluded: chain R residue 1033 SER Chi-restraints excluded: chain R residue 1072 VAL Chi-restraints excluded: chain R residue 1138 GLU Chi-restraints excluded: chain R residue 1145 GLU Chi-restraints excluded: chain R residue 1158 MET Chi-restraints excluded: chain S residue 967 SER Chi-restraints excluded: chain S residue 1004 LYS Chi-restraints excluded: chain S residue 1018 GLU Chi-restraints excluded: chain S residue 1028 MET Chi-restraints excluded: chain S residue 1036 VAL Chi-restraints excluded: chain S residue 1106 SER Chi-restraints excluded: chain S residue 1108 LEU Chi-restraints excluded: chain S residue 1150 GLU Chi-restraints excluded: chain T residue 1118 SER Chi-restraints excluded: chain T residue 1150 GLU Chi-restraints excluded: chain T residue 1157 ILE Chi-restraints excluded: chain T residue 1158 MET Chi-restraints excluded: chain U residue 947 ASN Chi-restraints excluded: chain U residue 953 THR Chi-restraints excluded: chain U residue 959 SER Chi-restraints excluded: chain U residue 1004 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 160 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 301 optimal weight: 20.0000 chunk 402 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 356 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 479 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 388 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 GLN A 973 GLN A1109 GLN B 941 ASN B1037 ASN B1069 ASN ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 966 GLN D1156 GLN E 941 ASN E 947 ASN E 993 ASN E1022 ASN F1093 HIS ** F1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1146 GLN ** H1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 947 ASN L 884 ASN M1002 ASN R 937 GLN R 973 GLN S 937 GLN S 941 ASN S1069 ASN T 880 GLN T 937 GLN T 947 ASN T 966 GLN T 993 ASN T1093 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.162713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114628 restraints weight = 42828.835| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.39 r_work: 0.3168 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.302 45939 Z= 0.175 Angle : 0.535 18.274 61797 Z= 0.284 Chirality : 0.043 0.140 6460 Planarity : 0.004 0.046 8040 Dihedral : 5.036 80.438 6286 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.17 % Allowed : 15.13 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.11), residues: 5640 helix: 0.74 (0.12), residues: 2040 sheet: -0.43 (0.13), residues: 1360 loop : -0.22 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG T1027 TYR 0.018 0.002 TYR Q1139 PHE 0.023 0.001 PHE U1107 TRP 0.007 0.002 TRP M1006 HIS 0.025 0.001 HIS M1084 Details of bonding type rmsd covalent geometry : bond 0.00393 (45860) covalent geometry : angle 0.50127 (61740) hydrogen bonds : bond 0.04871 ( 1917) hydrogen bonds : angle 4.56668 ( 5232) metal coordination : bond 0.07028 ( 79) metal coordination : angle 6.14631 ( 57) *********************** 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 927 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 781 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 977 ARG cc_start: 0.6082 (mmt-90) cc_final: 0.5881 (mmt-90) REVERT: A 1109 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6416 (tt0) REVERT: B 928 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7882 (mmtm) REVERT: B 1113 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6823 (tpp) REVERT: C 888 GLU cc_start: 0.8210 (tt0) cc_final: 0.7588 (pm20) REVERT: C 947 ASN cc_start: 0.7584 (m-40) cc_final: 0.7139 (m110) REVERT: C 969 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: D 947 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7279 (m-40) REVERT: D 972 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8018 (ttt) REVERT: D 1067 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7949 (tttp) REVERT: D 1072 VAL cc_start: 0.7605 (m) cc_final: 0.7195 (t) REVERT: D 1087 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7350 (mtm-85) REVERT: D 1113 MET cc_start: 0.7984 (ptm) cc_final: 0.7657 (ptt) REVERT: E 977 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7354 (mpt180) REVERT: F 972 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7240 (tpt) REVERT: H 883 ARG cc_start: 0.8592 (ttp-170) cc_final: 0.8291 (ttp-170) REVERT: H 902 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8474 (p0) REVERT: H 947 ASN cc_start: 0.7804 (t0) cc_final: 0.7339 (m-40) REVERT: H 1113 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7605 (ptm) REVERT: I 1143 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8078 (mtt180) REVERT: J 972 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.6966 (tpt) REVERT: L 1004 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7937 (mtpp) REVERT: L 1054 MET cc_start: 0.8151 (ttm) cc_final: 0.7828 (ttt) REVERT: L 1138 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6857 (tp30) REVERT: M 1004 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7891 (mppt) REVERT: M 1063 GLU cc_start: 0.7884 (pm20) cc_final: 0.7608 (pm20) REVERT: M 1067 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8402 (ttmm) REVERT: O 896 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.7537 (ttp-170) REVERT: O 963 LYS cc_start: 0.8389 (pttt) cc_final: 0.7364 (tptt) REVERT: O 1063 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: O 1087 ARG cc_start: 0.6262 (mtm-85) cc_final: 0.5811 (mtm-85) REVERT: P 932 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7939 (mtp180) REVERT: P 977 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7641 (tpp-160) REVERT: P 1018 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: P 1138 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: Q 931 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: Q 1007 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8552 (mt-10) REVERT: Q 1028 MET cc_start: 0.9174 (mmt) cc_final: 0.8890 (mmt) REVERT: Q 1113 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6495 (tpp) REVERT: R 876 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.6612 (t80) REVERT: R 966 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.5847 (mt0) REVERT: R 1004 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7863 (ttpm) REVERT: R 1022 ASN cc_start: 0.8761 (t0) cc_final: 0.8102 (t0) REVERT: R 1113 MET cc_start: 0.7487 (pmm) cc_final: 0.7252 (pmm) REVERT: R 1138 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7423 (tp30) REVERT: R 1145 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: S 964 GLU cc_start: 0.8141 (tt0) cc_final: 0.7788 (tt0) REVERT: S 967 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.8022 (p) REVERT: S 990 ASN cc_start: 0.7634 (t0) cc_final: 0.7153 (p0) REVERT: S 1004 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7754 (mtpp) REVERT: S 1028 MET cc_start: 0.8631 (mmm) cc_final: 0.8378 (mmt) REVERT: S 1113 MET cc_start: 0.7967 (tpp) cc_final: 0.7176 (ttp) REVERT: T 1087 ARG cc_start: 0.6508 (ttm170) cc_final: 0.5824 (ttm170) REVERT: T 1109 GLN cc_start: 0.7220 (mt0) cc_final: 0.6473 (tt0) REVERT: T 1113 MET cc_start: 0.7770 (mmm) cc_final: 0.7071 (mmm) REVERT: T 1115 MET cc_start: 0.7082 (mtm) cc_final: 0.6201 (mtt) REVERT: U 888 GLU cc_start: 0.7904 (tp30) cc_final: 0.7247 (mm-30) REVERT: U 964 GLU cc_start: 0.7790 (tt0) cc_final: 0.7394 (tt0) REVERT: U 1004 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7320 (UNCLASSIFIED) REVERT: U 1094 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7439 (mtm180) REVERT: U 1109 GLN cc_start: 0.7455 (tt0) cc_final: 0.6575 (tt0) REVERT: U 1113 MET cc_start: 0.7757 (tpp) cc_final: 0.7498 (tpp) outliers start: 146 outliers final: 79 residues processed: 845 average time/residue: 0.4850 time to fit residues: 499.7556 Evaluate side-chains 876 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 764 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1098 PHE Chi-restraints excluded: chain C residue 1126 THR Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1067 LYS Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain E residue 957 ASP Chi-restraints excluded: chain E residue 977 ARG Chi-restraints excluded: chain F residue 882 VAL Chi-restraints excluded: chain F residue 902 ASP Chi-restraints excluded: chain F residue 947 ASN Chi-restraints excluded: chain F residue 957 ASP Chi-restraints excluded: chain F residue 972 MET Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 1036 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1106 SER Chi-restraints excluded: chain F residue 1113 MET Chi-restraints excluded: chain F residue 1118 SER Chi-restraints excluded: chain F residue 1126 THR Chi-restraints excluded: chain F residue 1143 ARG Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain G residue 1143 ARG Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 910 LYS Chi-restraints excluded: chain H residue 957 ASP Chi-restraints excluded: chain H residue 977 ARG Chi-restraints excluded: chain H residue 1004 LYS Chi-restraints excluded: chain H residue 1108 LEU Chi-restraints excluded: chain H residue 1109 GLN Chi-restraints excluded: chain H residue 1113 MET Chi-restraints excluded: chain H residue 1126 THR Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1143 ARG Chi-restraints excluded: chain I residue 1150 GLU Chi-restraints excluded: chain J residue 913 LYS Chi-restraints excluded: chain J residue 963 LYS Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1036 VAL Chi-restraints excluded: chain L residue 931 GLU Chi-restraints excluded: chain L residue 1004 LYS Chi-restraints excluded: chain L residue 1108 LEU Chi-restraints excluded: chain L residue 1138 GLU Chi-restraints excluded: chain L residue 1154 THR Chi-restraints excluded: chain M residue 947 ASN Chi-restraints excluded: chain M residue 1004 LYS Chi-restraints excluded: chain M residue 1067 LYS Chi-restraints excluded: chain M residue 1092 CYS Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain M residue 1118 SER Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 988 ILE Chi-restraints excluded: chain N residue 1017 SER Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain N residue 1158 MET Chi-restraints excluded: chain O residue 902 ASP Chi-restraints excluded: chain O residue 1017 SER Chi-restraints excluded: chain O residue 1063 GLU Chi-restraints excluded: chain O residue 1099 CYS Chi-restraints excluded: chain P residue 932 ARG Chi-restraints excluded: chain P residue 957 ASP Chi-restraints excluded: chain P residue 977 ARG Chi-restraints excluded: chain P residue 1018 GLU Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain P residue 1098 PHE Chi-restraints excluded: chain P residue 1115 MET Chi-restraints excluded: chain P residue 1138 GLU Chi-restraints excluded: chain Q residue 931 GLU Chi-restraints excluded: chain Q residue 990 ASN Chi-restraints excluded: chain Q residue 1007 GLU Chi-restraints excluded: chain Q residue 1018 GLU Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1113 MET Chi-restraints excluded: chain R residue 876 PHE Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 944 LEU Chi-restraints excluded: chain R residue 966 GLN Chi-restraints excluded: chain R residue 1004 LYS Chi-restraints excluded: chain R residue 1033 SER Chi-restraints excluded: chain R residue 1072 VAL Chi-restraints excluded: chain R residue 1138 GLU Chi-restraints excluded: chain R residue 1145 GLU Chi-restraints excluded: chain R residue 1158 MET Chi-restraints excluded: chain S residue 967 SER Chi-restraints excluded: chain S residue 1004 LYS Chi-restraints excluded: chain S residue 1018 GLU Chi-restraints excluded: chain S residue 1036 VAL Chi-restraints excluded: chain S residue 1106 SER Chi-restraints excluded: chain S residue 1108 LEU Chi-restraints excluded: chain S residue 1150 GLU Chi-restraints excluded: chain T residue 1118 SER Chi-restraints excluded: chain T residue 1150 GLU Chi-restraints excluded: chain T residue 1158 MET Chi-restraints excluded: chain U residue 947 ASN Chi-restraints excluded: chain U residue 953 THR Chi-restraints excluded: chain U residue 959 SER Chi-restraints excluded: chain U residue 1004 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 167 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 267 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 470 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 399 optimal weight: 7.9990 chunk 243 optimal weight: 0.9990 chunk 271 optimal weight: 4.9990 chunk 446 optimal weight: 2.9990 chunk 474 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 898 GLN B 941 ASN B 979 HIS B1037 ASN B1069 ASN C 889 HIS C1048 HIS ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 937 GLN D 966 GLN E 947 ASN E 993 ASN E1022 ASN F1093 HIS ** F1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1146 GLN ** H1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 947 ASN L 884 ASN M1002 ASN R 937 GLN R 973 GLN S 937 GLN S1069 ASN T 880 GLN T 937 GLN T 947 ASN T 966 GLN T 993 ASN T1093 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115018 restraints weight = 43503.185| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.40 r_work: 0.3174 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.327 45939 Z= 0.160 Angle : 0.534 20.331 61797 Z= 0.279 Chirality : 0.043 0.138 6460 Planarity : 0.004 0.060 8040 Dihedral : 4.978 80.005 6286 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.09 % Allowed : 15.48 % Favored : 81.43 % 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: 0.82 (0.12), residues: 2040 sheet: -0.20 (0.13), residues: 1280 loop : -0.29 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG T1027 TYR 0.019 0.002 TYR B1090 PHE 0.024 0.001 PHE U1107 TRP 0.006 0.001 TRP M1006 HIS 0.028 0.001 HIS M1084 Details of bonding type rmsd covalent geometry : bond 0.00350 (45860) covalent geometry : angle 0.49142 (61740) hydrogen bonds : bond 0.04662 ( 1917) hydrogen bonds : angle 4.51571 ( 5232) metal coordination : bond 0.07340 ( 79) metal coordination : angle 6.88809 ( 57) *********************** 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 916 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 774 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 928 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7854 (mmtm) REVERT: B 1113 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6815 (tpp) REVERT: C 888 GLU cc_start: 0.8186 (tt0) cc_final: 0.7562 (pm20) REVERT: C 947 ASN cc_start: 0.7555 (m-40) cc_final: 0.7083 (m110) REVERT: C 1138 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6932 (mt-10) REVERT: D 947 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7262 (m-40) REVERT: D 972 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8019 (ttt) REVERT: D 1067 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7912 (tttp) REVERT: D 1072 VAL cc_start: 0.7577 (m) cc_final: 0.7172 (t) REVERT: D 1087 ARG cc_start: 0.7712 (mtm-85) cc_final: 0.7353 (mtm-85) REVERT: D 1113 MET cc_start: 0.7951 (ptm) cc_final: 0.7598 (ptt) REVERT: E 977 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7360 (mpt180) REVERT: E 1113 MET cc_start: 0.7460 (tpt) cc_final: 0.7217 (tpt) REVERT: F 972 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7233 (tpt) REVERT: H 883 ARG cc_start: 0.8582 (ttp-170) cc_final: 0.8330 (ttp-170) REVERT: H 902 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8493 (p0) REVERT: H 947 ASN cc_start: 0.7805 (t0) cc_final: 0.7356 (m-40) REVERT: I 1143 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8065 (mtt180) REVERT: J 972 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.6982 (tpt) REVERT: L 1004 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7889 (mtpp) REVERT: L 1054 MET cc_start: 0.8136 (ttm) cc_final: 0.7816 (ttt) REVERT: L 1138 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6835 (tp30) REVERT: M 1004 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7867 (mppt) REVERT: M 1063 GLU cc_start: 0.7879 (pm20) cc_final: 0.7046 (pp20) REVERT: M 1067 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8375 (ttmm) REVERT: O 963 LYS cc_start: 0.8385 (pttt) cc_final: 0.7363 (tptt) REVERT: O 1063 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: O 1087 ARG cc_start: 0.6310 (mtm-85) cc_final: 0.5840 (mtm-85) REVERT: P 977 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7630 (tpp-160) REVERT: P 1018 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: Q 931 GLU cc_start: 0.7751 (tt0) cc_final: 0.7396 (tt0) REVERT: Q 963 LYS cc_start: 0.7371 (tppt) cc_final: 0.7116 (ttpp) REVERT: Q 1007 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8518 (mt-10) REVERT: Q 1028 MET cc_start: 0.9155 (mmt) cc_final: 0.8914 (mmt) REVERT: Q 1113 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6459 (tpp) REVERT: R 876 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6573 (t80) REVERT: R 966 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.5812 (mt0) REVERT: R 1004 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7834 (ttpm) REVERT: R 1022 ASN cc_start: 0.8759 (t0) cc_final: 0.8083 (t0) REVERT: R 1138 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7428 (tp30) REVERT: R 1145 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8259 (pm20) REVERT: S 967 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8023 (p) REVERT: S 990 ASN cc_start: 0.7646 (t0) cc_final: 0.7167 (p0) REVERT: S 1004 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7729 (mtpp) REVERT: S 1113 MET cc_start: 0.7965 (tpp) cc_final: 0.7245 (ttp) REVERT: T 1109 GLN cc_start: 0.7255 (mt0) cc_final: 0.6516 (tt0) REVERT: T 1113 MET cc_start: 0.7754 (mmm) cc_final: 0.7065 (mmm) REVERT: T 1115 MET cc_start: 0.7107 (mtm) cc_final: 0.6263 (mtt) REVERT: U 888 GLU cc_start: 0.7900 (tp30) cc_final: 0.7255 (mm-30) REVERT: U 937 GLN cc_start: 0.4861 (mt0) cc_final: 0.3772 (mt0) REVERT: U 964 GLU cc_start: 0.7742 (tt0) cc_final: 0.7334 (tt0) REVERT: U 1004 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7311 (UNCLASSIFIED) REVERT: U 1109 GLN cc_start: 0.7467 (tt0) cc_final: 0.6582 (tt0) REVERT: U 1113 MET cc_start: 0.7766 (tpp) cc_final: 0.7405 (tpp) outliers start: 142 outliers final: 68 residues processed: 836 average time/residue: 0.4800 time to fit residues: 490.3706 Evaluate side-chains 856 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 761 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 1098 PHE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 1067 LYS Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain E residue 957 ASP Chi-restraints excluded: chain E residue 977 ARG Chi-restraints excluded: chain F residue 882 VAL Chi-restraints excluded: chain F residue 902 ASP Chi-restraints excluded: chain F residue 947 ASN Chi-restraints excluded: chain F residue 957 ASP Chi-restraints excluded: chain F residue 972 MET Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 1036 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1106 SER Chi-restraints excluded: chain F residue 1113 MET Chi-restraints excluded: chain F residue 1118 SER Chi-restraints excluded: chain F residue 1126 THR Chi-restraints excluded: chain F residue 1143 ARG Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain G residue 1143 ARG Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 910 LYS Chi-restraints excluded: chain H residue 957 ASP Chi-restraints excluded: chain H residue 1004 LYS Chi-restraints excluded: chain H residue 1108 LEU Chi-restraints excluded: chain H residue 1126 THR Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1143 ARG Chi-restraints excluded: chain I residue 1150 GLU Chi-restraints excluded: chain J residue 913 LYS Chi-restraints excluded: chain J residue 963 LYS Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1036 VAL Chi-restraints excluded: chain L residue 1004 LYS Chi-restraints excluded: chain L residue 1108 LEU Chi-restraints excluded: chain L residue 1138 GLU Chi-restraints excluded: chain L residue 1154 THR Chi-restraints excluded: chain M residue 947 ASN Chi-restraints excluded: chain M residue 1004 LYS Chi-restraints excluded: chain M residue 1067 LYS Chi-restraints excluded: chain M residue 1092 CYS Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain M residue 1118 SER Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 988 ILE Chi-restraints excluded: chain N residue 1017 SER Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain O residue 902 ASP Chi-restraints excluded: chain O residue 1017 SER Chi-restraints excluded: chain O residue 1063 GLU Chi-restraints excluded: chain O residue 1099 CYS Chi-restraints excluded: chain P residue 977 ARG Chi-restraints excluded: chain P residue 1018 GLU Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain P residue 1098 PHE Chi-restraints excluded: chain P residue 1108 LEU Chi-restraints excluded: chain P residue 1115 MET Chi-restraints excluded: chain Q residue 990 ASN Chi-restraints excluded: chain Q residue 1007 GLU Chi-restraints excluded: chain Q residue 1018 GLU Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1113 MET Chi-restraints excluded: chain R residue 876 PHE Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 944 LEU Chi-restraints excluded: chain R residue 966 GLN Chi-restraints excluded: chain R residue 1004 LYS Chi-restraints excluded: chain R residue 1033 SER Chi-restraints excluded: chain R residue 1072 VAL Chi-restraints excluded: chain R residue 1138 GLU Chi-restraints excluded: chain R residue 1145 GLU Chi-restraints excluded: chain R residue 1158 MET Chi-restraints excluded: chain S residue 967 SER Chi-restraints excluded: chain S residue 1004 LYS Chi-restraints excluded: chain S residue 1018 GLU Chi-restraints excluded: chain S residue 1036 VAL Chi-restraints excluded: chain S residue 1106 SER Chi-restraints excluded: chain S residue 1108 LEU Chi-restraints excluded: chain T residue 1118 SER Chi-restraints excluded: chain U residue 947 ASN Chi-restraints excluded: chain U residue 953 THR Chi-restraints excluded: chain U residue 959 SER Chi-restraints excluded: chain U residue 1004 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 428 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 chunk 554 optimal weight: 10.0000 chunk 543 optimal weight: 8.9990 chunk 424 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 289 optimal weight: 0.9980 chunk 331 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1109 GLN ** B 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1037 ASN B1069 ASN B1109 GLN ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 993 ASN D1022 ASN E 947 ASN E 993 ASN E1022 ASN F 889 HIS ** F1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1093 HIS G1146 GLN ** H1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 947 ASN L 884 ASN M1002 ASN O 941 ASN P 941 ASN R 937 GLN R 973 GLN S 937 GLN S 941 ASN S1069 ASN T 880 GLN T 937 GLN T 947 ASN T 966 GLN T1093 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114839 restraints weight = 43103.167| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.38 r_work: 0.3171 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.355 45939 Z= 0.170 Angle : 0.551 21.870 61797 Z= 0.285 Chirality : 0.043 0.137 6460 Planarity : 0.004 0.054 8040 Dihedral : 4.996 79.147 6286 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.91 % Allowed : 15.83 % Favored : 81.26 % 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: 0.09 (0.11), residues: 5640 helix: 0.82 (0.12), residues: 2040 sheet: -0.34 (0.14), residues: 1300 loop : -0.24 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T1027 TYR 0.019 0.002 TYR Q1139 PHE 0.024 0.001 PHE U1107 TRP 0.008 0.002 TRP T1006 HIS 0.029 0.001 HIS M1084 Details of bonding type rmsd covalent geometry : bond 0.00375 (45860) covalent geometry : angle 0.49931 (61740) hydrogen bonds : bond 0.04751 ( 1917) hydrogen bonds : angle 4.51746 ( 5232) metal coordination : bond 0.07880 ( 79) metal coordination : angle 7.67311 ( 57) *********************** 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 902 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 768 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1109 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.6346 (tt0) REVERT: B 928 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7862 (mmtm) REVERT: B 1113 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6832 (tpp) REVERT: C 888 GLU cc_start: 0.8197 (tt0) cc_final: 0.7575 (pm20) REVERT: C 947 ASN cc_start: 0.7586 (m-40) cc_final: 0.7112 (m110) REVERT: C 969 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: C 1138 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6979 (mt-10) REVERT: D 947 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.7277 (m-40) REVERT: D 972 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8009 (ttt) REVERT: D 1067 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7923 (tttp) REVERT: D 1072 VAL cc_start: 0.7575 (m) cc_final: 0.7174 (t) REVERT: D 1087 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7354 (mtm-85) REVERT: E 977 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7369 (mpt180) REVERT: E 1093 HIS cc_start: 0.7785 (m170) cc_final: 0.7425 (m170) REVERT: E 1113 MET cc_start: 0.7427 (tpt) cc_final: 0.7214 (tpt) REVERT: F 972 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7228 (tpt) REVERT: F 1109 GLN cc_start: 0.7902 (tp40) cc_final: 0.7481 (tp-100) REVERT: H 883 ARG cc_start: 0.8582 (ttp-170) cc_final: 0.8318 (ttp-170) REVERT: H 902 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8495 (p0) REVERT: H 947 ASN cc_start: 0.7802 (t0) cc_final: 0.7349 (m-40) REVERT: H 1113 MET cc_start: 0.7875 (ptm) cc_final: 0.7590 (ptm) REVERT: I 1143 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8072 (mtt180) REVERT: J 972 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.6981 (tpt) REVERT: L 1004 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7899 (mtpp) REVERT: L 1037 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8341 (t0) REVERT: L 1054 MET cc_start: 0.8127 (ttm) cc_final: 0.7815 (ttt) REVERT: L 1138 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6850 (tp30) REVERT: M 1004 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7878 (mppt) REVERT: M 1063 GLU cc_start: 0.7883 (pm20) cc_final: 0.7049 (pp20) REVERT: M 1067 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8382 (ttmm) REVERT: O 963 LYS cc_start: 0.8391 (pttt) cc_final: 0.7373 (tptt) REVERT: O 1063 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: O 1087 ARG cc_start: 0.6294 (mtm-85) cc_final: 0.5837 (mtm-85) REVERT: P 932 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7923 (mtp180) REVERT: P 943 TYR cc_start: 0.7894 (t80) cc_final: 0.7687 (t80) REVERT: P 977 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7636 (tpp-160) REVERT: P 1018 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: P 1138 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: Q 931 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: Q 963 LYS cc_start: 0.7369 (tppt) cc_final: 0.7107 (ttpp) REVERT: Q 1007 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: Q 1113 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6507 (tpp) REVERT: R 876 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.6579 (t80) REVERT: R 1004 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7843 (ttpm) REVERT: R 1022 ASN cc_start: 0.8772 (t0) cc_final: 0.8091 (t0) REVERT: R 1138 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: R 1145 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: S 967 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.8003 (p) REVERT: S 990 ASN cc_start: 0.7643 (t0) cc_final: 0.7164 (p0) REVERT: S 1004 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7750 (mtpp) REVERT: S 1113 MET cc_start: 0.7943 (tpp) cc_final: 0.7271 (ttp) REVERT: T 1109 GLN cc_start: 0.7236 (mt0) cc_final: 0.6485 (tt0) REVERT: T 1113 MET cc_start: 0.7753 (mmm) cc_final: 0.7037 (mmm) REVERT: T 1115 MET cc_start: 0.7056 (mtm) cc_final: 0.6230 (mtt) REVERT: U 888 GLU cc_start: 0.7891 (tp30) cc_final: 0.7249 (mm-30) REVERT: U 937 GLN cc_start: 0.4822 (mt0) cc_final: 0.3752 (mt0) REVERT: U 964 GLU cc_start: 0.7722 (tt0) cc_final: 0.7316 (tt0) REVERT: U 1004 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7307 (UNCLASSIFIED) REVERT: U 1109 GLN cc_start: 0.7478 (tt0) cc_final: 0.6579 (tt0) REVERT: U 1113 MET cc_start: 0.7725 (tpp) cc_final: 0.7424 (tpp) outliers start: 134 outliers final: 71 residues processed: 829 average time/residue: 0.4755 time to fit residues: 481.0211 Evaluate side-chains 865 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 762 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain B residue 928 LYS Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1098 PHE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain D residue 947 ASN Chi-restraints excluded: chain D residue 972 MET Chi-restraints excluded: chain D residue 993 ASN Chi-restraints excluded: chain D residue 1067 LYS Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain E residue 947 ASN Chi-restraints excluded: chain E residue 977 ARG Chi-restraints excluded: chain F residue 882 VAL Chi-restraints excluded: chain F residue 902 ASP Chi-restraints excluded: chain F residue 947 ASN Chi-restraints excluded: chain F residue 957 ASP Chi-restraints excluded: chain F residue 972 MET Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 1036 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1106 SER Chi-restraints excluded: chain F residue 1118 SER Chi-restraints excluded: chain F residue 1126 THR Chi-restraints excluded: chain F residue 1143 ARG Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain G residue 1143 ARG Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 910 LYS Chi-restraints excluded: chain H residue 957 ASP Chi-restraints excluded: chain H residue 1004 LYS Chi-restraints excluded: chain H residue 1108 LEU Chi-restraints excluded: chain H residue 1126 THR Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1111 SER Chi-restraints excluded: chain I residue 1143 ARG Chi-restraints excluded: chain I residue 1150 GLU Chi-restraints excluded: chain J residue 913 LYS Chi-restraints excluded: chain J residue 963 LYS Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1036 VAL Chi-restraints excluded: chain L residue 1004 LYS Chi-restraints excluded: chain L residue 1037 ASN Chi-restraints excluded: chain L residue 1108 LEU Chi-restraints excluded: chain L residue 1138 GLU Chi-restraints excluded: chain L residue 1154 THR Chi-restraints excluded: chain M residue 947 ASN Chi-restraints excluded: chain M residue 1004 LYS Chi-restraints excluded: chain M residue 1067 LYS Chi-restraints excluded: chain M residue 1092 CYS Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain M residue 1118 SER Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 988 ILE Chi-restraints excluded: chain N residue 1017 SER Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain O residue 902 ASP Chi-restraints excluded: chain O residue 1017 SER Chi-restraints excluded: chain O residue 1063 GLU Chi-restraints excluded: chain O residue 1099 CYS Chi-restraints excluded: chain P residue 932 ARG Chi-restraints excluded: chain P residue 977 ARG Chi-restraints excluded: chain P residue 1018 GLU Chi-restraints excluded: chain P residue 1036 VAL Chi-restraints excluded: chain P residue 1098 PHE Chi-restraints excluded: chain P residue 1108 LEU Chi-restraints excluded: chain P residue 1115 MET Chi-restraints excluded: chain P residue 1138 GLU Chi-restraints excluded: chain Q residue 931 GLU Chi-restraints excluded: chain Q residue 990 ASN Chi-restraints excluded: chain Q residue 1007 GLU Chi-restraints excluded: chain Q residue 1018 GLU Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1113 MET Chi-restraints excluded: chain R residue 876 PHE Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 944 LEU Chi-restraints excluded: chain R residue 1004 LYS Chi-restraints excluded: chain R residue 1033 SER Chi-restraints excluded: chain R residue 1072 VAL Chi-restraints excluded: chain R residue 1138 GLU Chi-restraints excluded: chain R residue 1145 GLU Chi-restraints excluded: chain R residue 1158 MET Chi-restraints excluded: chain S residue 967 SER Chi-restraints excluded: chain S residue 1004 LYS Chi-restraints excluded: chain S residue 1018 GLU Chi-restraints excluded: chain S residue 1036 VAL Chi-restraints excluded: chain S residue 1106 SER Chi-restraints excluded: chain S residue 1108 LEU Chi-restraints excluded: chain T residue 1118 SER Chi-restraints excluded: chain U residue 947 ASN Chi-restraints excluded: chain U residue 953 THR Chi-restraints excluded: chain U residue 959 SER Chi-restraints excluded: chain U residue 1004 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 33 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 120 optimal weight: 0.0270 chunk 128 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 301 optimal weight: 0.3980 chunk 308 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1109 GLN B 941 ASN B1037 ASN B1069 ASN C 979 HIS ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1156 GLN E 947 ASN E 993 ASN E1022 ASN ** F1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1093 HIS G1146 GLN ** H1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 947 ASN L 884 ASN M1002 ASN O 941 ASN R 937 GLN R 973 GLN S 937 GLN S1069 ASN T 880 GLN T 937 GLN T 947 ASN T 966 GLN T1093 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.117602 restraints weight = 43513.566| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.28 r_work: 0.3217 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.319 45939 Z= 0.107 Angle : 0.502 19.055 61797 Z= 0.258 Chirality : 0.041 0.200 6460 Planarity : 0.003 0.052 8040 Dihedral : 4.715 81.251 6286 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.93 % Allowed : 16.87 % Favored : 81.20 % 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: 0.42 (0.11), residues: 5640 helix: 1.15 (0.12), residues: 2040 sheet: 0.04 (0.14), residues: 1160 loop : -0.24 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG T1027 TYR 0.018 0.001 TYR B1090 PHE 0.025 0.001 PHE U1107 TRP 0.007 0.001 TRP T1006 HIS 0.033 0.001 HIS M1084 Details of bonding type rmsd covalent geometry : bond 0.00193 (45860) covalent geometry : angle 0.45187 (61740) hydrogen bonds : bond 0.03691 ( 1917) hydrogen bonds : angle 4.29285 ( 5232) metal coordination : bond 0.07291 ( 79) metal coordination : angle 7.23854 ( 57) ********************** 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 910 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 821 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1113 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6702 (tpt) REVERT: C 888 GLU cc_start: 0.8094 (tt0) cc_final: 0.7452 (pm20) REVERT: C 947 ASN cc_start: 0.7500 (m-40) cc_final: 0.7003 (m110) REVERT: C 969 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: C 972 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.6712 (tpt) REVERT: C 1113 MET cc_start: 0.7817 (ptm) cc_final: 0.7516 (ptp) REVERT: C 1138 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6909 (mt-10) REVERT: D 1067 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7820 (tttp) REVERT: D 1072 VAL cc_start: 0.7497 (m) cc_final: 0.7160 (t) REVERT: D 1087 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7374 (mtm-85) REVERT: D 1113 MET cc_start: 0.7924 (ptm) cc_final: 0.7592 (ptt) REVERT: E 977 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7419 (mpt180) REVERT: E 1093 HIS cc_start: 0.7788 (m170) cc_final: 0.7454 (m170) REVERT: E 1113 MET cc_start: 0.7310 (tpt) cc_final: 0.7099 (tpt) REVERT: F 891 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8396 (tpt) REVERT: F 1109 GLN cc_start: 0.7610 (tp40) cc_final: 0.7152 (tp-100) REVERT: G 1070 GLN cc_start: 0.8679 (mt0) cc_final: 0.8420 (mt0) REVERT: H 883 ARG cc_start: 0.8552 (ttp-170) cc_final: 0.8340 (ttp-170) REVERT: H 902 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8461 (p0) REVERT: H 947 ASN cc_start: 0.7538 (t0) cc_final: 0.7196 (m-40) REVERT: H 1109 GLN cc_start: 0.8498 (mt0) cc_final: 0.8071 (tt0) REVERT: J 972 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7088 (tpt) REVERT: J 1063 GLU cc_start: 0.7631 (tt0) cc_final: 0.6889 (tm-30) REVERT: L 1004 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7844 (mtpp) REVERT: L 1054 MET cc_start: 0.8048 (ttm) cc_final: 0.7746 (ttt) REVERT: M 896 ARG cc_start: 0.8035 (mtt-85) cc_final: 0.7412 (mtp180) REVERT: M 1004 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7829 (mppt) REVERT: M 1063 GLU cc_start: 0.7869 (pm20) cc_final: 0.6977 (pp20) REVERT: M 1067 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8235 (ttmm) REVERT: N 888 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8256 (tp30) REVERT: N 1113 MET cc_start: 0.7752 (ttt) cc_final: 0.7443 (ttm) REVERT: O 910 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7769 (ttpp) REVERT: O 963 LYS cc_start: 0.8363 (pttt) cc_final: 0.7374 (tptt) REVERT: O 1087 ARG cc_start: 0.6266 (mtm-85) cc_final: 0.5839 (mtm-85) REVERT: P 943 TYR cc_start: 0.7857 (t80) cc_final: 0.7650 (t80) REVERT: P 971 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7174 (mm-30) REVERT: P 1018 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6914 (tt0) REVERT: Q 931 GLU cc_start: 0.7696 (tt0) cc_final: 0.7324 (tt0) REVERT: Q 963 LYS cc_start: 0.7322 (tppt) cc_final: 0.7024 (ttpp) REVERT: Q 1007 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8476 (mt-10) REVERT: Q 1028 MET cc_start: 0.8998 (mmt) cc_final: 0.8583 (mmt) REVERT: Q 1113 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6412 (tpp) REVERT: Q 1115 MET cc_start: 0.7823 (mtm) cc_final: 0.7475 (mtt) REVERT: R 876 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.6500 (t80) REVERT: R 1004 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7788 (ttpm) REVERT: R 1022 ASN cc_start: 0.8731 (t0) cc_final: 0.8013 (t0) REVERT: R 1138 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7403 (tp30) REVERT: S 990 ASN cc_start: 0.7654 (t0) cc_final: 0.7190 (p0) REVERT: S 1113 MET cc_start: 0.7937 (tpp) cc_final: 0.7316 (ttp) REVERT: T 1004 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7462 (mppt) REVERT: T 1109 GLN cc_start: 0.7195 (mt0) cc_final: 0.6484 (tt0) REVERT: T 1113 MET cc_start: 0.7733 (mmm) cc_final: 0.7014 (mmm) REVERT: T 1115 MET cc_start: 0.7077 (mtm) cc_final: 0.6332 (mtt) REVERT: U 888 GLU cc_start: 0.7843 (tp30) cc_final: 0.7268 (mm-30) REVERT: U 937 GLN cc_start: 0.4759 (mt0) cc_final: 0.3696 (mt0) REVERT: U 940 LEU cc_start: 0.7320 (mp) cc_final: 0.7106 (mt) REVERT: U 964 GLU cc_start: 0.7691 (tt0) cc_final: 0.7280 (tt0) REVERT: U 1004 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7293 (UNCLASSIFIED) REVERT: U 1027 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7531 (mmm-85) REVERT: U 1109 GLN cc_start: 0.7476 (tt0) cc_final: 0.6557 (tt0) REVERT: U 1113 MET cc_start: 0.7741 (tpp) cc_final: 0.7464 (tpp) outliers start: 89 outliers final: 42 residues processed: 856 average time/residue: 0.4717 time to fit residues: 492.2015 Evaluate side-chains 837 residues out of total 4860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 777 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 972 MET Chi-restraints excluded: chain C residue 1098 PHE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain D residue 1067 LYS Chi-restraints excluded: chain D residue 1126 THR Chi-restraints excluded: chain E residue 947 ASN Chi-restraints excluded: chain E residue 977 ARG Chi-restraints excluded: chain F residue 882 VAL Chi-restraints excluded: chain F residue 891 MET Chi-restraints excluded: chain F residue 902 ASP Chi-restraints excluded: chain F residue 947 ASN Chi-restraints excluded: chain F residue 957 ASP Chi-restraints excluded: chain F residue 1036 VAL Chi-restraints excluded: chain F residue 1098 PHE Chi-restraints excluded: chain F residue 1126 THR Chi-restraints excluded: chain F residue 1143 ARG Chi-restraints excluded: chain G residue 1126 THR Chi-restraints excluded: chain G residue 1143 ARG Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 1108 LEU Chi-restraints excluded: chain I residue 1036 VAL Chi-restraints excluded: chain I residue 1098 PHE Chi-restraints excluded: chain I residue 1150 GLU Chi-restraints excluded: chain J residue 913 LYS Chi-restraints excluded: chain J residue 963 LYS Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain L residue 1004 LYS Chi-restraints excluded: chain M residue 947 ASN Chi-restraints excluded: chain M residue 1004 LYS Chi-restraints excluded: chain M residue 1067 LYS Chi-restraints excluded: chain M residue 1098 PHE Chi-restraints excluded: chain N residue 988 ILE Chi-restraints excluded: chain N residue 1018 GLU Chi-restraints excluded: chain O residue 902 ASP Chi-restraints excluded: chain P residue 1018 GLU Chi-restraints excluded: chain P residue 1098 PHE Chi-restraints excluded: chain P residue 1115 MET Chi-restraints excluded: chain Q residue 990 ASN Chi-restraints excluded: chain Q residue 1007 GLU Chi-restraints excluded: chain Q residue 1018 GLU Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1113 MET Chi-restraints excluded: chain R residue 876 PHE Chi-restraints excluded: chain R residue 944 LEU Chi-restraints excluded: chain R residue 1004 LYS Chi-restraints excluded: chain R residue 1033 SER Chi-restraints excluded: chain R residue 1138 GLU Chi-restraints excluded: chain R residue 1145 GLU Chi-restraints excluded: chain R residue 1158 MET Chi-restraints excluded: chain S residue 1018 GLU Chi-restraints excluded: chain S residue 1106 SER Chi-restraints excluded: chain T residue 1118 SER Chi-restraints excluded: chain U residue 947 ASN Chi-restraints excluded: chain U residue 953 THR Chi-restraints excluded: chain U residue 959 SER Chi-restraints excluded: chain U residue 1004 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 151 optimal weight: 0.5980 chunk 474 optimal weight: 6.9990 chunk 517 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 459 optimal weight: 5.9990 chunk 273 optimal weight: 8.9990 chunk 533 optimal weight: 9.9990 chunk 529 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 476 optimal weight: 8.9990 chunk 504 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 898 GLN B 941 ASN B1037 ASN B1069 ASN C 993 ASN ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 941 ASN E 947 ASN E 993 ASN E1022 ASN F1109 GLN G1093 HIS G1146 GLN ** H1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 889 HIS I 966 GLN J 947 ASN L 884 ASN L1022 ASN L1109 GLN M1002 ASN O 941 ASN R 937 GLN R 973 GLN S 937 GLN S1069 ASN T 937 GLN T 947 ASN T 966 GLN T1093 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114182 restraints weight = 43357.592| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.26 r_work: 0.3158 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.350 45939 Z= 0.250 Angle : 0.615 21.498 61797 Z= 0.319 Chirality : 0.046 0.155 6460 Planarity : 0.004 0.043 8040 Dihedral : 5.147 76.956 6286 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.85 % Allowed : 17.30 % Favored : 80.85 % 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: 0.05 (0.11), residues: 5640 helix: 0.76 (0.12), residues: 2040 sheet: -0.32 (0.14), residues: 1300 loop : -0.25 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T1027 TYR 0.023 0.002 TYR Q1139 PHE 0.026 0.002 PHE U1107 TRP 0.009 0.002 TRP T1006 HIS 0.026 0.002 HIS P1084 Details of bonding type rmsd covalent geometry : bond 0.00574 (45860) covalent geometry : angle 0.56521 (61740) hydrogen bonds : bond 0.05547 ( 1917) hydrogen bonds : angle 4.64901 ( 5232) metal coordination : bond 0.09024 ( 79) metal coordination : angle 7.96876 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17668.89 seconds wall clock time: 300 minutes 29.62 seconds (18029.62 seconds total)