Starting phenix.real_space_refine on Wed Jan 22 10:18:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7egq_31138/01_2025/7egq_31138_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7egq_31138/01_2025/7egq_31138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7egq_31138/01_2025/7egq_31138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7egq_31138/01_2025/7egq_31138.map" model { file = "/net/cci-nas-00/data/ceres_data/7egq_31138/01_2025/7egq_31138_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7egq_31138/01_2025/7egq_31138_neut.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17521 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 26 6.06 5 P 116 5.49 5 Mg 3 5.21 5 S 416 5.16 5 C 34193 2.51 5 N 9243 2.21 5 O 10550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 54547 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7462 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Chain: "B" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1400 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1418 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 4567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4559 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 556} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 588, 4559 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 556} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 4653 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 121} Chain: "K" Number of atoms: 4169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4169 Classifications: {'peptide': 523} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PTRANS': 26, 'TRANS': 492} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 7462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7462 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Chain: "O" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1400 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "P" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "Q" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1418 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "R" Number of atoms: 4567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4559 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 556} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 588, 4559 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 556} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 4653 Chain: "T" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "U" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 947 Classifications: {'peptide': 130} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 121} Chain: "X" Number of atoms: 4177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4177 Classifications: {'peptide': 524} Link IDs: {'CIS': 5, 'PTRANS': 26, 'TRANS': 492} Chain: "F" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 692 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 19} Link IDs: {'rna2p': 2, 'rna3p': 30} Chain: "L" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "M" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 692 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 18} Link IDs: {'rna2p': 3, 'rna3p': 29} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 2, ' ZN': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 65.490 68.697 176.860 1.00 55.74 S ATOM 2487 SG CYS A 306 66.286 68.110 173.167 1.00 53.32 S ATOM 2519 SG CYS A 310 62.714 68.903 174.340 1.00 49.59 S ATOM 3927 SG CYS A 487 80.661 75.931 189.877 1.00 51.82 S ATOM 5180 SG CYS A 645 81.798 75.317 186.237 1.00 57.87 S ATOM 5186 SG CYS A 646 78.785 73.434 187.678 1.00 61.40 S ATOM 10937 SG CYS E 16 78.491 121.771 244.477 1.00243.61 S ATOM 10952 SG CYS E 19 75.010 120.289 245.496 1.00249.46 S ATOM 10855 SG CYS E 5 73.085 131.165 240.359 1.00247.81 S ATOM 10876 SG CYS E 8 72.312 134.666 241.819 1.00250.69 S ATOM 11014 SG CYS E 26 75.953 133.722 240.625 1.00246.27 S ATOM 11031 SG CYS E 29 74.427 132.436 243.660 1.00246.73 S ATOM 11196 SG CYS E 50 98.173 120.253 238.814 1.00233.68 S ATOM 11226 SG CYS E 55 99.254 118.079 241.896 1.00242.96 S ATOM 11359 SG CYS E 72 100.288 121.848 241.913 1.00232.45 S ATOM 16788 SG CYS H 74 39.543 40.119 115.225 1.00 79.74 S ATOM 16814 SG CYS H 77 39.047 42.783 117.881 1.00 79.74 S ATOM 16919 SG CYS H 90 36.074 40.913 116.442 1.00 91.16 S ATOM 17122 SG CYS H 117 24.815 26.980 109.500 1.00159.18 S ATOM 17142 SG CYS H 120 24.201 25.972 110.284 1.00169.69 S ATOM 17215 SG CYS H 130 22.377 25.808 106.454 1.00202.41 S ATOM 18840 SG CYS K 207 57.079 48.951 89.738 1.00 79.74 S ATOM 18860 SG CYS K 210 58.226 50.781 87.155 1.00 79.74 S ATOM 18981 SG CYS K 226 60.566 51.647 89.814 1.00 79.74 S ATOM 19281 SG CYS K 261 84.088 62.095 111.841 1.00 79.74 S ATOM 19411 SG CYS K 279 82.504 58.673 110.606 1.00 79.74 S ATOM 20801 SG CYS K 452 104.169 61.577 59.938 1.00108.12 S ATOM 21028 SG CYS K 484 101.170 64.406 60.832 1.00 93.58 S ATOM 23838 SG CYS N 301 59.381 129.390 110.662 1.00 46.56 S ATOM 23879 SG CYS N 306 60.006 130.130 114.361 1.00 46.29 S ATOM 23911 SG CYS N 310 56.683 128.622 113.159 1.00 40.34 S ATOM 25319 SG CYS N 487 75.830 125.404 97.798 1.00 48.93 S ATOM 26572 SG CYS N 645 76.783 126.241 101.446 1.00 53.10 S ATOM 26578 SG CYS N 646 73.463 127.466 99.974 1.00 52.49 S ATOM 32329 SG CYS R 16 84.414 80.250 43.627 1.00170.29 S ATOM 32344 SG CYS R 19 80.901 80.039 42.081 1.00172.43 S ATOM 32247 SG CYS R 5 80.068 69.401 47.992 1.00171.68 S ATOM 32268 SG CYS R 8 80.074 65.830 46.423 1.00175.29 S ATOM 32406 SG CYS R 26 83.268 67.508 47.283 1.00171.25 S ATOM 32423 SG CYS R 29 81.357 68.710 44.362 1.00169.36 S ATOM 32588 SG CYS R 50 102.498 86.034 49.244 1.00156.57 S ATOM 32618 SG CYS R 55 102.116 87.719 45.880 1.00179.22 S ATOM 32751 SG CYS R 72 104.722 85.004 46.261 1.00161.23 S ATOM 38180 SG CYS U 74 27.606 152.095 172.061 1.00103.80 S ATOM 38206 SG CYS U 77 28.124 149.358 169.483 1.00 99.95 S ATOM 38311 SG CYS U 90 24.678 150.768 170.150 1.00126.49 S ATOM 38514 SG CYS U 117 10.285 160.545 179.106 1.00193.93 S ATOM 38534 SG CYS U 120 9.983 162.879 177.105 1.00202.41 S ATOM 38607 SG CYS U 130 7.877 163.003 180.427 1.00228.75 S ATOM 40238 SG CYS X 207 47.202 147.519 197.699 1.00 79.74 S ATOM 40258 SG CYS X 210 49.146 147.425 200.688 1.00 79.74 S ATOM 40379 SG CYS X 226 50.396 145.277 197.816 1.00 79.74 S ATOM 40679 SG CYS X 261 76.297 139.908 176.697 1.00 83.92 S ATOM 40809 SG CYS X 279 73.647 142.860 176.940 1.00 79.74 S ATOM 42199 SG CYS X 452 95.966 144.369 227.709 1.00156.03 S ATOM 42431 SG CYS X 484 92.646 142.177 228.637 1.00151.49 S ATOM 42811 SG CYS F 5 91.002 73.398 236.317 1.00275.65 S ATOM 42832 SG CYS F 8 91.728 75.710 239.006 1.00278.91 S ATOM 42970 SG CYS F 26 94.467 75.571 236.534 1.00291.20 S ATOM 42991 SG CYS F 29 94.193 72.502 238.028 1.00294.83 S ATOM 43156 SG CYS F 50 104.359 74.205 212.662 1.00290.42 S ATOM 43186 SG CYS F 55 106.588 71.274 211.799 1.00282.78 S ATOM 43319 SG CYS F 72 108.080 74.392 213.206 1.00292.75 S ATOM 42893 SG CYS F 16 94.031 66.730 229.199 1.00296.46 S ATOM 42908 SG CYS F 19 93.580 63.086 229.977 1.00301.84 S ATOM 47441 SG CYS S 5 86.019 129.997 51.719 1.00244.24 S ATOM 47462 SG CYS S 8 87.351 127.766 49.144 1.00247.73 S ATOM 47600 SG CYS S 26 89.847 128.738 51.561 1.00247.83 S ATOM 47621 SG CYS S 29 89.148 131.443 49.836 1.00248.91 S ATOM 47786 SG CYS S 50 98.901 131.785 75.289 1.00262.30 S ATOM 47816 SG CYS S 55 100.384 135.149 76.132 1.00272.21 S ATOM 47949 SG CYS S 72 102.688 132.616 75.079 1.00265.36 S ATOM 47523 SG CYS S 16 88.223 137.641 59.452 1.00250.57 S ATOM 47538 SG CYS S 19 85.825 140.283 57.850 1.00253.85 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET E 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.59 residue: pdb=" N AMET R 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET R 474 " occ=0.59 Time building chain proxies: 25.88, per 1000 atoms: 0.47 Number of scatterers: 54547 At special positions: 0 Unit cell: (149.46, 200.34, 288.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 26 29.99 S 416 16.00 P 116 15.00 Mg 3 11.99 O 10550 8.00 N 9243 7.00 C 34193 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.11 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb=" ZN H 200 " pdb="ZN ZN H 200 " - pdb=" NE2 HIS H 83 " pdb="ZN ZN H 200 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 200 " - pdb=" SG CYS H 74 " pdb="ZN ZN H 200 " - pdb=" SG CYS H 77 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 120 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 117 " pdb=" ZN K 600 " pdb="ZN ZN K 600 " - pdb=" SG CYS K 226 " pdb="ZN ZN K 600 " - pdb=" SG CYS K 210 " pdb="ZN ZN K 600 " - pdb=" ND1 HIS K 229 " pdb="ZN ZN K 600 " - pdb=" SG CYS K 207 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" ND1 HIS K 264 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 257 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 261 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 279 " pdb=" ZN K 602 " pdb="ZN ZN K 602 " - pdb=" ND1 HIS K 487 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 452 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 484 " pdb=" ZN N1001 " pdb="ZN ZN N1001 " - pdb=" ND1 HIS N 295 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 310 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 301 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 306 " pdb=" ZN N1002 " pdb="ZN ZN N1002 " - pdb=" ND1 HIS N 642 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 487 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 646 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 645 " pdb=" ZN R 701 " pdb="ZN ZN R 701 " - pdb=" NE2 HIS R 33 " pdb="ZN ZN R 701 " - pdb=" ND1 HIS R 39 " pdb="ZN ZN R 701 " - pdb=" SG CYS R 16 " pdb="ZN ZN R 701 " - pdb=" SG CYS R 19 " pdb=" ZN R 702 " pdb="ZN ZN R 702 " - pdb=" SG CYS R 26 " pdb="ZN ZN R 702 " - pdb=" SG CYS R 8 " pdb="ZN ZN R 702 " - pdb=" SG CYS R 29 " pdb="ZN ZN R 702 " - pdb=" SG CYS R 5 " pdb=" ZN R 703 " pdb="ZN ZN R 703 " - pdb=" ND1 HIS R 75 " pdb="ZN ZN R 703 " - pdb=" SG CYS R 55 " pdb="ZN ZN R 703 " - pdb=" SG CYS R 50 " pdb="ZN ZN R 703 " - pdb=" SG CYS R 72 " pdb=" ZN S1000 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 26 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 8 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 29 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 5 " pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" ND1 HIS S 75 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 55 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 72 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 50 " pdb=" ZN S1002 " pdb="ZN ZN S1002 " - pdb=" ND1 HIS S 39 " pdb="ZN ZN S1002 " - pdb=" ND1 HIS S 33 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 19 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 16 " pdb=" ZN U 200 " pdb="ZN ZN U 200 " - pdb=" NE2 HIS U 83 " pdb="ZN ZN U 200 " - pdb=" SG CYS U 74 " pdb="ZN ZN U 200 " - pdb=" SG CYS U 90 " pdb="ZN ZN U 200 " - pdb=" SG CYS U 77 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 120 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 130 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 117 " pdb=" ZN X 600 " pdb="ZN ZN X 600 " - pdb=" SG CYS X 210 " pdb="ZN ZN X 600 " - pdb=" NE2 HIS X 229 " pdb="ZN ZN X 600 " - pdb=" SG CYS X 226 " pdb="ZN ZN X 600 " - pdb=" SG CYS X 207 " pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" NE2 HIS X 257 " pdb="ZN ZN X 601 " - pdb=" NE2 HIS X 264 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 261 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 279 " pdb=" ZN X 602 " pdb="ZN ZN X 602 " - pdb=" SG CYS X 484 " pdb="ZN ZN X 602 " - pdb=" SG CYS X 452 " pdb="ZN ZN X 602 " - pdb=" NE2 HIS X 487 " Number of angles added : 71 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12620 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 76 sheets defined 39.6% alpha, 11.8% beta 42 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 15.13 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 removed outlier: 3.863A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.548A pdb=" N ASN A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.987A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 248 Proline residue: A 243 - end of helix removed outlier: 4.059A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.636A pdb=" N THR A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 removed outlier: 3.892A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.880A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.657A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.611A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.781A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 4.038A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.702A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 518 removed outlier: 4.085A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.628A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.604A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.503A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.514A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.690A pdb=" N CYS A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 855 through 867 removed outlier: 4.021A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 875 through 903 removed outlier: 3.535A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.687A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 31 through 52 removed outlier: 3.664A pdb=" N LEU B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 96 Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.737A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 26 through 42 removed outlier: 3.690A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.724A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.842A pdb=" N LYS C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 28 Processing helix chain 'D' and resid 33 through 82 removed outlier: 3.724A pdb=" N LEU D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 4.324A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 59 through 63 removed outlier: 3.926A pdb=" N LEU E 63 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.612A pdb=" N THR E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 removed outlier: 3.687A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 145 Processing helix chain 'E' and resid 259 through 264 removed outlier: 3.861A pdb=" N SER E 264 " --> pdb=" O ASP E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 274 Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.950A pdb=" N ALA E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 325 removed outlier: 3.596A pdb=" N VAL E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 328 No H-bonds generated for 'chain 'E' and resid 326 through 328' Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 424 through 431 Processing helix chain 'E' and resid 445 through 457 Processing helix chain 'E' and resid 490 through 503 Processing helix chain 'E' and resid 504 through 508 removed outlier: 3.995A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 526 Processing helix chain 'E' and resid 533 through 537 Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 579 through 585 Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'H' and resid 7 through 9 No H-bonds generated for 'chain 'H' and resid 7 through 9' Processing helix chain 'H' and resid 10 through 19 Processing helix chain 'H' and resid 22 through 33 Processing helix chain 'H' and resid 74 through 80 Processing helix chain 'H' and resid 106 through 114 removed outlier: 3.650A pdb=" N PHE H 110 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 76 through 82 removed outlier: 3.724A pdb=" N HIS K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 155 removed outlier: 4.153A pdb=" N HIS K 148 " --> pdb=" O GLN K 145 " (cutoff:3.500A) Proline residue: K 151 - end of helix removed outlier: 3.748A pdb=" N TYR K 154 " --> pdb=" O PRO K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 175 removed outlier: 3.502A pdb=" N VAL K 162 " --> pdb=" O PRO K 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 195 removed outlier: 3.942A pdb=" N GLU K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 248 removed outlier: 3.582A pdb=" N GLY K 248 " --> pdb=" O GLN K 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 245 through 248' Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 270 through 287 removed outlier: 3.711A pdb=" N CYS K 285 " --> pdb=" O ALA K 281 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL K 287 " --> pdb=" O HIS K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 325 removed outlier: 3.963A pdb=" N ILE K 305 " --> pdb=" O ASP K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 374 removed outlier: 3.827A pdb=" N SER K 374 " --> pdb=" O TYR K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 437 removed outlier: 3.508A pdb=" N VAL K 437 " --> pdb=" O SER K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 485 through 504 Processing helix chain 'K' and resid 516 through 524 removed outlier: 3.699A pdb=" N TRP K 520 " --> pdb=" O THR K 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 12 Processing helix chain 'N' and resid 61 through 63 No H-bonds generated for 'chain 'N' and resid 61 through 63' Processing helix chain 'N' and resid 76 through 91 Processing helix chain 'N' and resid 123 through 133 Processing helix chain 'N' and resid 139 through 149 Processing helix chain 'N' and resid 153 through 159 removed outlier: 3.548A pdb=" N ASN N 158 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 177 Processing helix chain 'N' and resid 178 through 199 Processing helix chain 'N' and resid 206 through 210 removed outlier: 3.988A pdb=" N ASN N 209 " --> pdb=" O THR N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 248 Proline residue: N 243 - end of helix removed outlier: 4.059A pdb=" N THR N 246 " --> pdb=" O MET N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 254 removed outlier: 3.635A pdb=" N THR N 252 " --> pdb=" O ARG N 249 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA N 253 " --> pdb=" O ALA N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 288 removed outlier: 3.892A pdb=" N ARG N 279 " --> pdb=" O PHE N 275 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS N 288 " --> pdb=" O ASP N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 301 Processing helix chain 'N' and resid 303 through 318 removed outlier: 3.881A pdb=" N PHE N 313 " --> pdb=" O HIS N 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 326 removed outlier: 3.656A pdb=" N SER N 325 " --> pdb=" O PRO N 322 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE N 326 " --> pdb=" O PRO N 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 322 through 326' Processing helix chain 'N' and resid 367 through 376 Processing helix chain 'N' and resid 377 through 384 removed outlier: 4.611A pdb=" N HIS N 381 " --> pdb=" O ASP N 377 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 426 Processing helix chain 'N' and resid 448 through 454 Processing helix chain 'N' and resid 455 through 459 removed outlier: 3.780A pdb=" N TYR N 458 " --> pdb=" O TYR N 455 " (cutoff:3.500A) Processing helix chain 'N' and resid 465 through 479 removed outlier: 4.038A pdb=" N GLU N 474 " --> pdb=" O LEU N 470 " (cutoff:3.500A) Processing helix chain 'N' and resid 489 through 493 removed outlier: 3.702A pdb=" N VAL N 493 " --> pdb=" O ALA N 490 " (cutoff:3.500A) Processing helix chain 'N' and resid 505 through 509 Processing helix chain 'N' and resid 511 through 518 removed outlier: 4.085A pdb=" N TYR N 515 " --> pdb=" O LYS N 511 " (cutoff:3.500A) Processing helix chain 'N' and resid 520 through 532 Processing helix chain 'N' and resid 561 through 580 removed outlier: 3.628A pdb=" N THR N 565 " --> pdb=" O SER N 561 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR N 567 " --> pdb=" O CYS N 563 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN N 570 " --> pdb=" O MET N 566 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS N 574 " --> pdb=" O GLN N 570 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU N 575 " --> pdb=" O PHE N 571 " (cutoff:3.500A) Processing helix chain 'N' and resid 596 through 606 Processing helix chain 'N' and resid 621 through 626 removed outlier: 3.605A pdb=" N MET N 626 " --> pdb=" O CYS N 622 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 640 removed outlier: 3.503A pdb=" N ARG N 631 " --> pdb=" O PRO N 627 " (cutoff:3.500A) Processing helix chain 'N' and resid 647 through 663 Processing helix chain 'N' and resid 686 through 709 Processing helix chain 'N' and resid 717 through 733 Processing helix chain 'N' and resid 738 through 753 Processing helix chain 'N' and resid 768 through 774 Processing helix chain 'N' and resid 778 through 791 removed outlier: 3.514A pdb=" N PHE N 782 " --> pdb=" O SER N 778 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN N 791 " --> pdb=" O TYR N 787 " (cutoff:3.500A) Processing helix chain 'N' and resid 795 through 799 removed outlier: 3.689A pdb=" N CYS N 799 " --> pdb=" O GLU N 796 " (cutoff:3.500A) Processing helix chain 'N' and resid 833 through 842 Processing helix chain 'N' and resid 856 through 867 Processing helix chain 'N' and resid 868 through 872 Processing helix chain 'N' and resid 875 through 903 removed outlier: 3.535A pdb=" N ASP N 879 " --> pdb=" O GLN N 875 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE N 881 " --> pdb=" O TYR N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 912 through 917 removed outlier: 3.687A pdb=" N TRP N 916 " --> pdb=" O SER N 913 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU N 917 " --> pdb=" O ARG N 914 " (cutoff:3.500A) Processing helix chain 'N' and resid 921 through 926 Processing helix chain 'O' and resid 9 through 29 Processing helix chain 'O' and resid 31 through 96 removed outlier: 3.752A pdb=" N ARG O 51 " --> pdb=" O SER O 47 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLN O 56 " --> pdb=" O ASP O 52 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG O 96 " --> pdb=" O PHE O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 110 removed outlier: 4.283A pdb=" N ASN O 104 " --> pdb=" O ASN O 100 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA O 110 " --> pdb=" O ILE O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 125 removed outlier: 4.022A pdb=" N LEU O 122 " --> pdb=" O ASN O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 142 removed outlier: 3.588A pdb=" N TYR O 138 " --> pdb=" O ASP O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 172 removed outlier: 3.521A pdb=" N ILE O 172 " --> pdb=" O LEU O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 180 Processing helix chain 'P' and resid 3 through 20 Processing helix chain 'P' and resid 21 through 25 Processing helix chain 'P' and resid 26 through 42 removed outlier: 3.562A pdb=" N ALA P 30 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU P 41 " --> pdb=" O ASN P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 61 removed outlier: 3.724A pdb=" N ALA P 48 " --> pdb=" O ASP P 44 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU P 59 " --> pdb=" O LEU P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 71 removed outlier: 3.841A pdb=" N LYS P 70 " --> pdb=" O VAL P 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 32 through 41 removed outlier: 3.960A pdb=" N LEU Q 38 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS Q 39 " --> pdb=" O LEU Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 81 removed outlier: 3.564A pdb=" N ARG Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 99 removed outlier: 3.848A pdb=" N GLN Q 88 " --> pdb=" O THR Q 84 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 112 removed outlier: 4.467A pdb=" N ILE Q 106 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 141 removed outlier: 3.646A pdb=" N TYR Q 138 " --> pdb=" O ASP Q 134 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN Q 140 " --> pdb=" O ASN Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 180 removed outlier: 3.783A pdb=" N LEU Q 180 " --> pdb=" O SER Q 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 36 Processing helix chain 'R' and resid 59 through 61 No H-bonds generated for 'chain 'R' and resid 59 through 61' Processing helix chain 'R' and resid 102 through 112 removed outlier: 4.071A pdb=" N PHE R 106 " --> pdb=" O ASN R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 125 removed outlier: 3.910A pdb=" N TYR R 120 " --> pdb=" O ASN R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 145 Processing helix chain 'R' and resid 265 through 274 Processing helix chain 'R' and resid 287 through 299 Processing helix chain 'R' and resid 310 through 325 removed outlier: 4.189A pdb=" N VAL R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 328 No H-bonds generated for 'chain 'R' and resid 326 through 328' Processing helix chain 'R' and resid 380 through 391 Processing helix chain 'R' and resid 423 through 431 Processing helix chain 'R' and resid 445 through 456 Processing helix chain 'R' and resid 490 through 503 Processing helix chain 'R' and resid 504 through 507 Processing helix chain 'R' and resid 515 through 526 Processing helix chain 'R' and resid 557 through 566 Processing helix chain 'R' and resid 579 through 585 Processing helix chain 'T' and resid 95 through 110 Processing helix chain 'U' and resid 7 through 9 No H-bonds generated for 'chain 'U' and resid 7 through 9' Processing helix chain 'U' and resid 10 through 20 removed outlier: 3.823A pdb=" N ALA U 20 " --> pdb=" O PHE U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 33 Processing helix chain 'U' and resid 70 through 74 removed outlier: 3.813A pdb=" N CYS U 74 " --> pdb=" O GLY U 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 70 through 74' Processing helix chain 'U' and resid 74 through 80 Processing helix chain 'U' and resid 106 through 114 removed outlier: 3.647A pdb=" N PHE U 110 " --> pdb=" O ASP U 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 82 Processing helix chain 'X' and resid 143 through 155 removed outlier: 4.110A pdb=" N HIS X 148 " --> pdb=" O GLN X 145 " (cutoff:3.500A) Proline residue: X 151 - end of helix removed outlier: 3.579A pdb=" N LYS X 155 " --> pdb=" O LEU X 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 175 removed outlier: 4.330A pdb=" N ILE X 164 " --> pdb=" O ASN X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 195 removed outlier: 3.719A pdb=" N GLU X 191 " --> pdb=" O ALA X 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 198 No H-bonds generated for 'chain 'X' and resid 196 through 198' Processing helix chain 'X' and resid 245 through 248 removed outlier: 3.564A pdb=" N GLY X 248 " --> pdb=" O GLN X 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 245 through 248' Processing helix chain 'X' and resid 252 through 258 Processing helix chain 'X' and resid 269 through 287 removed outlier: 3.757A pdb=" N ASP X 273 " --> pdb=" O VAL X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 302 through 325 Processing helix chain 'X' and resid 372 through 376 removed outlier: 3.612A pdb=" N ASP X 375 " --> pdb=" O THR X 372 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS X 376 " --> pdb=" O HIS X 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 372 through 376' Processing helix chain 'X' and resid 484 through 504 Processing helix chain 'X' and resid 516 through 524 removed outlier: 3.584A pdb=" N TRP X 520 " --> pdb=" O THR X 516 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR X 524 " --> pdb=" O TRP X 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.506A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR F 37 " --> pdb=" O HIS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 102 through 111 removed outlier: 3.719A pdb=" N PHE F 106 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 removed outlier: 4.072A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 273 removed outlier: 4.467A pdb=" N ASN F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.611A pdb=" N ALA F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 5.149A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA F 321 " --> pdb=" O LEU F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 380 through 391 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 445 through 449 Processing helix chain 'F' and resid 451 through 455 removed outlier: 3.606A pdb=" N ALA F 454 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 494 Processing helix chain 'F' and resid 515 through 525 removed outlier: 3.811A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 536 Processing helix chain 'F' and resid 557 through 566 Processing helix chain 'F' and resid 580 through 585 removed outlier: 4.021A pdb=" N LYS F 584 " --> pdb=" O ASP F 580 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 580 through 585' Processing helix chain 'S' and resid 26 through 37 removed outlier: 3.665A pdb=" N THR S 37 " --> pdb=" O HIS S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 112 Processing helix chain 'S' and resid 116 through 125 Processing helix chain 'S' and resid 127 through 149 removed outlier: 3.680A pdb=" N TYR S 149 " --> pdb=" O PHE S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 259 through 261 No H-bonds generated for 'chain 'S' and resid 259 through 261' Processing helix chain 'S' and resid 262 through 275 removed outlier: 4.066A pdb=" N ALA S 267 " --> pdb=" O SER S 263 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN S 268 " --> pdb=" O SER S 264 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS S 271 " --> pdb=" O ALA S 267 " (cutoff:3.500A) Processing helix chain 'S' and resid 289 through 299 Processing helix chain 'S' and resid 310 through 319 Processing helix chain 'S' and resid 361 through 363 No H-bonds generated for 'chain 'S' and resid 361 through 363' Processing helix chain 'S' and resid 380 through 391 Processing helix chain 'S' and resid 418 through 422 Processing helix chain 'S' and resid 423 through 432 Processing helix chain 'S' and resid 445 through 449 Processing helix chain 'S' and resid 489 through 494 Processing helix chain 'S' and resid 515 through 525 removed outlier: 3.682A pdb=" N ILE S 525 " --> pdb=" O VAL S 521 " (cutoff:3.500A) Processing helix chain 'S' and resid 532 through 537 removed outlier: 3.817A pdb=" N GLN S 537 " --> pdb=" O VAL S 533 " (cutoff:3.500A) Processing helix chain 'S' and resid 557 through 566 Processing helix chain 'S' and resid 580 through 584 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 59 removed outlier: 5.191A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.233A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.665A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.815A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.565A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 544 Processing sheet with id=AB1, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB2, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.682A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB5, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AB6, first strand: chain 'E' and resid 64 through 66 removed outlier: 3.572A pdb=" N GLY E 66 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.620A pdb=" N GLU E 156 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 347 through 348 removed outlier: 7.442A pdb=" N CYS E 330 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR E 367 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA E 393 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP E 369 " --> pdb=" O ALA E 393 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLY E 400 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU E 280 " --> pdb=" O GLY E 400 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 530 through 532 removed outlier: 6.296A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP E 542 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 480 through 481 Processing sheet with id=AC2, first strand: chain 'G' and resid 67 through 68 removed outlier: 3.549A pdb=" N THR G 67 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ALA G 16 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP G 26 " --> pdb=" O ALA G 16 " (cutoff:3.500A) removed outlier: 10.639A pdb=" N ASN G 27 " --> pdb=" O SER G 46 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER G 46 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU G 29 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU G 44 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR G 31 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY G 38 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 65 through 69 Processing sheet with id=AC4, first strand: chain 'K' and resid 34 through 35 Processing sheet with id=AC5, first strand: chain 'K' and resid 116 through 118 removed outlier: 3.700A pdb=" N GLN K 108 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE K 87 " --> pdb=" O VAL K 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 95 through 96 Processing sheet with id=AC7, first strand: chain 'K' and resid 122 through 126 Processing sheet with id=AC8, first strand: chain 'K' and resid 216 through 218 removed outlier: 3.536A pdb=" N ALA K 225 " --> pdb=" O CYS K 216 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR K 223 " --> pdb=" O SER K 218 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 347 through 348 removed outlier: 3.685A pdb=" N ILE K 332 " --> pdb=" O LEU K 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 351 through 352 Processing sheet with id=AD2, first strand: chain 'K' and resid 399 through 401 Processing sheet with id=AD3, first strand: chain 'K' and resid 411 through 412 Processing sheet with id=AD4, first strand: chain 'K' and resid 439 through 440 Processing sheet with id=AD5, first strand: chain 'K' and resid 446 through 447 removed outlier: 6.385A pdb=" N TYR K 446 " --> pdb=" O ILE K 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'N' and resid 18 through 21 removed outlier: 4.407A pdb=" N ARG N 18 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER N 68 " --> pdb=" O GLU N 58 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 31 through 38 Processing sheet with id=AD8, first strand: chain 'N' and resid 223 through 224 removed outlier: 7.233A pdb=" N VAL N 233 " --> pdb=" O ILE N 201 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY N 203 " --> pdb=" O VAL N 233 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 353 through 355 removed outlier: 6.665A pdb=" N LEU N 329 " --> pdb=" O THR N 344 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 334 through 335 Processing sheet with id=AE2, first strand: chain 'N' and resid 387 through 390 removed outlier: 6.864A pdb=" N ILE O 185 " --> pdb=" O VAL O 159 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL O 159 " --> pdb=" O ILE O 185 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR O 187 " --> pdb=" O GLN O 157 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU O 153 " --> pdb=" O ALA O 191 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 397 through 400 removed outlier: 6.564A pdb=" N SER N 397 " --> pdb=" O VAL N 675 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL N 675 " --> pdb=" O SER N 397 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA N 399 " --> pdb=" O LEU N 673 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 414 through 415 Processing sheet with id=AE5, first strand: chain 'N' and resid 540 through 544 Processing sheet with id=AE6, first strand: chain 'N' and resid 755 through 758 Processing sheet with id=AE7, first strand: chain 'N' and resid 816 through 822 Processing sheet with id=AE8, first strand: chain 'Q' and resid 115 through 116 removed outlier: 3.785A pdb=" N VAL Q 115 " --> pdb=" O VAL Q 131 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL Q 130 " --> pdb=" O VAL Q 186 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 3 through 4 Processing sheet with id=AF1, first strand: chain 'R' and resid 15 through 16 Processing sheet with id=AF2, first strand: chain 'R' and resid 63 through 66 Processing sheet with id=AF3, first strand: chain 'R' and resid 84 through 85 Processing sheet with id=AF4, first strand: chain 'R' and resid 193 through 198 removed outlier: 5.830A pdb=" N GLN R 194 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG R 186 " --> pdb=" O GLN R 194 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY R 196 " --> pdb=" O GLY R 184 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP R 223 " --> pdb=" O VAL R 154 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N HIS R 164 " --> pdb=" O ARG R 155 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL R 157 " --> pdb=" O GLU R 162 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLU R 162 " --> pdb=" O VAL R 157 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 277 through 279 removed outlier: 6.767A pdb=" N SER R 278 " --> pdb=" O TYR R 398 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL R 305 " --> pdb=" O VAL R 372 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA R 308 " --> pdb=" O CYS R 358 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER R 331 " --> pdb=" O PHE R 357 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N THR R 359 " --> pdb=" O SER R 331 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N CYS R 330 " --> pdb=" O LYS R 347 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 440 through 441 removed outlier: 7.078A pdb=" N LYS R 462 " --> pdb=" O CYS R 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'R' and resid 530 through 531 removed outlier: 5.985A pdb=" N PHE R 511 " --> pdb=" O GLN R 531 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS R 471 " --> pdb=" O THR R 588 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 480 through 483 removed outlier: 3.685A pdb=" N SER R 486 " --> pdb=" O ASP R 483 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 67 through 68 removed outlier: 3.549A pdb=" N THR T 67 " --> pdb=" O ALA T 54 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA T 15 " --> pdb=" O ARG T 55 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG T 10 " --> pdb=" O TYR T 32 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR T 32 " --> pdb=" O ARG T 10 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA T 16 " --> pdb=" O ASP T 26 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP T 26 " --> pdb=" O ALA T 16 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N ASN T 27 " --> pdb=" O SER T 46 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER T 46 " --> pdb=" O ASN T 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU T 29 " --> pdb=" O LEU T 44 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU T 44 " --> pdb=" O LEU T 29 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR T 31 " --> pdb=" O LEU T 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY T 38 " --> pdb=" O THR T 35 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE T 75 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 65 through 69 Processing sheet with id=AG2, first strand: chain 'X' and resid 53 through 54 removed outlier: 3.591A pdb=" N ARG X 53 " --> pdb=" O ASP X 126 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 117 through 118 removed outlier: 7.732A pdb=" N ASN X 104 " --> pdb=" O ALA X 96 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA X 96 " --> pdb=" O ASN X 104 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS X 94 " --> pdb=" O PRO X 106 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP X 90 " --> pdb=" O GLY X 110 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 184 through 185 Processing sheet with id=AG5, first strand: chain 'X' and resid 216 through 218 removed outlier: 3.587A pdb=" N SER X 218 " --> pdb=" O THR X 223 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR X 223 " --> pdb=" O SER X 218 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 347 through 348 removed outlier: 6.328A pdb=" N VAL X 328 " --> pdb=" O VAL X 381 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 351 through 352 Processing sheet with id=AG8, first strand: chain 'X' and resid 398 through 401 removed outlier: 3.705A pdb=" N VAL X 398 " --> pdb=" O TRP X 509 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 418 through 421 Processing sheet with id=AH1, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AH2, first strand: chain 'F' and resid 70 through 72 removed outlier: 3.563A pdb=" N PHE F 81 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.688A pdb=" N ALA F 85 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 154 through 156 removed outlier: 7.127A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.230A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR F 307 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 472 through 473 removed outlier: 6.355A pdb=" N PHE F 472 " --> pdb=" O LEU F 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'F' and resid 511 through 512 removed outlier: 6.239A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU F 573 " --> pdb=" O PHE F 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'S' and resid 3 through 4 Processing sheet with id=AH9, first strand: chain 'S' and resid 15 through 16 Processing sheet with id=AI1, first strand: chain 'S' and resid 70 through 71 Processing sheet with id=AI2, first strand: chain 'S' and resid 154 through 156 removed outlier: 3.565A pdb=" N ARG S 212 " --> pdb=" O THR S 199 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN S 194 " --> pdb=" O ARG S 186 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG S 186 " --> pdb=" O GLN S 194 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY S 196 " --> pdb=" O GLY S 184 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'S' and resid 277 through 280 removed outlier: 6.379A pdb=" N VAL S 371 " --> pdb=" O VAL S 397 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE S 399 " --> pdb=" O VAL S 371 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE S 373 " --> pdb=" O ILE S 399 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE S 304 " --> pdb=" O VAL S 356 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N CYS S 358 " --> pdb=" O ILE S 304 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR S 306 " --> pdb=" O CYS S 358 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'S' and resid 511 through 512 removed outlier: 5.977A pdb=" N ILE S 512 " --> pdb=" O THR S 547 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE S 575 " --> pdb=" O PHE S 546 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS S 574 " --> pdb=" O CYS S 471 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE S 472 " --> pdb=" O LEU S 590 " (cutoff:3.500A) 2041 hydrogen bonds defined for protein. 5670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 21.27 Time building geometry restraints manager: 11.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 8617 1.29 - 1.42: 15445 1.42 - 1.56: 31114 1.56 - 1.69: 239 1.69 - 1.83: 578 Bond restraints: 55993 Sorted by residual: bond pdb=" CA HIS A 810 " pdb=" C HIS A 810 " ideal model delta sigma weight residual 1.525 1.414 0.111 1.29e-02 6.01e+03 7.40e+01 bond pdb=" N HIS A 810 " pdb=" CA HIS A 810 " ideal model delta sigma weight residual 1.458 1.360 0.098 1.27e-02 6.20e+03 5.92e+01 bond pdb=" CA SER A 607 " pdb=" C SER A 607 " ideal model delta sigma weight residual 1.526 1.423 0.103 1.35e-02 5.49e+03 5.78e+01 bond pdb=" C1' G M 21 " pdb=" N9 G M 21 " ideal model delta sigma weight residual 1.475 1.371 0.104 1.50e-02 4.44e+03 4.83e+01 bond pdb=" C HIS A 810 " pdb=" O HIS A 810 " ideal model delta sigma weight residual 1.235 1.149 0.085 1.23e-02 6.61e+03 4.82e+01 ... (remaining 55988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.30: 76258 9.30 - 18.60: 292 18.60 - 27.90: 58 27.90 - 37.19: 18 37.19 - 46.49: 10 Bond angle restraints: 76636 Sorted by residual: angle pdb=" N ASP T 25 " pdb=" CA ASP T 25 " pdb=" C ASP T 25 " ideal model delta sigma weight residual 110.97 157.46 -46.49 1.09e+00 8.42e-01 1.82e+03 angle pdb=" N GLY R 170 " pdb=" CA GLY R 170 " pdb=" C GLY R 170 " ideal model delta sigma weight residual 112.64 158.62 -45.98 1.21e+00 6.83e-01 1.44e+03 angle pdb=" N CYS X 208 " pdb=" CA CYS X 208 " pdb=" C CYS X 208 " ideal model delta sigma weight residual 111.11 152.10 -40.99 1.20e+00 6.94e-01 1.17e+03 angle pdb=" N TYR A 217 " pdb=" CA TYR A 217 " pdb=" C TYR A 217 " ideal model delta sigma weight residual 114.04 154.65 -40.61 1.24e+00 6.50e-01 1.07e+03 angle pdb=" N SER S 536 " pdb=" CA SER S 536 " pdb=" C SER S 536 " ideal model delta sigma weight residual 113.23 148.46 -35.23 1.24e+00 6.50e-01 8.07e+02 ... (remaining 76631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 31873 33.95 - 67.89: 1629 67.89 - 101.84: 121 101.84 - 135.79: 2 135.79 - 169.73: 1 Dihedral angle restraints: 33626 sinusoidal: 14036 harmonic: 19590 Sorted by residual: dihedral pdb=" C MET N 855 " pdb=" N MET N 855 " pdb=" CA MET N 855 " pdb=" CB MET N 855 " ideal model delta harmonic sigma weight residual -122.60 -77.65 -44.95 0 2.50e+00 1.60e-01 3.23e+02 dihedral pdb=" C SER F 536 " pdb=" N SER F 536 " pdb=" CA SER F 536 " pdb=" CB SER F 536 " ideal model delta harmonic sigma weight residual -122.60 -79.39 -43.21 0 2.50e+00 1.60e-01 2.99e+02 dihedral pdb=" C LYS K 469 " pdb=" N LYS K 469 " pdb=" CA LYS K 469 " pdb=" CB LYS K 469 " ideal model delta harmonic sigma weight residual -122.60 -79.52 -43.08 0 2.50e+00 1.60e-01 2.97e+02 ... (remaining 33623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 8649 0.352 - 0.704: 96 0.704 - 1.056: 11 1.056 - 1.409: 6 1.409 - 1.761: 8 Chirality restraints: 8770 Sorted by residual: chirality pdb=" CA LYS X 423 " pdb=" N LYS X 423 " pdb=" C LYS X 423 " pdb=" CB LYS X 423 " both_signs ideal model delta sigma weight residual False 2.51 0.75 1.76 2.00e-01 2.50e+01 7.75e+01 chirality pdb=" CA LEU R 147 " pdb=" N LEU R 147 " pdb=" C LEU R 147 " pdb=" CB LEU R 147 " both_signs ideal model delta sigma weight residual False 2.51 0.77 1.74 2.00e-01 2.50e+01 7.58e+01 chirality pdb=" CA CYS X 208 " pdb=" N CYS X 208 " pdb=" C CYS X 208 " pdb=" CB CYS X 208 " both_signs ideal model delta sigma weight residual False 2.51 0.84 1.67 2.00e-01 2.50e+01 6.97e+01 ... (remaining 8767 not shown) Planarity restraints: 9378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY N 808 " -0.094 5.00e-02 4.00e+02 1.39e-01 3.10e+01 pdb=" N PRO N 809 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO N 809 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO N 809 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 808 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C GLY A 808 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY A 808 " 0.030 2.00e-02 2.50e+03 pdb=" N PRO A 809 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP O 182 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO O 183 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO O 183 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO O 183 " 0.059 5.00e-02 4.00e+02 ... (remaining 9375 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 41 2.12 - 2.81: 18176 2.81 - 3.51: 77754 3.51 - 4.20: 131738 4.20 - 4.90: 218617 Nonbonded interactions: 446326 Sorted by model distance: nonbonded pdb=" OE1 GLU N 83 " pdb=" O PHE N 219 " model vdw 1.423 3.040 nonbonded pdb=" OE1 GLN A 822 " pdb=" OG1 THR A 926 " model vdw 1.511 3.040 nonbonded pdb=" CE1 TYR A 606 " pdb=" CD2 LEU A 805 " model vdw 1.637 3.760 nonbonded pdb=" N GLY N 23 " pdb=" O GLY N 23 " model vdw 1.721 2.496 nonbonded pdb=" O ASP T 26 " pdb=" OD1 ASP T 26 " model vdw 1.730 3.040 ... (remaining 446321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'N' } ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 191)) selection = (chain 'O' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'Q' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 191)) } ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = (chain 'E' and (resid 2 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 226 or (resid 227 and (name N or \ name CA or name C or name O or name CB )) or resid 228 through 287 or (resid 28 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 289 through \ 441 or (resid 442 through 443 and (name N or name CA or name C or name O or name \ CB )) or resid 444 through 473 or resid 475 through 592 or resid 701 through 70 \ 3)) selection = (chain 'F' and (resid 2 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 93 or (resid 94 and (name N or name \ CA or name C or name O or name CB )) or resid 95 through 100 or (resid 101 thro \ ugh 102 and (name N or name CA or name C or name O or name CB )) or resid 103 th \ rough 336 or resid 340 through 391 or (resid 392 through 393 and (name N or name \ CA or name C or name O or name CB )) or resid 394 through 473 or resid 475 thro \ ugh 523 or (resid 524 and (name N or name CA or name C or name O or name CB )) o \ r resid 525 through 590 or (resid 591 and (name N or name CA or name C or name O \ or name CB )) or resid 592 or resid 1000 through 1002)) selection = (chain 'R' and (resid 2 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 226 or (resid 227 and (name N or \ name CA or name C or name O or name CB )) or resid 228 through 287 or (resid 28 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 289 through \ 441 or (resid 442 through 443 and (name N or name CA or name C or name O or name \ CB )) or resid 444 through 473 or resid 475 through 592 or resid 701 through 70 \ 3)) selection = (chain 'S' and (resid 2 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 93 or (resid 94 and (name N or name \ CA or name C or name O or name CB )) or resid 95 through 100 or (resid 101 thro \ ugh 102 and (name N or name CA or name C or name O or name CB )) or resid 103 th \ rough 336 or resid 340 through 391 or (resid 392 through 393 and (name N or name \ CA or name C or name O or name CB )) or resid 394 through 473 or resid 475 thro \ ugh 523 or (resid 524 and (name N or name CA or name C or name O or name CB )) o \ r resid 525 through 590 or (resid 591 and (name N or name CA or name C or name O \ or name CB )) or resid 592 or resid 1000 through 1002)) } ncs_group { reference = chain 'G' selection = chain 'T' } ncs_group { reference = (chain 'H' and (resid 1 through 130 or resid 200 through 201)) selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = (chain 'K' and (resid 3 through 524 or resid 601 through 602 or resid 604)) selection = (chain 'X' and (resid 3 through 454 or (resid 455 and (name N or name CA or name \ C or name O or name CB )) or resid 456 through 524 or resid 600 through 601 or \ resid 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.320 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 111.400 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.008 0.111 55993 Z= 0.506 Angle : 1.560 46.492 76636 Z= 0.968 Chirality : 0.101 1.761 8770 Planarity : 0.006 0.139 9378 Dihedral : 18.689 169.732 21006 Min Nonbonded Distance : 1.423 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.49 % Favored : 88.93 % Rotamer: Outliers : 9.99 % Allowed : 17.51 % Favored : 72.51 % Cbeta Deviations : 2.46 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 1.07 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.09), residues: 6610 helix: -1.63 (0.09), residues: 2317 sheet: -2.48 (0.15), residues: 905 loop : -3.31 (0.09), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 182 HIS 0.016 0.002 HIS X 229 PHE 0.047 0.003 PHE A 881 TYR 0.038 0.002 TYR N 595 ARG 0.018 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 5781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 571 poor density : 426 time to evaluate : 4.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8219 (p0) REVERT: A 63 ASP cc_start: 0.8569 (m-30) cc_final: 0.7673 (t0) REVERT: A 138 ASN cc_start: 0.8767 (p0) cc_final: 0.8546 (p0) REVERT: A 583 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8763 (mpt180) REVERT: A 609 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7956 (t) REVERT: A 721 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8091 (mtp85) REVERT: A 847 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8924 (tt) REVERT: A 848 VAL cc_start: 0.9483 (OUTLIER) cc_final: 0.9237 (t) REVERT: A 899 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8291 (ttp) REVERT: A 904 SER cc_start: 0.7909 (OUTLIER) cc_final: 0.7367 (t) REVERT: B 69 GLN cc_start: 0.8412 (tm130) cc_final: 0.8109 (tm-30) REVERT: B 72 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8594 (pttm) REVERT: B 174 MET cc_start: 0.8502 (tpt) cc_final: 0.8163 (tpt) REVERT: D 49 PHE cc_start: 0.6903 (t80) cc_final: 0.6615 (t80) REVERT: D 55 MET cc_start: 0.8169 (ppp) cc_final: 0.7934 (ppp) REVERT: D 56 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: D 69 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7976 (tm-30) REVERT: E 167 TRP cc_start: 0.7220 (m-90) cc_final: 0.6963 (m-90) REVERT: G 66 TYR cc_start: 0.8050 (m-10) cc_final: 0.7425 (m-80) REVERT: G 92 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7428 (ttmm) REVERT: K 170 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8581 (mp) REVERT: K 241 MET cc_start: 0.9042 (mtt) cc_final: 0.8661 (mtt) REVERT: K 493 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8643 (mp) REVERT: N 103 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7526 (mtpp) REVERT: N 154 ASP cc_start: 0.8160 (t70) cc_final: 0.7809 (t0) REVERT: N 219 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: N 624 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8783 (mtt90) REVERT: N 714 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8504 (mmtm) REVERT: N 729 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: O 42 LEU cc_start: 0.4214 (OUTLIER) cc_final: 0.3929 (tt) REVERT: O 51 ARG cc_start: 0.3624 (OUTLIER) cc_final: 0.3142 (mmt180) REVERT: T 50 ASP cc_start: 0.6591 (OUTLIER) cc_final: 0.5520 (p0) REVERT: X 395 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7469 (p0) REVERT: X 400 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7616 (tpp80) REVERT: X 457 LYS cc_start: 0.6995 (tptt) cc_final: 0.6534 (tptt) REVERT: F 233 MET cc_start: 0.4745 (ptp) cc_final: 0.4517 (ppp) REVERT: S 164 HIS cc_start: 0.3590 (OUTLIER) cc_final: 0.3015 (m90) REVERT: S 554 HIS cc_start: -0.0049 (OUTLIER) cc_final: -0.0604 (t-170) outliers start: 571 outliers final: 285 residues processed: 934 average time/residue: 0.5279 time to fit residues: 819.4200 Evaluate side-chains 639 residues out of total 5781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 307 poor density : 332 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 HIS Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 221 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 261 CYS Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 291 ASP Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 303 LEU Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 462 ASP Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 470 SER Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 484 CYS Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 21 PRO Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 53 CYS Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 115 SER Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 160 LYS Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 277 GLU Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 325 SER Chi-restraints excluded: chain N residue 335 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 496 ASN Chi-restraints excluded: chain N residue 504 PHE Chi-restraints excluded: chain N residue 621 LYS Chi-restraints excluded: chain N residue 624 ARG Chi-restraints excluded: chain N residue 644 THR Chi-restraints excluded: chain N residue 667 VAL Chi-restraints excluded: chain N residue 680 THR Chi-restraints excluded: chain N residue 686 THR Chi-restraints excluded: chain N residue 708 LEU Chi-restraints excluded: chain N residue 710 THR Chi-restraints excluded: chain N residue 715 ILE Chi-restraints excluded: chain N residue 718 LYS Chi-restraints excluded: chain N residue 729 GLU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 740 ASP Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain N residue 807 LYS Chi-restraints excluded: chain N residue 820 VAL Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 919 GLU Chi-restraints excluded: chain N residue 926 THR Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 4 SER Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 114 CYS Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 159 VAL Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 383 ASP Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 458 ASP Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 55 ARG Chi-restraints excluded: chain T residue 68 GLU Chi-restraints excluded: chain T residue 75 PHE Chi-restraints excluded: chain T residue 81 LYS Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 47 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 90 CYS Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 193 THR Chi-restraints excluded: chain X residue 194 SER Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 207 CYS Chi-restraints excluded: chain X residue 212 ARG Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 317 VAL Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 387 CYS Chi-restraints excluded: chain X residue 395 ASN Chi-restraints excluded: chain X residue 396 SER Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 400 ARG Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 407 SER Chi-restraints excluded: chain X residue 414 CYS Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 437 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 470 SER Chi-restraints excluded: chain X residue 476 ARG Chi-restraints excluded: chain X residue 503 SER Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 255 THR Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 315 ASP Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 351 THR Chi-restraints excluded: chain S residue 383 ASP Chi-restraints excluded: chain S residue 387 VAL Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 455 LEU Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 549 THR Chi-restraints excluded: chain S residue 554 HIS Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 562 optimal weight: 6.9990 chunk 504 optimal weight: 0.5980 chunk 280 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 340 optimal weight: 4.9990 chunk 269 optimal weight: 0.0270 chunk 522 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 317 optimal weight: 0.8980 chunk 388 optimal weight: 20.0000 chunk 604 optimal weight: 5.9990 overall best weight: 1.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 HIS ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 HIS B 43 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 107 ASN E 164 HIS ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN G 11 GLN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 ASN ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 133 HIS ** N 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 408 GLN N 725 HIS ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 GLN U 62 ASN X 104 ASN X 228 HIS ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 478 ASN ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 489 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 HIS ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 GLN F 531 GLN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 404 GLN ** S 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.130634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.080716 restraints weight = 179989.310| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.27 r_work: 0.2963 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 55993 Z= 0.266 Angle : 0.731 14.116 76636 Z= 0.383 Chirality : 0.045 0.266 8770 Planarity : 0.005 0.086 9378 Dihedral : 13.735 162.517 9563 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.24 % Favored : 92.66 % Rotamer: Outliers : 5.61 % Allowed : 20.11 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 1.07 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.10), residues: 6610 helix: -0.32 (0.10), residues: 2346 sheet: -2.04 (0.15), residues: 923 loop : -2.65 (0.10), residues: 3341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 520 HIS 0.012 0.001 HIS X 487 PHE 0.026 0.002 PHE X 367 TYR 0.041 0.002 TYR X 465 ARG 0.010 0.001 ARG T 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 5781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 321 poor density : 359 time to evaluate : 4.499 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 63 ASP cc_start: 0.8567 (m-30) cc_final: 0.7794 (t0) REVERT: A 758 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8189 (tt) REVERT: A 806 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9053 (t) REVERT: A 899 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8204 (ttp) REVERT: A 904 SER cc_start: 0.7885 (OUTLIER) cc_final: 0.7264 (t) REVERT: B 48 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6374 (mm-30) REVERT: B 55 MET cc_start: 0.6402 (ptm) cc_final: 0.6147 (mmm) REVERT: B 69 GLN cc_start: 0.8347 (tm130) cc_final: 0.8013 (tm-30) REVERT: B 90 MET cc_start: 0.9158 (tmm) cc_final: 0.8528 (tmm) REVERT: C 67 ASP cc_start: 0.9391 (p0) cc_final: 0.9190 (p0) REVERT: D 60 GLU cc_start: 0.8503 (tp30) cc_final: 0.8224 (tp30) REVERT: D 64 ASP cc_start: 0.8662 (m-30) cc_final: 0.8307 (m-30) REVERT: D 69 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8121 (tm-30) REVERT: E 167 TRP cc_start: 0.7189 (m-90) cc_final: 0.6927 (m-90) REVERT: G 25 ASP cc_start: 0.7850 (t70) cc_final: 0.7530 (t70) REVERT: G 31 TYR cc_start: 0.7528 (m-80) cc_final: 0.7247 (m-80) REVERT: G 66 TYR cc_start: 0.8196 (m-10) cc_final: 0.7639 (m-80) REVERT: K 170 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8981 (mp) REVERT: N 63 ASP cc_start: 0.8822 (m-30) cc_final: 0.8349 (m-30) REVERT: N 83 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: N 154 ASP cc_start: 0.9043 (t70) cc_final: 0.8491 (t0) REVERT: N 219 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: N 463 MET cc_start: 0.8674 (ttt) cc_final: 0.8421 (ttt) REVERT: N 640 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8388 (ttt180) REVERT: N 714 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8422 (mmtm) REVERT: N 906 MET cc_start: 0.9052 (ttt) cc_final: 0.8834 (ttt) REVERT: O 55 MET cc_start: 0.8076 (mtp) cc_final: 0.7724 (ppp) REVERT: Q 155 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8277 (mm-30) REVERT: R 233 MET cc_start: 0.6956 (tpp) cc_final: 0.6747 (tpp) REVERT: T 40 PHE cc_start: 0.8735 (t80) cc_final: 0.8519 (t80) REVERT: T 50 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.5963 (p0) REVERT: U 29 ASP cc_start: 0.9060 (t0) cc_final: 0.8755 (t0) REVERT: F 511 PHE cc_start: -0.0379 (OUTLIER) cc_final: -0.0639 (m-80) REVERT: S 70 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7456 (p90) outliers start: 321 outliers final: 206 residues processed: 655 average time/residue: 0.5035 time to fit residues: 561.5065 Evaluate side-chains 544 residues out of total 5781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 327 time to evaluate : 4.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 188 HIS Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 291 ASP Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 484 CYS Chi-restraints excluded: chain K residue 489 ASN Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 160 LYS Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 335 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 640 ARG Chi-restraints excluded: chain N residue 644 THR Chi-restraints excluded: chain N residue 680 THR Chi-restraints excluded: chain N residue 710 THR Chi-restraints excluded: chain N residue 715 ILE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 740 ASP Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain N residue 807 LYS Chi-restraints excluded: chain N residue 820 VAL Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 883 LEU Chi-restraints excluded: chain N residue 899 MET Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 15 PHE Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 145 THR Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 290 HIS Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 75 PHE Chi-restraints excluded: chain T residue 92 LYS Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 51 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 207 CYS Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 236 VAL Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 279 CYS Chi-restraints excluded: chain X residue 317 VAL Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 255 THR Chi-restraints excluded: chain S residue 270 GLN Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 484 VAL Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 575 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 181 optimal weight: 10.0000 chunk 182 optimal weight: 30.0000 chunk 203 optimal weight: 8.9990 chunk 372 optimal weight: 0.0050 chunk 442 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 445 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 304 optimal weight: 0.3980 chunk 267 optimal weight: 0.9990 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 HIS N 356 ASN N 599 HIS N 790 ASN Q 158 GLN ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 290 HIS U 48 HIS X 82 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 478 ASN ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 519 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.130696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080459 restraints weight = 218797.747| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.57 r_work: 0.2937 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 55993 Z= 0.242 Angle : 0.658 14.265 76636 Z= 0.342 Chirality : 0.043 0.256 8770 Planarity : 0.005 0.058 9378 Dihedral : 12.826 161.067 9272 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.31 % Favored : 92.61 % Rotamer: Outliers : 5.00 % Allowed : 21.32 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 0.71 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.10), residues: 6610 helix: 0.19 (0.11), residues: 2357 sheet: -1.72 (0.16), residues: 884 loop : -2.25 (0.10), residues: 3369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 182 HIS 0.010 0.001 HIS S 554 PHE 0.019 0.002 PHE A 275 TYR 0.033 0.002 TYR B 71 ARG 0.006 0.001 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 5781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 286 poor density : 353 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8795 (m-30) cc_final: 0.7993 (t0) REVERT: A 758 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8271 (tt) REVERT: A 904 SER cc_start: 0.7806 (OUTLIER) cc_final: 0.7316 (t) REVERT: B 55 MET cc_start: 0.6616 (ptm) cc_final: 0.6404 (mmp) REVERT: B 155 GLU cc_start: 0.7945 (mp0) cc_final: 0.7710 (mp0) REVERT: B 174 MET cc_start: 0.9239 (tpt) cc_final: 0.8951 (tpt) REVERT: C 47 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: C 67 ASP cc_start: 0.9383 (p0) cc_final: 0.9156 (p0) REVERT: D 60 GLU cc_start: 0.8532 (tp30) cc_final: 0.8100 (tp30) REVERT: D 64 ASP cc_start: 0.8807 (m-30) cc_final: 0.8459 (m-30) REVERT: D 69 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8143 (tm-30) REVERT: E 167 TRP cc_start: 0.7093 (m-90) cc_final: 0.6890 (m-90) REVERT: E 240 LEU cc_start: 0.5281 (mp) cc_final: 0.4971 (tp) REVERT: E 288 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6516 (mtmm) REVERT: G 31 TYR cc_start: 0.7472 (m-80) cc_final: 0.7125 (m-80) REVERT: G 66 TYR cc_start: 0.8082 (m-10) cc_final: 0.7492 (m-80) REVERT: G 74 ARG cc_start: 0.8379 (tpt90) cc_final: 0.8049 (tpt90) REVERT: G 106 LEU cc_start: 0.8183 (tp) cc_final: 0.7942 (tt) REVERT: K 490 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8475 (mm-30) REVERT: N 63 ASP cc_start: 0.8957 (m-30) cc_final: 0.8475 (m-30) REVERT: N 154 ASP cc_start: 0.9101 (t70) cc_final: 0.8559 (t0) REVERT: N 219 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8230 (m-80) REVERT: N 463 MET cc_start: 0.8805 (ttt) cc_final: 0.8526 (ttt) REVERT: N 640 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8474 (ttt180) REVERT: O 23 GLU cc_start: 0.6227 (mt-10) cc_final: 0.5875 (pp20) REVERT: O 55 MET cc_start: 0.8076 (mtp) cc_final: 0.7534 (ppp) REVERT: Q 155 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8395 (mm-30) REVERT: Q 158 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7509 (tm130) REVERT: R 436 MET cc_start: 0.4561 (mmt) cc_final: 0.4181 (mmm) REVERT: R 475 PHE cc_start: 0.8952 (p90) cc_final: 0.8531 (p90) REVERT: T 50 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6036 (p0) REVERT: X 390 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7762 (t0) REVERT: X 460 VAL cc_start: 0.7486 (OUTLIER) cc_final: 0.7113 (p) REVERT: F 332 ARG cc_start: 0.1427 (OUTLIER) cc_final: -0.1464 (mtm110) REVERT: F 333 ILE cc_start: 0.5104 (OUTLIER) cc_final: 0.3827 (tp) REVERT: F 511 PHE cc_start: -0.0371 (OUTLIER) cc_final: -0.0637 (m-80) REVERT: S 70 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.7227 (p90) outliers start: 286 outliers final: 191 residues processed: 610 average time/residue: 0.5094 time to fit residues: 530.1318 Evaluate side-chains 531 residues out of total 5781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 325 time to evaluate : 4.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 188 HIS Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 490 GLU Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 335 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 394 THR Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 640 ARG Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 790 ASN Chi-restraints excluded: chain N residue 820 VAL Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 883 LEU Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 145 THR Chi-restraints excluded: chain Q residue 158 GLN Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 223 ASP Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain R residue 581 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 75 PHE Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 47 THR Chi-restraints excluded: chain U residue 51 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 207 CYS Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 279 CYS Chi-restraints excluded: chain X residue 317 VAL Chi-restraints excluded: chain X residue 390 ASP Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 460 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 470 SER Chi-restraints excluded: chain X residue 478 ASN Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 270 GLN Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 496 VAL Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 417 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 492 optimal weight: 0.9990 chunk 363 optimal weight: 9.9990 chunk 355 optimal weight: 0.6980 chunk 636 optimal weight: 30.0000 chunk 314 optimal weight: 0.9990 chunk 450 optimal weight: 40.0000 chunk 233 optimal weight: 2.9990 chunk 652 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN B 65 GLN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 492 GLN N 790 ASN ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 GLN X 82 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 455 HIS ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 ASN F 518 GLN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.130574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.080061 restraints weight = 218537.013| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 4.44 r_work: 0.2940 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 55993 Z= 0.234 Angle : 0.629 14.220 76636 Z= 0.326 Chirality : 0.043 0.243 8770 Planarity : 0.004 0.062 9378 Dihedral : 12.511 163.304 9208 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.62 % Favored : 93.34 % Rotamer: Outliers : 5.04 % Allowed : 21.58 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 1.07 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.10), residues: 6610 helix: 0.40 (0.11), residues: 2339 sheet: -1.57 (0.16), residues: 886 loop : -2.09 (0.10), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 182 HIS 0.006 0.001 HIS P 36 PHE 0.017 0.001 PHE A 275 TYR 0.038 0.001 TYR B 71 ARG 0.005 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 5781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 288 poor density : 349 time to evaluate : 5.683 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: A 63 ASP cc_start: 0.8877 (m-30) cc_final: 0.8090 (t0) REVERT: A 658 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8338 (mt-10) REVERT: A 758 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8246 (tt) REVERT: B 12 TYR cc_start: 0.5904 (t80) cc_final: 0.5656 (t80) REVERT: B 55 MET cc_start: 0.6507 (ptm) cc_final: 0.6300 (mmp) REVERT: B 90 MET cc_start: 0.9115 (tmm) cc_final: 0.8609 (tmm) REVERT: B 95 LEU cc_start: 0.8176 (tp) cc_final: 0.7880 (tp) REVERT: B 96 ARG cc_start: 0.9087 (mtm110) cc_final: 0.8885 (mtm110) REVERT: B 155 GLU cc_start: 0.7887 (mp0) cc_final: 0.7603 (mp0) REVERT: C 47 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: C 67 ASP cc_start: 0.9368 (p0) cc_final: 0.9088 (p0) REVERT: D 60 GLU cc_start: 0.8513 (tp30) cc_final: 0.8071 (tp30) REVERT: D 64 ASP cc_start: 0.8820 (m-30) cc_final: 0.8457 (m-30) REVERT: D 69 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8168 (tm-30) REVERT: E 240 LEU cc_start: 0.5298 (mp) cc_final: 0.4939 (tp) REVERT: E 288 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6482 (mtmm) REVERT: G 74 ARG cc_start: 0.8394 (tpt90) cc_final: 0.8039 (tpt90) REVERT: G 106 LEU cc_start: 0.8146 (tp) cc_final: 0.7918 (tt) REVERT: K 170 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8956 (mp) REVERT: K 490 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8454 (mm-30) REVERT: N 40 ASP cc_start: 0.8646 (p0) cc_final: 0.8171 (t0) REVERT: N 63 ASP cc_start: 0.9043 (m-30) cc_final: 0.8568 (m-30) REVERT: N 154 ASP cc_start: 0.9063 (t70) cc_final: 0.8511 (t0) REVERT: N 219 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: N 350 GLU cc_start: 0.9016 (mp0) cc_final: 0.8785 (mp0) REVERT: N 463 MET cc_start: 0.8800 (ttt) cc_final: 0.8538 (ttt) REVERT: N 613 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.8192 (m170) REVERT: N 640 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8479 (ttt180) REVERT: O 23 GLU cc_start: 0.6086 (mt-10) cc_final: 0.5689 (pp20) REVERT: O 55 MET cc_start: 0.8153 (mtp) cc_final: 0.7699 (ppp) REVERT: Q 65 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7931 (tm-30) REVERT: Q 155 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8417 (mm-30) REVERT: Q 158 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: T 50 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6202 (p0) REVERT: T 68 GLU cc_start: 0.7648 (pp20) cc_final: 0.7416 (pp20) REVERT: T 92 LYS cc_start: 0.7642 (mmtp) cc_final: 0.7402 (ttmm) REVERT: X 390 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7909 (t0) REVERT: X 460 VAL cc_start: 0.7594 (OUTLIER) cc_final: 0.7260 (p) REVERT: F 332 ARG cc_start: 0.1392 (OUTLIER) cc_final: -0.1344 (mtm110) REVERT: F 511 PHE cc_start: -0.0232 (OUTLIER) cc_final: -0.0455 (m-80) REVERT: S 70 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6693 (p90) REVERT: S 429 MET cc_start: 0.0107 (ptt) cc_final: -0.2121 (ttp) REVERT: S 474 MET cc_start: 0.3972 (mmt) cc_final: 0.3714 (mmm) outliers start: 288 outliers final: 205 residues processed: 611 average time/residue: 0.5232 time to fit residues: 543.3611 Evaluate side-chains 547 residues out of total 5781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 327 time to evaluate : 4.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 188 HIS Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 490 GLU Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 335 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 394 THR Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 482 CYS Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 613 HIS Chi-restraints excluded: chain N residue 640 ARG Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 820 VAL Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 883 LEU Chi-restraints excluded: chain N residue 899 MET Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 129 MET Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 15 PHE Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 145 THR Chi-restraints excluded: chain Q residue 158 GLN Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain R residue 581 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 73 CYS Chi-restraints excluded: chain T residue 75 PHE Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 41 CYS Chi-restraints excluded: chain U residue 51 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 87 ILE Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 236 VAL Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 279 CYS Chi-restraints excluded: chain X residue 390 ASP Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 460 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 476 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 255 THR Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 496 VAL Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 575 ILE Chi-restraints excluded: chain S residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.3363 > 50: distance: 37 - 56: 20.370 distance: 41 - 68: 28.410 distance: 50 - 56: 20.972 distance: 56 - 57: 8.194 distance: 57 - 58: 9.142 distance: 57 - 60: 6.820 distance: 58 - 59: 15.178 distance: 58 - 68: 17.997 distance: 60 - 61: 7.294 distance: 61 - 62: 16.203 distance: 61 - 63: 10.210 distance: 62 - 64: 16.479 distance: 63 - 65: 9.579 distance: 64 - 66: 14.341 distance: 65 - 66: 19.526 distance: 66 - 67: 20.902 distance: 68 - 69: 27.015 distance: 69 - 70: 51.342 distance: 69 - 72: 32.903 distance: 70 - 71: 35.206 distance: 70 - 76: 28.641 distance: 72 - 73: 28.445 distance: 73 - 74: 28.396 distance: 73 - 75: 19.448 distance: 76 - 77: 12.275 distance: 77 - 78: 20.236 distance: 77 - 80: 20.010 distance: 78 - 88: 3.210 distance: 80 - 81: 15.469 distance: 81 - 82: 20.021 distance: 81 - 83: 32.382 distance: 82 - 84: 14.505 distance: 83 - 85: 13.352 distance: 84 - 86: 20.800 distance: 85 - 86: 21.922 distance: 86 - 87: 6.749 distance: 88 - 89: 36.490 distance: 89 - 90: 6.454 distance: 89 - 92: 23.469 distance: 90 - 91: 22.831 distance: 90 - 100: 48.073 distance: 91 - 123: 38.830 distance: 92 - 93: 8.862 distance: 93 - 94: 18.261 distance: 93 - 95: 6.174 distance: 94 - 96: 10.077 distance: 95 - 97: 12.154 distance: 96 - 98: 3.522 distance: 97 - 98: 13.821 distance: 98 - 99: 12.142 distance: 100 - 101: 17.308 distance: 101 - 102: 18.424 distance: 101 - 104: 25.368 distance: 102 - 103: 13.133 distance: 102 - 111: 19.829 distance: 104 - 105: 6.721 distance: 105 - 106: 7.210 distance: 106 - 107: 6.730 distance: 107 - 108: 9.625 distance: 108 - 110: 9.800 distance: 111 - 112: 14.703 distance: 112 - 113: 17.535 distance: 112 - 115: 5.988 distance: 113 - 114: 16.063 distance: 113 - 123: 5.061 distance: 115 - 116: 7.629 distance: 116 - 117: 4.774 distance: 116 - 118: 7.814 distance: 117 - 119: 5.171 distance: 118 - 120: 3.555 distance: 119 - 121: 7.023 distance: 120 - 121: 4.174 distance: 121 - 122: 5.716 distance: 123 - 124: 3.411 distance: 124 - 125: 8.993 distance: 124 - 127: 3.015 distance: 125 - 126: 30.877 distance: 125 - 131: 20.753 distance: 127 - 128: 12.603 distance: 128 - 129: 6.365 distance: 128 - 130: 17.984 distance: 131 - 132: 24.745 distance: 132 - 133: 35.326 distance: 132 - 135: 28.693 distance: 133 - 134: 52.020 distance: 133 - 139: 39.689 distance: 135 - 136: 11.220 distance: 136 - 137: 13.947 distance: 136 - 138: 29.883 distance: 139 - 140: 15.596 distance: 139 - 145: 43.417 distance: 140 - 141: 39.688 distance: 140 - 143: 20.229 distance: 141 - 142: 10.820 distance: 141 - 146: 6.164 distance: 143 - 144: 8.109 distance: 144 - 145: 15.538 distance: 146 - 147: 20.832 distance: 147 - 148: 12.321 distance: 147 - 150: 8.192 distance: 148 - 149: 8.161 distance: 148 - 153: 25.247 distance: 150 - 151: 22.609 distance: 150 - 152: 31.337