Starting phenix.real_space_refine on Sun Sep 29 11:57:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4i_12719/09_2024/7o4i_12719.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4i_12719/09_2024/7o4i_12719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4i_12719/09_2024/7o4i_12719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4i_12719/09_2024/7o4i_12719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4i_12719/09_2024/7o4i_12719.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4i_12719/09_2024/7o4i_12719.cif" } resolution = 3.2 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 10 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 17 6.06 5 P 135 5.49 5 Mg 2 5.21 5 S 401 5.16 5 Be 1 3.05 5 C 46402 2.51 5 N 12786 2.21 5 O 14198 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 73949 Number of models: 1 Model: "" Number of chains: 43 Chain: "0" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6091 Classifications: {'peptide': 752} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 719} Chain: "1" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4214 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 503} Chain breaks: 6 Chain: "2" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3597 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain breaks: 4 Chain: "3" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "4" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2274 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 Chain: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "6" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2794 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 334} Chain breaks: 1 Chain: "7" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4954 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 24, 'TRANS': 590} Chain breaks: 2 Chain: "A" Number of atoms: 11254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1430, 11254 Classifications: {'peptide': 1430} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1363} Chain breaks: 3 Chain: "B" Number of atoms: 9404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9404 Classifications: {'peptide': 1180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1127} Chain breaks: 5 Chain: "C" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2092 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1343 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 697 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2360 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Chain: "N" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1374 Classifications: {'DNA': 67} Link IDs: {'rna3p': 66} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 172} Chain: "Q" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1871 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 2 Chain: "R" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2230 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "T" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1370 Classifications: {'DNA': 67} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 66} Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 885 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain breaks: 2 Chain: "V" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Link IDs: {'TRANS': 103} Chain breaks: 1 Chain: "W" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2532 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 15, 'TRANS': 296} Chain breaks: 3 Chain: "X" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1708 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" 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: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 938 SG CYS 0 115 74.889 90.120 188.605 1.00 98.99 S ATOM 1265 SG CYS 0 156 69.744 89.613 192.571 1.00111.49 S ATOM 1080 SG CYS 0 133 71.951 95.483 190.495 1.00105.83 S ATOM 1566 SG CYS 0 191 74.817 92.566 194.839 1.00 99.63 S ATOM 13941 SG CYS 3 13 59.277 120.078 142.735 1.00141.02 S ATOM 13962 SG CYS 3 16 60.361 119.638 139.127 1.00141.24 S ATOM 14157 SG CYS 3 39 61.715 122.606 141.110 1.00143.22 S ATOM 14178 SG CYS 3 42 58.195 122.595 139.993 1.00144.81 S ATOM 14110 SG CYS 3 34 52.657 124.982 151.827 1.00138.63 S ATOM 14268 SG CYS 3 54 51.735 124.462 148.122 1.00141.95 S ATOM 14306 SG CYS 3 59 49.070 123.876 150.842 1.00144.83 S ATOM 16970 SG CYS 4 289 123.756 50.493 209.083 1.00116.36 S ATOM 16989 SG CYS 4 292 127.241 51.324 210.146 1.00111.46 S ATOM 17081 SG CYS 4 305 124.920 49.328 212.491 1.00125.25 S ATOM 17099 SG CYS 4 308 124.338 53.017 211.919 1.00122.71 S ATOM 19766 SG CYS 6 349 127.373 33.267 195.852 1.00113.95 S ATOM 19787 SG CYS 6 352 125.557 30.811 193.564 1.00128.66 S ATOM 19866 SG CYS 6 363 126.104 34.320 192.385 1.00116.99 S ATOM 19885 SG CYS 6 366 123.678 33.730 195.229 1.00124.19 S ATOM 20187 SG CYS 6 403 155.060 68.638 206.188 1.00129.74 S ATOM 20210 SG CYS 6 406 157.087 67.369 203.187 1.00119.61 S ATOM 20404 SG CYS 6 437 154.479 70.303 202.722 1.00127.55 S ATOM 20425 SG CYS 6 440 153.464 66.998 203.092 1.00118.67 S ATOM 20337 SG CYS 6 429 144.842 66.610 212.663 1.00131.47 S ATOM 20360 SG CYS 6 432 148.202 65.502 214.247 1.00130.98 S ATOM 20518 SG CYS 6 451 147.194 64.128 210.971 1.00119.70 S ATOM 20535 SG CYS 6 454 145.230 63.085 214.029 1.00121.74 S ATOM 19665 SG CYS 6 336 131.022 33.624 181.917 1.00139.19 S ATOM 19677 SG CYS 6 338 129.787 36.423 184.223 1.00128.59 S ATOM 19825 SG CYS 6 357 133.493 36.119 183.412 1.00117.29 S ATOM 26347 SG CYS A 107 98.813 114.846 115.238 1.00 61.45 S ATOM 26371 SG CYS A 110 97.676 116.323 118.511 1.00 63.64 S ATOM 26676 SG CYS A 148 101.376 115.529 118.020 1.00 72.55 S ATOM 26814 SG CYS A 167 98.895 112.719 118.404 1.00 77.32 S ATOM 26042 SG CYS A 67 59.974 139.322 100.879 1.00 63.14 S ATOM 26064 SG CYS A 70 60.554 142.950 101.915 1.00 59.53 S ATOM 26117 SG CYS A 77 62.623 141.431 99.089 1.00 51.81 S ATOM 45691 SG CYS B1163 73.247 144.292 112.977 1.00 45.82 S ATOM 45709 SG CYS B1166 74.416 141.317 110.736 1.00 46.12 S ATOM 45834 SG CYS B1182 70.784 141.612 111.739 1.00 52.45 S ATOM 45853 SG CYS B1185 73.495 140.705 114.253 1.00 55.87 S ATOM 46838 SG CYS C 86 43.535 178.687 46.819 1.00 59.89 S ATOM 46855 SG CYS C 88 43.041 175.237 48.339 1.00 72.75 S ATOM 46888 SG CYS C 92 41.548 176.113 44.891 1.00 58.09 S ATOM 46911 SG CYS C 95 45.293 175.633 45.367 1.00 50.52 S ATOM 54581 SG CYS I 7 131.528 89.639 59.533 1.00114.07 S ATOM 54606 SG CYS I 10 127.972 89.053 61.048 1.00113.41 S ATOM 54772 SG CYS I 29 130.445 91.175 63.061 1.00131.96 S ATOM 54796 SG CYS I 32 131.189 87.672 62.377 1.00132.18 S ATOM 55123 SG CYS I 75 134.544 122.880 30.787 1.00106.13 S ATOM 55145 SG CYS I 78 134.008 121.875 27.122 1.00114.45 S ATOM 55361 SG CYS I 103 130.992 122.390 29.322 1.00 99.70 S ATOM 55381 SG CYS I 106 133.294 119.427 29.921 1.00105.53 S ATOM 55526 SG CYS J 7 72.960 165.301 33.767 1.00 30.37 S ATOM 55549 SG CYS J 10 72.496 168.977 32.808 1.00 30.65 S ATOM 55829 SG CYS J 45 75.930 167.232 32.466 1.00 32.74 S ATOM 55835 SG CYS J 46 73.099 166.371 30.143 1.00 32.88 S ATOM 57015 SG CYS L 31 48.412 129.644 43.727 1.00 57.45 S ATOM 57035 SG CYS L 34 46.278 129.329 40.638 1.00 62.75 S ATOM 57139 SG CYS L 48 45.010 128.020 43.956 1.00 64.32 S ATOM 57162 SG CYS L 51 47.940 126.222 42.274 1.00 64.29 S ATOM 57406 SG CYS M 24 46.391 159.342 90.066 1.00 86.34 S ATOM 57428 SG CYS M 27 43.682 160.840 87.934 1.00 92.81 S ATOM 57572 SG CYS M 45 46.040 158.349 86.307 1.00 77.06 S ATOM 57591 SG CYS M 48 47.379 161.764 87.510 1.00 75.83 S ATOM 70661 SG CYS W 124 46.359 136.834 110.086 1.00126.99 S ATOM 70682 SG CYS W 127 49.602 136.196 108.600 1.00124.89 S ATOM 70867 SG CYS W 149 48.517 139.827 109.654 1.00114.01 S ATOM 70887 SG CYS W 152 47.044 138.042 106.522 1.00113.01 S Time building chain proxies: 29.99, per 1000 atoms: 0.41 Number of scatterers: 73949 At special positions: 0 Unit cell: (213.15, 228.9, 243.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 17 29.99 Fe 4 26.01 S 401 16.00 P 135 15.00 Mg 2 11.99 F 3 9.00 O 14198 8.00 N 12786 7.00 C 46402 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.11 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " Number of angles added : 93 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16900 Finding SS restraints... Secondary structure from input PDB file: 355 helices and 72 sheets defined 45.9% alpha, 12.6% beta 60 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 19.64 Creating SS restraints... Processing helix chain '0' and resid 18 through 35 Processing helix chain '0' and resid 48 through 63 Processing helix chain '0' and resid 75 through 98 Processing helix chain '0' and resid 125 through 138 removed outlier: 3.604A pdb=" N VAL 0 129 " --> pdb=" O LYS 0 125 " (cutoff:3.500A) Processing helix chain '0' and resid 139 through 148 Processing helix chain '0' and resid 156 through 165 removed outlier: 3.667A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN 0 164 " --> pdb=" O GLU 0 160 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE 0 165 " --> pdb=" O ASN 0 161 " (cutoff:3.500A) Processing helix chain '0' and resid 166 through 170 Processing helix chain '0' and resid 177 through 189 Processing helix chain '0' and resid 191 through 200 Processing helix chain '0' and resid 210 through 215 Processing helix chain '0' and resid 215 through 224 removed outlier: 3.768A pdb=" N GLU 0 220 " --> pdb=" O PRO 0 216 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG 0 221 " --> pdb=" O LYS 0 217 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL 0 222 " --> pdb=" O ILE 0 218 " (cutoff:3.500A) Processing helix chain '0' and resid 239 through 248 removed outlier: 4.049A pdb=" N VAL 0 243 " --> pdb=" O ASN 0 239 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 278 Processing helix chain '0' and resid 279 through 292 removed outlier: 3.565A pdb=" N GLN 0 291 " --> pdb=" O GLU 0 287 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY 0 292 " --> pdb=" O LYS 0 288 " (cutoff:3.500A) Processing helix chain '0' and resid 294 through 299 Processing helix chain '0' and resid 312 through 316 Processing helix chain '0' and resid 327 through 346 Processing helix chain '0' and resid 355 through 367 Processing helix chain '0' and resid 370 through 376 removed outlier: 3.536A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) Processing helix chain '0' and resid 376 through 388 Processing helix chain '0' and resid 394 through 397 Processing helix chain '0' and resid 398 through 410 removed outlier: 3.942A pdb=" N ILE 0 402 " --> pdb=" O ALA 0 398 " (cutoff:3.500A) Processing helix chain '0' and resid 446 through 453 Processing helix chain '0' and resid 467 through 473 removed outlier: 3.603A pdb=" N ARG 0 471 " --> pdb=" O ASP 0 467 " (cutoff:3.500A) Processing helix chain '0' and resid 509 through 513 Processing helix chain '0' and resid 515 through 533 removed outlier: 3.567A pdb=" N ILE 0 532 " --> pdb=" O GLU 0 528 " (cutoff:3.500A) Processing helix chain '0' and resid 543 through 558 Processing helix chain '0' and resid 558 through 567 removed outlier: 3.609A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS 0 566 " --> pdb=" O GLU 0 562 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 592 Processing helix chain '0' and resid 605 through 609 removed outlier: 3.559A pdb=" N GLU 0 608 " --> pdb=" O LYS 0 605 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY 0 609 " --> pdb=" O VAL 0 606 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 605 through 609' Processing helix chain '0' and resid 632 through 646 Processing helix chain '0' and resid 649 through 667 Processing helix chain '0' and resid 668 through 670 No H-bonds generated for 'chain '0' and resid 668 through 670' Processing helix chain '0' and resid 684 through 693 removed outlier: 3.641A pdb=" N SER 0 687 " --> pdb=" O ARG 0 684 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG 0 688 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) Processing helix chain '0' and resid 694 through 701 removed outlier: 3.809A pdb=" N GLY 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 702 through 706 Processing helix chain '0' and resid 709 through 725 Processing helix chain '0' and resid 729 through 734 Processing helix chain '0' and resid 740 through 752 Processing helix chain '1' and resid 93 through 121 removed outlier: 3.640A pdb=" N THR 1 103 " --> pdb=" O ASN 1 99 " (cutoff:3.500A) Processing helix chain '1' and resid 170 through 177 Processing helix chain '1' and resid 177 through 188 removed outlier: 3.523A pdb=" N LYS 1 186 " --> pdb=" O GLN 1 182 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY 1 187 " --> pdb=" O SER 1 183 " (cutoff:3.500A) Processing helix chain '1' and resid 188 through 200 removed outlier: 3.658A pdb=" N MET 1 192 " --> pdb=" O ASN 1 188 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU 1 197 " --> pdb=" O LYS 1 193 " (cutoff:3.500A) Processing helix chain '1' and resid 205 through 212 removed outlier: 4.102A pdb=" N THR 1 212 " --> pdb=" O GLU 1 208 " (cutoff:3.500A) Processing helix chain '1' and resid 213 through 225 removed outlier: 3.871A pdb=" N THR 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 232 through 237 removed outlier: 3.716A pdb=" N THR 1 236 " --> pdb=" O ASN 1 232 " (cutoff:3.500A) Processing helix chain '1' and resid 252 through 263 Processing helix chain '1' and resid 263 through 272 removed outlier: 3.525A pdb=" N LYS 1 267 " --> pdb=" O TYR 1 263 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP 1 272 " --> pdb=" O LYS 1 268 " (cutoff:3.500A) Processing helix chain '1' and resid 279 through 290 Processing helix chain '1' and resid 290 through 297 removed outlier: 3.939A pdb=" N ARG 1 294 " --> pdb=" O SER 1 290 " (cutoff:3.500A) Processing helix chain '1' and resid 308 through 313 removed outlier: 3.846A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) Processing helix chain '1' and resid 314 through 330 Processing helix chain '1' and resid 334 through 337 Processing helix chain '1' and resid 338 through 345 removed outlier: 3.663A pdb=" N ASN 1 342 " --> pdb=" O ASP 1 338 " (cutoff:3.500A) Processing helix chain '1' and resid 355 through 359 removed outlier: 3.500A pdb=" N GLN 1 359 " --> pdb=" O PHE 1 356 " (cutoff:3.500A) Processing helix chain '1' and resid 370 through 390 removed outlier: 3.811A pdb=" N ILE 1 374 " --> pdb=" O GLY 1 370 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU 1 375 " --> pdb=" O THR 1 371 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS 1 390 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) Processing helix chain '1' and resid 414 through 420 Processing helix chain '1' and resid 421 through 425 removed outlier: 3.584A pdb=" N LEU 1 424 " --> pdb=" O ILE 1 421 " (cutoff:3.500A) Processing helix chain '1' and resid 465 through 483 Processing helix chain '1' and resid 485 through 490 removed outlier: 3.551A pdb=" N GLN 1 488 " --> pdb=" O ASP 1 485 " (cutoff:3.500A) Processing helix chain '1' and resid 495 through 515 removed outlier: 3.696A pdb=" N ILE 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 569 Processing helix chain '1' and resid 572 through 574 No H-bonds generated for 'chain '1' and resid 572 through 574' Processing helix chain '1' and resid 575 through 605 Processing helix chain '1' and resid 608 through 616 Processing helix chain '1' and resid 616 through 639 Processing helix chain '2' and resid 6 through 17 removed outlier: 3.541A pdb=" N ILE 2 17 " --> pdb=" O TYR 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 26 removed outlier: 3.561A pdb=" N ARG 2 24 " --> pdb=" O GLN 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 39 removed outlier: 3.751A pdb=" N ARG 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU 2 39 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 52 removed outlier: 4.111A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 66 removed outlier: 3.794A pdb=" N VAL 2 66 " --> pdb=" O LEU 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 84 removed outlier: 3.569A pdb=" N LEU 2 84 " --> pdb=" O SER 2 80 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 114 Processing helix chain '2' and resid 134 through 152 Processing helix chain '2' and resid 160 through 170 Processing helix chain '2' and resid 185 through 194 Processing helix chain '2' and resid 195 through 211 removed outlier: 3.593A pdb=" N LEU 2 203 " --> pdb=" O GLN 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 217 through 231 Processing helix chain '2' and resid 243 through 255 removed outlier: 3.827A pdb=" N ILE 2 248 " --> pdb=" O GLU 2 244 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP 2 255 " --> pdb=" O GLN 2 251 " (cutoff:3.500A) Processing helix chain '2' and resid 272 through 280 removed outlier: 3.529A pdb=" N LEU 2 276 " --> pdb=" O THR 2 272 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER 2 280 " --> pdb=" O LEU 2 276 " (cutoff:3.500A) Processing helix chain '2' and resid 353 through 362 removed outlier: 3.514A pdb=" N LEU 2 362 " --> pdb=" O ALA 2 358 " (cutoff:3.500A) Processing helix chain '2' and resid 379 through 389 Processing helix chain '2' and resid 392 through 403 Processing helix chain '2' and resid 405 through 423 Processing helix chain '2' and resid 434 through 449 removed outlier: 3.917A pdb=" N VAL 2 438 " --> pdb=" O PRO 2 434 " (cutoff:3.500A) Processing helix chain '2' and resid 464 through 478 Processing helix chain '2' and resid 495 through 507 removed outlier: 4.484A pdb=" N SER 2 499 " --> pdb=" O LYS 2 495 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLN 2 500 " --> pdb=" O GLU 2 496 " (cutoff:3.500A) Processing helix chain '3' and resid 40 through 48 Processing helix chain '3' and resid 64 through 68 Processing helix chain '3' and resid 75 through 90 Processing helix chain '3' and resid 95 through 100 Processing helix chain '3' and resid 102 through 123 Processing helix chain '3' and resid 125 through 139 removed outlier: 3.503A pdb=" N GLU 3 138 " --> pdb=" O ARG 3 134 " (cutoff:3.500A) Processing helix chain '4' and resid 33 through 44 removed outlier: 3.578A pdb=" N PHE 4 40 " --> pdb=" O LEU 4 36 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 68 removed outlier: 4.090A pdb=" N LYS 4 52 " --> pdb=" O GLY 4 48 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN 4 68 " --> pdb=" O HIS 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 115 through 139 removed outlier: 3.508A pdb=" N VAL 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR 4 124 " --> pdb=" O ASN 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 148 through 167 Processing helix chain '4' and resid 189 through 191 No H-bonds generated for 'chain '4' and resid 189 through 191' Processing helix chain '4' and resid 192 through 206 Processing helix chain '4' and resid 221 through 231 Processing helix chain '4' and resid 243 through 251 removed outlier: 4.196A pdb=" N TYR 4 247 " --> pdb=" O GLY 4 243 " (cutoff:3.500A) Processing helix chain '4' and resid 255 through 259 removed outlier: 3.704A pdb=" N ARG 4 259 " --> pdb=" O PRO 4 256 " (cutoff:3.500A) Processing helix chain '4' and resid 300 through 304 removed outlier: 3.958A pdb=" N LYS 4 304 " --> pdb=" O PRO 4 301 " (cutoff:3.500A) Processing helix chain '4' and resid 313 through 322 removed outlier: 3.626A pdb=" N LYS 4 319 " --> pdb=" O HIS 4 315 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU 4 320 " --> pdb=" O VAL 4 316 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 27 Processing helix chain '5' and resid 46 through 60 removed outlier: 3.759A pdb=" N HIS 5 52 " --> pdb=" O GLU 5 48 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) Processing helix chain '6' and resid 97 through 114 removed outlier: 3.823A pdb=" N ALA 6 111 " --> pdb=" O LYS 6 107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS 6 112 " --> pdb=" O LYS 6 108 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN 6 114 " --> pdb=" O THR 6 110 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 removed outlier: 3.945A pdb=" N GLU 6 138 " --> pdb=" O ALA 6 135 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 164 Processing helix chain '6' and resid 188 through 200 removed outlier: 3.796A pdb=" N HIS 6 192 " --> pdb=" O ASN 6 188 " (cutoff:3.500A) Processing helix chain '6' and resid 209 through 222 Processing helix chain '6' and resid 246 through 258 Processing helix chain '6' and resid 270 through 280 Processing helix chain '6' and resid 293 through 304 Processing helix chain '6' and resid 372 through 378 removed outlier: 3.573A pdb=" N LEU 6 376 " --> pdb=" O LEU 6 372 " (cutoff:3.500A) Processing helix chain '6' and resid 379 through 383 Processing helix chain '6' and resid 437 through 447 removed outlier: 3.644A pdb=" N VAL 6 442 " --> pdb=" O VAL 6 438 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE 6 443 " --> pdb=" O ASP 6 439 " (cutoff:3.500A) Processing helix chain '6' and resid 451 through 457 Processing helix chain '7' and resid 109 through 113 Processing helix chain '7' and resid 149 through 161 removed outlier: 3.966A pdb=" N ASP 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE 7 156 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) Processing helix chain '7' and resid 176 through 186 removed outlier: 3.839A pdb=" N SER 7 185 " --> pdb=" O TYR 7 181 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL 7 186 " --> pdb=" O ALA 7 182 " (cutoff:3.500A) Processing helix chain '7' and resid 189 through 201 Processing helix chain '7' and resid 206 through 218 removed outlier: 3.616A pdb=" N ALA 7 216 " --> pdb=" O PHE 7 212 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE 7 218 " --> pdb=" O LYS 7 214 " (cutoff:3.500A) Processing helix chain '7' and resid 241 through 246 Processing helix chain '7' and resid 322 through 333 removed outlier: 3.741A pdb=" N LYS 7 328 " --> pdb=" O GLU 7 324 " (cutoff:3.500A) Processing helix chain '7' and resid 363 through 375 Processing helix chain '7' and resid 391 through 404 Processing helix chain '7' and resid 413 through 428 removed outlier: 3.518A pdb=" N VAL 7 417 " --> pdb=" O SER 7 413 " (cutoff:3.500A) Processing helix chain '7' and resid 431 through 433 No H-bonds generated for 'chain '7' and resid 431 through 433' Processing helix chain '7' and resid 456 through 462 removed outlier: 3.762A pdb=" N ASN 7 462 " --> pdb=" O SER 7 458 " (cutoff:3.500A) Processing helix chain '7' and resid 467 through 480 Processing helix chain '7' and resid 490 through 493 Processing helix chain '7' and resid 498 through 505 removed outlier: 4.265A pdb=" N VAL 7 502 " --> pdb=" O PHE 7 498 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER 7 503 " --> pdb=" O ARG 7 499 " (cutoff:3.500A) Processing helix chain '7' and resid 521 through 525 removed outlier: 4.080A pdb=" N ILE 7 524 " --> pdb=" O ASP 7 521 " (cutoff:3.500A) Processing helix chain '7' and resid 526 through 531 Processing helix chain '7' and resid 540 through 546 Processing helix chain '7' and resid 562 through 572 removed outlier: 3.847A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG 7 571 " --> pdb=" O GLN 7 567 " (cutoff:3.500A) Processing helix chain '7' and resid 573 through 583 removed outlier: 3.736A pdb=" N MET 7 578 " --> pdb=" O ALA 7 574 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) Processing helix chain '7' and resid 584 through 601 removed outlier: 3.660A pdb=" N PHE 7 588 " --> pdb=" O ASN 7 584 " (cutoff:3.500A) Processing helix chain '7' and resid 611 through 623 Processing helix chain '7' and resid 632 through 646 Processing helix chain '7' and resid 655 through 659 Processing helix chain '7' and resid 679 through 688 Processing helix chain '7' and resid 689 through 693 removed outlier: 4.280A pdb=" N ARG 7 692 " --> pdb=" O ARG 7 689 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA 7 693 " --> pdb=" O ILE 7 690 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 689 through 693' Processing helix chain '7' and resid 713 through 722 removed outlier: 3.899A pdb=" N TYR 7 717 " --> pdb=" O THR 7 713 " (cutoff:3.500A) Processing helix chain '7' and resid 723 through 730 Processing helix chain '7' and resid 752 through 767 removed outlier: 4.314A pdb=" N ASN 7 767 " --> pdb=" O VAL 7 763 " (cutoff:3.500A) Processing helix chain '7' and resid 831 through 837 removed outlier: 3.832A pdb=" N LYS 7 835 " --> pdb=" O LEU 7 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 261 through 282 removed outlier: 3.542A pdb=" N ASN A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.758A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.567A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.553A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 845 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.847A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.545A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.160A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 removed outlier: 3.558A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix removed outlier: 3.700A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.799A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1165 through 1176 removed outlier: 4.525A pdb=" N ILE A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 4.006A pdb=" N LYS A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.634A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 removed outlier: 3.533A pdb=" N GLU A1253 " --> pdb=" O ALA A1250 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A1254 " --> pdb=" O GLU A1251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1250 through 1254' Processing helix chain 'A' and resid 1255 through 1270 Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.773A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 removed outlier: 3.656A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.299A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 4.012A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 3.710A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.667A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 64 removed outlier: 4.734A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.716A pdb=" N SER B 182 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.855A pdb=" N ARG B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 439 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 463 Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 668 removed outlier: 3.875A pdb=" N ASP B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 688 Processing helix chain 'B' and resid 695 through 699 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.734A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 808 through 813 removed outlier: 3.511A pdb=" N LEU B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.581A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.931A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.590A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.738A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 268 removed outlier: 3.516A pdb=" N ASP C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.784A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.758A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.708A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.526A pdb=" N TYR G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.879A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.689A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 116 removed outlier: 3.504A pdb=" N LYS M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 140 removed outlier: 3.600A pdb=" N GLU M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 158 Processing helix chain 'M' and resid 167 through 183 Processing helix chain 'M' and resid 188 through 196 removed outlier: 3.970A pdb=" N LEU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 221 Processing helix chain 'M' and resid 227 through 231 Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 237 through 247 removed outlier: 4.629A pdb=" N ARG M 241 " --> pdb=" O THR M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 264 removed outlier: 3.867A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 271 removed outlier: 4.208A pdb=" N GLY M 271 " --> pdb=" O LYS M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 289 Processing helix chain 'M' and resid 294 through 303 Processing helix chain 'M' and resid 305 through 318 removed outlier: 3.861A pdb=" N GLU M 318 " --> pdb=" O LYS M 314 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 324 removed outlier: 4.098A pdb=" N VAL M 324 " --> pdb=" O ASP M 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 332 Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 128 through 147 Processing helix chain 'O' and resid 171 through 179 Processing helix chain 'O' and resid 219 through 237 removed outlier: 3.799A pdb=" N ILE O 223 " --> pdb=" O GLN O 219 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR O 224 " --> pdb=" O ARG O 220 " (cutoff:3.500A) Proline residue: O 232 - end of helix removed outlier: 3.772A pdb=" N PHE O 237 " --> pdb=" O VAL O 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 35 Processing helix chain 'Q' and resid 152 through 168 Processing helix chain 'Q' and resid 336 through 347 Processing helix chain 'Q' and resid 405 through 414 Processing helix chain 'Q' and resid 423 through 432 Processing helix chain 'Q' and resid 436 through 450 Processing helix chain 'R' and resid 48 through 53 Processing helix chain 'R' and resid 74 through 82 removed outlier: 3.843A pdb=" N LYS R 80 " --> pdb=" O PHE R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 113 removed outlier: 4.097A pdb=" N ASN R 113 " --> pdb=" O GLU R 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 110 through 113' Processing helix chain 'R' and resid 234 through 246 removed outlier: 3.773A pdb=" N VAL R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 264 Processing helix chain 'R' and resid 279 through 286 Processing helix chain 'R' and resid 295 through 310 removed outlier: 3.608A pdb=" N ILE R 299 " --> pdb=" O PRO R 295 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP R 301 " --> pdb=" O LYS R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 323 Processing helix chain 'R' and resid 325 through 336 removed outlier: 3.943A pdb=" N GLU R 331 " --> pdb=" O ALA R 327 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS R 332 " --> pdb=" O HIS R 328 " (cutoff:3.500A) Processing helix chain 'R' and resid 352 through 357 Processing helix chain 'U' and resid 4 through 29 removed outlier: 3.811A pdb=" N ARG U 22 " --> pdb=" O VAL U 18 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 50 removed outlier: 3.764A pdb=" N GLN U 36 " --> pdb=" O GLU U 32 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS U 50 " --> pdb=" O LEU U 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 12 Processing helix chain 'V' and resid 13 through 30 Processing helix chain 'V' and resid 33 through 55 Processing helix chain 'W' and resid 3 through 21 Processing helix chain 'W' and resid 22 through 35 removed outlier: 3.670A pdb=" N VAL W 26 " --> pdb=" O GLY W 22 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 48 Processing helix chain 'W' and resid 50 through 64 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 90 through 118 removed outlier: 3.575A pdb=" N GLU W 118 " --> pdb=" O ASP W 114 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 138 removed outlier: 3.946A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 179 removed outlier: 3.693A pdb=" N GLN W 169 " --> pdb=" O ASN W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 192 removed outlier: 3.645A pdb=" N ILE W 183 " --> pdb=" O ILE W 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 204 removed outlier: 3.567A pdb=" N ALA W 204 " --> pdb=" O GLU W 200 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 289 Processing helix chain 'W' and resid 291 through 296 Processing helix chain 'W' and resid 350 through 369 Processing helix chain 'X' and resid 106 through 116 Processing helix chain 'X' and resid 123 through 137 removed outlier: 3.702A pdb=" N LYS X 127 " --> pdb=" O HIS X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 151 Processing helix chain 'X' and resid 157 through 166 Processing helix chain 'X' and resid 188 through 198 Processing helix chain 'X' and resid 206 through 212 removed outlier: 3.778A pdb=" N ASP X 212 " --> pdb=" O LYS X 208 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 227 Processing helix chain 'X' and resid 256 through 266 removed outlier: 3.910A pdb=" N MET X 262 " --> pdb=" O GLU X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 272 No H-bonds generated for 'chain 'X' and resid 270 through 272' Processing helix chain 'X' and resid 273 through 281 Processing helix chain 'X' and resid 289 through 293 Processing sheet with id=A, first strand: chain '0' and resid 2 through 4 Processing sheet with id=B, first strand: chain '0' and resid 174 through 176 removed outlier: 4.221A pdb=" N GLY 0 107 " --> pdb=" O PHE 0 176 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE 0 205 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE 0 69 " --> pdb=" O ILE 0 206 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR 0 208 " --> pdb=" O ILE 0 69 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR 0 71 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE 0 231 " --> pdb=" O ILE 0 70 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N CYS 0 72 " --> pdb=" O ILE 0 231 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE 0 233 " --> pdb=" O CYS 0 72 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 478 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN 0 480 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU 0 41 " --> pdb=" O GLN 0 480 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER 0 482 " --> pdb=" O GLU 0 41 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain '0' and resid 250 through 253 Processing sheet with id=D, first strand: chain '0' and resid 492 through 497 removed outlier: 6.847A pdb=" N GLY 0 677 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N MET 0 495 " --> pdb=" O GLY 0 677 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N MET 0 679 " --> pdb=" O MET 0 495 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE 0 497 " --> pdb=" O MET 0 679 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU 0 681 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR 0 619 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA 0 596 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL 0 539 " --> pdb=" O ALA 0 596 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU 0 598 " --> pdb=" O VAL 0 539 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE 0 541 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER 0 600 " --> pdb=" O PHE 0 541 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain '1' and resid 4 through 9 Processing sheet with id=F, first strand: chain '1' and resid 86 through 90 Processing sheet with id=G, first strand: chain '2' and resid 87 through 92 Processing sheet with id=H, first strand: chain '2' and resid 259 through 261 Processing sheet with id=I, first strand: chain '2' and resid 339 through 341 removed outlier: 3.665A pdb=" N LEU 2 375 " --> pdb=" O ALA 2 368 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA 2 368 " --> pdb=" O LEU 2 375 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN 2 377 " --> pdb=" O LEU 2 366 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU 2 366 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain '2' and resid 456 through 459 removed outlier: 3.648A pdb=" N SER 2 457 " --> pdb=" O ILE 2 493 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE 2 493 " --> pdb=" O SER 2 457 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP 2 483 " --> pdb=" O PHE 2 492 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER 2 494 " --> pdb=" O LEU 2 481 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU 2 481 " --> pdb=" O SER 2 494 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain '3' and resid 29 through 31 Processing sheet with id=L, first strand: chain '4' and resid 82 through 87 removed outlier: 6.416A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ALA 4 74 " --> pdb=" O SER 4 24 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU 4 26 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 26 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL 4 28 " --> pdb=" O ILE 4 76 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ALA 4 78 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE 4 30 " --> pdb=" O ALA 4 78 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS 4 173 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N THR 4 27 " --> pdb=" O LYS 4 173 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU 4 177 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain '5' and resid 8 through 11 Processing sheet with id=N, first strand: chain '6' and resid 178 through 183 removed outlier: 6.162A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP 6 131 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL 6 235 " --> pdb=" O ASP 6 131 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG 6 260 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE 6 234 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS 6 262 " --> pdb=" O ILE 6 234 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain '7' and resid 132 through 134 removed outlier: 5.978A pdb=" N LYS 7 174 " --> pdb=" O PRO 7 163 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain '7' and resid 224 through 228 removed outlier: 4.414A pdb=" N TYR 7 232 " --> pdb=" O ILE 7 318 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE 7 316 " --> pdb=" O VAL 7 234 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain '7' and resid 382 through 384 removed outlier: 6.191A pdb=" N ILE 7 485 " --> pdb=" O LEU 7 511 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU 7 513 " --> pdb=" O ILE 7 485 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU 7 487 " --> pdb=" O LEU 7 513 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain '7' and resid 734 through 736 removed outlier: 3.503A pdb=" N TRP 7 558 " --> pdb=" O ILE 7 736 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA 7 703 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA 7 555 " --> pdb=" O ALA 7 703 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE 7 705 " --> pdb=" O ALA 7 555 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL 7 557 " --> pdb=" O PHE 7 705 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER 7 707 " --> pdb=" O VAL 7 557 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS 7 559 " --> pdb=" O SER 7 707 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL 7 709 " --> pdb=" O CYS 7 559 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N SER 7 674 " --> pdb=" O LEU 7 708 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N SER 7 710 " --> pdb=" O SER 7 674 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'A' and resid 82 through 85 Processing sheet with id=T, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=U, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=V, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.799A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A 487 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.450A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=W Processing sheet with id=X, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.671A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.617A pdb=" N PHE A 614 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=Z, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AA, first strand: chain 'A' and resid 1115 through 1119 removed outlier: 3.500A pdb=" N ARG A1289 " --> pdb=" O GLU A1301 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.353A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'B' and resid 69 through 73 Processing sheet with id=AD, first strand: chain 'B' and resid 95 through 97 Processing sheet with id=AE, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AF, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AG, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AH, first strand: chain 'B' and resid 498 through 500 removed outlier: 6.273A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'B' and resid 224 through 227 removed outlier: 6.927A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG B 241 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER B 252 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AJ, first strand: chain 'B' and resid 543 through 545 Processing sheet with id=AK, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.530A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.646A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id=AM, first strand: chain 'B' and resid 1086 through 1092 removed outlier: 4.048A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B1010 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N MET B 839 " --> pdb=" O LYS B 987 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR B 989 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N MET B 841 " --> pdb=" O THR B 989 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N GLY B 991 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'B' and resid 872 through 874 Processing sheet with id=AO, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AP, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AQ, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.798A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AR, first strand: chain 'C' and resid 97 through 104 removed outlier: 5.933A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id=AS, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AT, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AU, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.730A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id=AV, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AW, first strand: chain 'F' and resid 133 through 137 Processing sheet with id=AX, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.299A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id=AY, first strand: chain 'G' and resid 142 through 146 removed outlier: 6.887A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE G 157 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N PHE G 109 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA G 159 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N THR G 111 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLY G 161 " --> pdb=" O THR G 111 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AZ, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.870A pdb=" N THR G 120 " --> pdb=" O GLN G 131 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.304A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'I' and resid 14 through 19 Processing sheet with id=BC, first strand: chain 'I' and resid 69 through 71 removed outlier: 3.743A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=BD, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=BE, first strand: chain 'L' and resid 37 through 40 Processing sheet with id=BF, first strand: chain 'M' and resid 34 through 37 removed outlier: 3.558A pdb=" N SER M 53 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS M 45 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL M 51 " --> pdb=" O CYS M 45 " (cutoff:3.500A) Processing sheet with id=BG, first strand: chain 'O' and resid 155 through 157 removed outlier: 4.249A pdb=" N LYS O 120 " --> pdb=" O PHE O 116 " (cutoff:3.500A) Processing sheet with id=BH, first strand: chain 'O' and resid 192 through 197 removed outlier: 4.152A pdb=" N LYS O 211 " --> pdb=" O PHE O 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE O 160 " --> pdb=" O GLY O 216 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER O 163 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU O 67 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing sheet with id=BI, first strand: chain 'Q' and resid 103 through 105 removed outlier: 6.319A pdb=" N PHE Q 384 " --> pdb=" O ARG Q 104 " (cutoff:3.500A) Processing sheet with id=BJ, first strand: chain 'Q' and resid 117 through 121 removed outlier: 6.754A pdb=" N LYS Q 391 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N LYS Q 120 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR Q 393 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL Q 392 " --> pdb=" O GLU Q 366 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) Processing sheet with id=BK, first strand: chain 'R' and resid 93 through 97 removed outlier: 4.459A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU R 70 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU R 221 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARG R 72 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLN R 223 " --> pdb=" O ARG R 72 " (cutoff:3.500A) Processing sheet with id=BL, first strand: chain 'R' and resid 337 through 340 removed outlier: 3.582A pdb=" N VAL R 340 " --> pdb=" O LYS R 348 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS R 348 " --> pdb=" O VAL R 340 " (cutoff:3.500A) Processing sheet with id=BM, first strand: chain 'R' and resid 133 through 138 removed outlier: 3.697A pdb=" N GLY R 216 " --> pdb=" O VAL R 134 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR R 136 " --> pdb=" O ILE R 214 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE R 214 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN R 138 " --> pdb=" O THR R 212 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR R 212 " --> pdb=" O GLN R 138 " (cutoff:3.500A) Processing sheet with id=BN, first strand: chain 'U' and resid 243 through 245 Processing sheet with id=BO, first strand: chain 'U' and resid 278 through 284 removed outlier: 3.579A pdb=" N LYS U 250 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS U 263 " --> pdb=" O TYR U 248 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR U 248 " --> pdb=" O LYS U 263 " (cutoff:3.500A) Processing sheet with id=BP, first strand: chain 'V' and resid 60 through 63 removed outlier: 3.907A pdb=" N VAL V 87 " --> pdb=" O SER V 104 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER V 104 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id=BQ, first strand: chain 'V' and resid 110 through 116 removed outlier: 3.551A pdb=" N THR V 68 " --> pdb=" O ILE V 79 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS V 81 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU V 66 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id=BR, first strand: chain 'W' and resid 68 through 74 Processing sheet with id=BS, first strand: chain 'X' and resid 169 through 172 Processing sheet with id=BT, first strand: chain 'X' and resid 230 through 232 3175 hydrogen bonds defined for protein. 9003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 142 hydrogen bonds 284 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 33.98 Time building geometry restraints manager: 16.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 31041 1.43 - 1.64: 43860 1.64 - 1.85: 628 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 75541 Sorted by residual: bond pdb=" C4 ADP 7 903 " pdb=" C5 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" F2 BEF 7 901 " pdb="BE BEF 7 901 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C5 ADP 7 903 " pdb=" C6 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" F3 BEF 7 901 " pdb="BE BEF 7 901 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C VAL O 208 " pdb=" N SER O 209 " ideal model delta sigma weight residual 1.333 1.382 -0.048 1.56e-02 4.11e+03 9.59e+00 ... (remaining 75536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 102011 2.48 - 4.95: 502 4.95 - 7.43: 13 7.43 - 9.90: 9 9.90 - 12.38: 2 Bond angle restraints: 102537 Sorted by residual: angle pdb=" N TYR 7 677 " pdb=" CA TYR 7 677 " pdb=" C TYR 7 677 " ideal model delta sigma weight residual 108.31 115.21 -6.90 1.52e+00 4.33e-01 2.06e+01 angle pdb=" N LYS Q 415 " pdb=" CA LYS Q 415 " pdb=" C LYS Q 415 " ideal model delta sigma weight residual 110.80 119.72 -8.92 2.13e+00 2.20e-01 1.76e+01 angle pdb=" C1' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C3' ADP 7 903 " ideal model delta sigma weight residual 111.00 98.62 12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" CA LYS Q 416 " pdb=" CB LYS Q 416 " pdb=" CG LYS Q 416 " ideal model delta sigma weight residual 114.10 122.34 -8.24 2.00e+00 2.50e-01 1.70e+01 angle pdb=" PA ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PB ADP 7 903 " ideal model delta sigma weight residual 120.50 131.89 -11.39 3.00e+00 1.11e-01 1.44e+01 ... (remaining 102532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.91: 44546 31.91 - 63.82: 1420 63.82 - 95.72: 107 95.72 - 127.63: 1 127.63 - 159.54: 2 Dihedral angle restraints: 46076 sinusoidal: 20057 harmonic: 26019 Sorted by residual: dihedral pdb=" O1B ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PB ADP 7 903 " pdb=" PA ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 99.54 -159.54 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" PB ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 76.54 -136.54 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" C5' ADP 7 903 " pdb=" O5' ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" O2A ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 -175.02 115.02 1 2.00e+01 2.50e-03 3.42e+01 ... (remaining 46073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 9983 0.054 - 0.108: 1283 0.108 - 0.162: 317 0.162 - 0.216: 2 0.216 - 0.270: 2 Chirality restraints: 11587 Sorted by residual: chirality pdb=" CA LYS Q 415 " pdb=" N LYS Q 415 " pdb=" C LYS Q 415 " pdb=" CB LYS Q 415 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA LYS Q 416 " pdb=" N LYS Q 416 " pdb=" C LYS Q 416 " pdb=" CB LYS Q 416 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C4' ADP 7 903 " pdb=" O3' ADP 7 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 11584 not shown) Planarity restraints: 12694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY 7 678 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C GLY 7 678 " 0.055 2.00e-02 2.50e+03 pdb=" O GLY 7 678 " -0.020 2.00e-02 2.50e+03 pdb=" N SER 7 679 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP 5 13 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO 5 14 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO 5 14 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO 5 14 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 245 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.029 5.00e-02 4.00e+02 ... (remaining 12691 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 269 2.49 - 3.09: 52326 3.09 - 3.69: 109524 3.69 - 4.30: 162249 4.30 - 4.90: 269747 Nonbonded interactions: 594115 Sorted by model distance: nonbonded pdb=" OD1 ASP B 326 " pdb=" OG1 THR B 329 " model vdw 1.885 3.040 nonbonded pdb=" OG1 THR A 595 " pdb=" OD1 ASN A 603 " model vdw 1.969 3.040 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1803 " model vdw 1.977 2.170 nonbonded pdb=" OH TYR W 21 " pdb=" OD2 ASP W 64 " model vdw 1.984 3.040 nonbonded pdb=" OG SER 4 90 " pdb=" OD2 ASP 6 402 " model vdw 1.992 3.040 ... (remaining 594110 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.060 Extract box with map and model: 2.410 Check model and map are aligned: 0.430 Set scattering table: 0.540 Process input model: 167.450 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.002 0.109 75541 Z= 0.159 Angle : 0.480 12.380 102537 Z= 0.276 Chirality : 0.040 0.270 11587 Planarity : 0.003 0.060 12694 Dihedral : 14.704 159.539 29176 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.03 % Allowed : 0.06 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.09), residues: 8762 helix: 1.87 (0.09), residues: 3619 sheet: 0.19 (0.14), residues: 1327 loop : -0.00 (0.10), residues: 3816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 466 HIS 0.006 0.001 HIS 7 314 PHE 0.018 0.001 PHE A 219 TYR 0.017 0.001 TYR 7 581 ARG 0.008 0.000 ARG 0 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1805 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1803 time to evaluate : 6.517 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: 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: 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: 0 42 MET cc_start: 0.8333 (mmm) cc_final: 0.8011 (mmm) REVERT: 0 76 MET cc_start: 0.8101 (ttp) cc_final: 0.7711 (ttt) REVERT: 0 134 ARG cc_start: 0.8702 (mtt90) cc_final: 0.7948 (mtt90) REVERT: 0 180 LYS cc_start: 0.7254 (tttt) cc_final: 0.6996 (ttpt) REVERT: 0 199 MET cc_start: 0.7833 (mtm) cc_final: 0.7596 (mtm) REVERT: 0 447 LYS cc_start: 0.8397 (tppt) cc_final: 0.8147 (tppt) REVERT: 0 481 LYS cc_start: 0.8338 (ptpt) cc_final: 0.8026 (ptmm) REVERT: 0 544 TYR cc_start: 0.7794 (t80) cc_final: 0.7389 (t80) REVERT: 1 97 MET cc_start: 0.8723 (ttp) cc_final: 0.8511 (ttm) REVERT: 1 102 MET cc_start: 0.7591 (mmm) cc_final: 0.7306 (mmm) REVERT: 1 169 LEU cc_start: 0.8383 (mp) cc_final: 0.7972 (pp) REVERT: 1 220 PHE cc_start: 0.8765 (t80) cc_final: 0.8116 (t80) REVERT: 1 469 MET cc_start: 0.7459 (ttp) cc_final: 0.7097 (ttm) REVERT: 1 601 LEU cc_start: 0.8321 (tp) cc_final: 0.8095 (tp) REVERT: 2 143 TRP cc_start: 0.8755 (t-100) cc_final: 0.8520 (t-100) REVERT: 2 223 HIS cc_start: 0.8100 (m90) cc_final: 0.7487 (m-70) REVERT: 3 12 MET cc_start: 0.8060 (ptm) cc_final: 0.7598 (mtm) REVERT: 3 25 ASP cc_start: 0.8043 (m-30) cc_final: 0.7740 (t0) REVERT: 3 28 PHE cc_start: 0.8567 (m-80) cc_final: 0.8040 (m-80) REVERT: 3 45 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7700 (ttp80) REVERT: 3 75 ASP cc_start: 0.8219 (t0) cc_final: 0.7863 (t0) REVERT: 3 106 TYR cc_start: 0.7838 (t80) cc_final: 0.7620 (t80) REVERT: 3 114 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8224 (tp30) REVERT: 4 146 ARG cc_start: 0.6694 (mtm110) cc_final: 0.5917 (mtp-110) REVERT: 4 191 PHE cc_start: 0.7486 (p90) cc_final: 0.7133 (p90) REVERT: 4 271 ASP cc_start: 0.6745 (p0) cc_final: 0.6477 (p0) REVERT: 5 38 THR cc_start: 0.7444 (p) cc_final: 0.6807 (p) REVERT: 6 198 SER cc_start: 0.8550 (m) cc_final: 0.8319 (p) REVERT: 7 194 ILE cc_start: 0.9043 (mm) cc_final: 0.8609 (pt) REVERT: 7 459 MET cc_start: 0.8308 (mmm) cc_final: 0.7310 (ttm) REVERT: A 41 MET cc_start: 0.7736 (mmm) cc_final: 0.7422 (mmm) REVERT: A 53 LEU cc_start: 0.8860 (mm) cc_final: 0.8659 (mt) REVERT: A 175 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.7024 (mtm110) REVERT: A 341 MET cc_start: 0.8764 (mmm) cc_final: 0.8501 (mmm) REVERT: A 417 TYR cc_start: 0.7640 (m-80) cc_final: 0.7375 (m-80) REVERT: A 487 MET cc_start: 0.8947 (mtp) cc_final: 0.8714 (mtm) REVERT: A 696 GLU cc_start: 0.7174 (tt0) cc_final: 0.6931 (tt0) REVERT: A 929 LEU cc_start: 0.8460 (mt) cc_final: 0.8240 (mt) REVERT: A 949 ASP cc_start: 0.7597 (t0) cc_final: 0.7366 (t0) REVERT: A 959 ASN cc_start: 0.7563 (t0) cc_final: 0.7089 (t0) REVERT: A 1038 THR cc_start: 0.8066 (m) cc_final: 0.7820 (p) REVERT: A 1140 HIS cc_start: 0.7988 (t-170) cc_final: 0.7448 (t-90) REVERT: A 1259 MET cc_start: 0.7720 (tpp) cc_final: 0.7511 (tpp) REVERT: A 1398 MET cc_start: 0.8354 (ttp) cc_final: 0.7973 (ttp) REVERT: B 45 SER cc_start: 0.8497 (t) cc_final: 0.8216 (p) REVERT: B 73 GLN cc_start: 0.7779 (tt0) cc_final: 0.7519 (mt0) REVERT: B 177 LYS cc_start: 0.8700 (mttt) cc_final: 0.8496 (mtmt) REVERT: B 390 LEU cc_start: 0.8046 (mt) cc_final: 0.7758 (mt) REVERT: B 391 ASP cc_start: 0.7345 (m-30) cc_final: 0.7105 (t0) REVERT: B 440 HIS cc_start: 0.7669 (m90) cc_final: 0.7270 (m-70) REVERT: B 451 LYS cc_start: 0.7691 (tttt) cc_final: 0.7183 (ttmm) REVERT: B 603 LEU cc_start: 0.8605 (mt) cc_final: 0.8392 (mt) REVERT: B 608 ASP cc_start: 0.7414 (m-30) cc_final: 0.7104 (m-30) REVERT: B 935 ARG cc_start: 0.7421 (ptm160) cc_final: 0.6907 (ttt90) REVERT: B 1057 LYS cc_start: 0.8105 (tttp) cc_final: 0.7803 (ttmm) REVERT: B 1190 ASP cc_start: 0.7436 (t0) cc_final: 0.7215 (t0) REVERT: C 94 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7943 (ttpp) REVERT: D 48 ILE cc_start: 0.8564 (mm) cc_final: 0.8356 (mt) REVERT: E 16 PHE cc_start: 0.8356 (t80) cc_final: 0.7860 (t80) REVERT: E 40 GLU cc_start: 0.8158 (pm20) cc_final: 0.7695 (pm20) REVERT: E 41 ASP cc_start: 0.8527 (m-30) cc_final: 0.7650 (m-30) REVERT: E 132 ILE cc_start: 0.8916 (mm) cc_final: 0.8695 (pt) REVERT: E 137 GLU cc_start: 0.7859 (tt0) cc_final: 0.7604 (mt-10) REVERT: F 76 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8133 (mtpp) REVERT: G 60 ARG cc_start: 0.8040 (ttt-90) cc_final: 0.7805 (ttt-90) REVERT: G 140 LYS cc_start: 0.8851 (tttt) cc_final: 0.8419 (mttp) REVERT: H 41 ASP cc_start: 0.7690 (m-30) cc_final: 0.7389 (m-30) REVERT: H 134 ASN cc_start: 0.8113 (m-40) cc_final: 0.7712 (m-40) REVERT: I 11 ASN cc_start: 0.8740 (t0) cc_final: 0.8419 (t0) REVERT: I 15 TYR cc_start: 0.7647 (m-80) cc_final: 0.7378 (m-80) REVERT: I 55 THR cc_start: 0.7037 (p) cc_final: 0.6807 (p) REVERT: I 113 ASP cc_start: 0.7967 (t0) cc_final: 0.7687 (t0) REVERT: J 38 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7973 (ttm-80) REVERT: L 39 SER cc_start: 0.8751 (m) cc_final: 0.8388 (p) REVERT: M 33 LYS cc_start: 0.7944 (mmmt) cc_final: 0.7639 (mmtp) REVERT: O 73 THR cc_start: 0.7715 (p) cc_final: 0.7445 (p) REVERT: O 97 LYS cc_start: 0.8518 (mttt) cc_final: 0.8290 (tptt) REVERT: O 224 TYR cc_start: 0.8073 (m-10) cc_final: 0.7459 (m-10) REVERT: Q 128 ASN cc_start: 0.7240 (t0) cc_final: 0.6481 (t0) REVERT: Q 133 PHE cc_start: 0.7626 (m-10) cc_final: 0.7392 (m-80) REVERT: R 76 PHE cc_start: 0.7151 (p90) cc_final: 0.6911 (p90) REVERT: R 118 HIS cc_start: 0.6605 (m90) cc_final: 0.6322 (m-70) REVERT: R 334 ASP cc_start: 0.7544 (m-30) cc_final: 0.7239 (p0) REVERT: U 9 VAL cc_start: 0.8847 (t) cc_final: 0.8440 (p) REVERT: U 26 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7160 (mp0) REVERT: U 242 ASN cc_start: 0.7297 (m-40) cc_final: 0.6966 (m-40) REVERT: U 252 THR cc_start: 0.8732 (p) cc_final: 0.8093 (m) REVERT: U 272 ASN cc_start: 0.8786 (m-40) cc_final: 0.8199 (m110) REVERT: U 276 PHE cc_start: 0.8199 (p90) cc_final: 0.7777 (p90) REVERT: U 278 LYS cc_start: 0.8541 (mttp) cc_final: 0.8203 (mmmt) REVERT: U 280 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7855 (tp40) REVERT: W 42 ASP cc_start: 0.8389 (m-30) cc_final: 0.8164 (m-30) REVERT: W 87 TYR cc_start: 0.8607 (m-80) cc_final: 0.7815 (m-80) REVERT: W 130 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7680 (mtmt) REVERT: W 187 LYS cc_start: 0.8450 (mttt) cc_final: 0.8095 (tmtt) REVERT: X 146 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7171 (mt-10) REVERT: X 191 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8257 (mt-10) REVERT: X 222 ASN cc_start: 0.8594 (m-40) cc_final: 0.8317 (m-40) REVERT: X 227 ASP cc_start: 0.7435 (t0) cc_final: 0.6945 (t0) outliers start: 2 outliers final: 0 residues processed: 1803 average time/residue: 0.7331 time to fit residues: 2210.4207 Evaluate side-chains 1191 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1191 time to evaluate : 6.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 751 optimal weight: 8.9990 chunk 674 optimal weight: 0.8980 chunk 374 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 455 optimal weight: 0.8980 chunk 360 optimal weight: 0.9990 chunk 697 optimal weight: 0.0670 chunk 269 optimal weight: 50.0000 chunk 424 optimal weight: 8.9990 chunk 519 optimal weight: 3.9990 chunk 808 optimal weight: 7.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 699 GLN ** 1 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 621 ASN ** 2 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 169 HIS ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 107 ASN 4 62 ASN ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 43 ASN 6 119 GLN 6 227 HIS 6 302 ASN 6 450 ASN 7 462 ASN 7 551 ASN 7 567 GLN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A 640 GLN A1004 ASN A1040 GLN A1218 GLN B 592 ASN B 822 ASN B1104 HIS B1179 GLN E 5 ASN E 8 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN K 110 ASN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 GLN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 353 ASN X 251 ASN X 279 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 75541 Z= 0.253 Angle : 0.571 10.357 102537 Z= 0.299 Chirality : 0.043 0.221 11587 Planarity : 0.004 0.060 12694 Dihedral : 12.371 179.048 11139 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.45 % Allowed : 7.75 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 8762 helix: 1.63 (0.09), residues: 3625 sheet: 0.16 (0.14), residues: 1329 loop : -0.09 (0.10), residues: 3808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 7 133 HIS 0.010 0.001 HIS 2 403 PHE 0.024 0.002 PHE A 219 TYR 0.025 0.001 TYR 7 581 ARG 0.008 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1353 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1238 time to evaluate : 6.533 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: 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: symmetry clash revert: symmetry clash REVERT: 0 7 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: 0 41 GLU cc_start: 0.7589 (tt0) cc_final: 0.7318 (tt0) REVERT: 0 42 MET cc_start: 0.8429 (mmm) cc_final: 0.8112 (mmm) REVERT: 0 76 MET cc_start: 0.7988 (ttp) cc_final: 0.7668 (ttt) REVERT: 0 85 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7582 (mm-30) REVERT: 0 134 ARG cc_start: 0.8678 (mtt90) cc_final: 0.8078 (mtt90) REVERT: 0 189 THR cc_start: 0.8850 (m) cc_final: 0.8431 (p) REVERT: 0 438 THR cc_start: 0.8921 (p) cc_final: 0.8646 (t) REVERT: 0 481 LYS cc_start: 0.8576 (ptpt) cc_final: 0.8267 (ptmm) REVERT: 0 544 TYR cc_start: 0.7927 (t80) cc_final: 0.7624 (t80) REVERT: 1 102 MET cc_start: 0.7462 (mmm) cc_final: 0.7026 (mmm) REVERT: 1 192 MET cc_start: 0.8184 (tpt) cc_final: 0.7837 (tpp) REVERT: 1 220 PHE cc_start: 0.8757 (t80) cc_final: 0.8163 (t80) REVERT: 1 379 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.6678 (m-40) REVERT: 1 616 LEU cc_start: 0.8631 (mp) cc_final: 0.8414 (mp) REVERT: 2 223 HIS cc_start: 0.8234 (m90) cc_final: 0.7633 (m-70) REVERT: 3 25 ASP cc_start: 0.8063 (m-30) cc_final: 0.7700 (t0) REVERT: 3 28 PHE cc_start: 0.8678 (m-80) cc_final: 0.8071 (m-80) REVERT: 3 80 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8619 (ttpt) REVERT: 3 99 PHE cc_start: 0.7082 (m-80) cc_final: 0.6265 (m-80) REVERT: 3 100 ASN cc_start: 0.8152 (m-40) cc_final: 0.7804 (p0) REVERT: 3 106 TYR cc_start: 0.7892 (t80) cc_final: 0.7644 (t80) REVERT: 3 114 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8166 (tp30) REVERT: 4 29 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8458 (pt) REVERT: 4 45 ASN cc_start: 0.7914 (p0) cc_final: 0.7427 (p0) REVERT: 4 116 ARG cc_start: 0.7573 (mmm160) cc_final: 0.7113 (mmm160) REVERT: 4 146 ARG cc_start: 0.6510 (mtm110) cc_final: 0.5952 (ptp90) REVERT: 4 228 THR cc_start: 0.8604 (p) cc_final: 0.8333 (t) REVERT: 4 273 ARG cc_start: 0.7349 (mtm-85) cc_final: 0.7106 (ttm170) REVERT: 6 188 ASN cc_start: 0.7590 (t0) cc_final: 0.7373 (t0) REVERT: 6 322 MET cc_start: 0.7301 (mtp) cc_final: 0.6991 (mtm) REVERT: 6 450 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7488 (p0) REVERT: 7 464 ARG cc_start: 0.5023 (OUTLIER) cc_final: 0.4304 (ptp-170) REVERT: 7 474 MET cc_start: 0.8819 (tpp) cc_final: 0.8345 (mmm) REVERT: 7 716 MET cc_start: 0.9184 (mmm) cc_final: 0.8880 (mmp) REVERT: A 41 MET cc_start: 0.7919 (mmm) cc_final: 0.7598 (mmm) REVERT: A 100 LYS cc_start: 0.8750 (tttt) cc_final: 0.8413 (ttpp) REVERT: A 175 ARG cc_start: 0.7259 (mtm-85) cc_final: 0.7007 (mtm110) REVERT: A 696 GLU cc_start: 0.7250 (tt0) cc_final: 0.6911 (tt0) REVERT: A 949 ASP cc_start: 0.7713 (t0) cc_final: 0.7405 (t0) REVERT: A 1038 THR cc_start: 0.8089 (m) cc_final: 0.7784 (p) REVERT: A 1135 ARG cc_start: 0.8036 (ttt180) cc_final: 0.7718 (ttt-90) REVERT: A 1140 HIS cc_start: 0.8053 (t-170) cc_final: 0.7675 (t-90) REVERT: A 1448 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6427 (tm-30) REVERT: B 45 SER cc_start: 0.8411 (t) cc_final: 0.8167 (p) REVERT: B 73 GLN cc_start: 0.7825 (tt0) cc_final: 0.7553 (mt0) REVERT: B 177 LYS cc_start: 0.8712 (mttt) cc_final: 0.8501 (mtmt) REVERT: B 277 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8098 (ptpt) REVERT: B 326 ASP cc_start: 0.7920 (p0) cc_final: 0.7590 (p0) REVERT: B 355 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7720 (tp) REVERT: B 373 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.8081 (mtt-85) REVERT: B 390 LEU cc_start: 0.8223 (mt) cc_final: 0.7976 (mt) REVERT: B 391 ASP cc_start: 0.7373 (m-30) cc_final: 0.6962 (t0) REVERT: B 440 HIS cc_start: 0.7913 (m90) cc_final: 0.7385 (m-70) REVERT: B 935 ARG cc_start: 0.7556 (ptm160) cc_final: 0.7032 (ttt90) REVERT: B 1021 MET cc_start: 0.8851 (mtm) cc_final: 0.8607 (mtm) REVERT: B 1190 ASP cc_start: 0.7480 (t0) cc_final: 0.7010 (t0) REVERT: D 48 ILE cc_start: 0.8569 (mm) cc_final: 0.8350 (mt) REVERT: E 16 PHE cc_start: 0.8395 (t80) cc_final: 0.7903 (t80) REVERT: E 40 GLU cc_start: 0.8164 (pm20) cc_final: 0.7815 (pm20) REVERT: E 41 ASP cc_start: 0.8481 (m-30) cc_final: 0.7671 (m-30) REVERT: E 93 MET cc_start: 0.6649 (mmt) cc_final: 0.6406 (mmp) REVERT: E 107 THR cc_start: 0.8238 (m) cc_final: 0.7873 (p) REVERT: F 76 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8121 (tttp) REVERT: G 44 TYR cc_start: 0.8403 (m-80) cc_final: 0.7400 (m-80) REVERT: G 50 ASP cc_start: 0.8376 (t0) cc_final: 0.8171 (t70) REVERT: G 53 ASN cc_start: 0.7341 (m110) cc_final: 0.6552 (t0) REVERT: G 71 ASN cc_start: 0.8799 (t0) cc_final: 0.8477 (t0) REVERT: G 100 GLU cc_start: 0.7379 (tt0) cc_final: 0.7098 (tt0) REVERT: G 140 LYS cc_start: 0.8826 (tttt) cc_final: 0.8408 (mttp) REVERT: G 148 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7249 (mt-10) REVERT: H 41 ASP cc_start: 0.7808 (m-30) cc_final: 0.7565 (m-30) REVERT: H 134 ASN cc_start: 0.8004 (m-40) cc_final: 0.7582 (m-40) REVERT: I 11 ASN cc_start: 0.8665 (t0) cc_final: 0.8356 (t0) REVERT: I 15 TYR cc_start: 0.7506 (m-80) cc_final: 0.7011 (m-80) REVERT: I 25 LEU cc_start: 0.8012 (tp) cc_final: 0.7148 (tp) REVERT: I 99 LEU cc_start: 0.8595 (mt) cc_final: 0.8378 (mp) REVERT: L 39 SER cc_start: 0.8772 (m) cc_final: 0.8383 (p) REVERT: M 33 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7630 (mmtp) REVERT: M 214 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7923 (mm) REVERT: M 300 GLN cc_start: 0.7989 (tp40) cc_final: 0.7670 (tp-100) REVERT: O 68 GLN cc_start: 0.7682 (mm110) cc_final: 0.7360 (mt0) REVERT: O 158 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8205 (mm-40) REVERT: O 179 HIS cc_start: 0.7393 (m90) cc_final: 0.7032 (m90) REVERT: O 181 THR cc_start: 0.8438 (p) cc_final: 0.8027 (t) REVERT: Q 101 PHE cc_start: 0.7479 (m-80) cc_final: 0.7018 (m-80) REVERT: Q 128 ASN cc_start: 0.7321 (t0) cc_final: 0.6934 (t0) REVERT: Q 327 ARG cc_start: 0.7057 (mmm160) cc_final: 0.6816 (tpp-160) REVERT: Q 347 PHE cc_start: 0.7879 (t80) cc_final: 0.7659 (t80) REVERT: Q 386 MET cc_start: 0.6948 (tmm) cc_final: 0.6610 (tmm) REVERT: R 129 VAL cc_start: 0.8720 (p) cc_final: 0.8476 (m) REVERT: R 334 ASP cc_start: 0.7604 (m-30) cc_final: 0.7333 (p0) REVERT: U 242 ASN cc_start: 0.7430 (m-40) cc_final: 0.6739 (m-40) REVERT: U 270 ASN cc_start: 0.8080 (p0) cc_final: 0.7423 (p0) REVERT: U 276 PHE cc_start: 0.8238 (p90) cc_final: 0.7613 (p90) REVERT: U 280 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7844 (tp40) REVERT: W 123 MET cc_start: 0.6068 (tpp) cc_final: 0.5665 (mmm) REVERT: W 187 LYS cc_start: 0.8486 (mttt) cc_final: 0.8146 (tmtt) REVERT: X 216 GLN cc_start: 0.7928 (pm20) cc_final: 0.7694 (pm20) REVERT: X 227 ASP cc_start: 0.7315 (t0) cc_final: 0.6929 (t0) outliers start: 115 outliers final: 65 residues processed: 1298 average time/residue: 0.7830 time to fit residues: 1729.0867 Evaluate side-chains 1167 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1094 time to evaluate : 6.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 7 ASP Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 280 GLU Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 364 ILE Chi-restraints excluded: chain 1 residue 379 ASN Chi-restraints excluded: chain 1 residue 475 LEU Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 166 LEU Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 3 residue 93 ASN Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 294 CYS Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 347 TYR Chi-restraints excluded: chain 6 residue 450 ASN Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 833 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 263 CYS Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 223 ILE Chi-restraints excluded: chain Q residue 329 THR Chi-restraints excluded: chain Q residue 360 THR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 193 ARG Chi-restraints excluded: chain X residue 186 VAL Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 279 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 449 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 672 optimal weight: 0.9990 chunk 550 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 809 optimal weight: 9.9990 chunk 874 optimal weight: 30.0000 chunk 721 optimal weight: 3.9990 chunk 802 optimal weight: 3.9990 chunk 276 optimal weight: 30.0000 chunk 649 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 379 ASN 1 513 GLN ** 1 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 500 GLN ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 93 ASN ** 4 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 ASN A 493 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN B 309 GLN B 415 GLN B 975 GLN B1062 HIS D 34 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN Q 117 HIS Q 150 GLN R 111 ASN R 118 HIS W 353 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 75541 Z= 0.436 Angle : 0.623 11.049 102537 Z= 0.327 Chirality : 0.045 0.226 11587 Planarity : 0.005 0.074 12694 Dihedral : 12.465 159.559 11139 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.10 % Allowed : 9.94 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.09), residues: 8762 helix: 1.37 (0.09), residues: 3634 sheet: 0.05 (0.14), residues: 1310 loop : -0.31 (0.10), residues: 3818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP 7 133 HIS 0.011 0.001 HIS 5 52 PHE 0.030 0.002 PHE A 219 TYR 0.044 0.002 TYR O 224 ARG 0.010 0.001 ARG I 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1138 time to evaluate : 6.611 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: 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: 0 7 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: 0 41 GLU cc_start: 0.7688 (tt0) cc_final: 0.7481 (tt0) REVERT: 0 42 MET cc_start: 0.8486 (mmm) cc_final: 0.8230 (mmm) REVERT: 0 76 MET cc_start: 0.8039 (ttp) cc_final: 0.7676 (ttt) REVERT: 0 78 GLU cc_start: 0.7666 (mp0) cc_final: 0.7153 (mp0) REVERT: 0 134 ARG cc_start: 0.8745 (mtt90) cc_final: 0.8151 (mtt90) REVERT: 0 180 LYS cc_start: 0.7541 (tttt) cc_final: 0.7277 (tttt) REVERT: 0 250 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7783 (mm) REVERT: 0 481 LYS cc_start: 0.8679 (ptpt) cc_final: 0.8382 (ptmm) REVERT: 0 525 MET cc_start: 0.7949 (ttm) cc_final: 0.7730 (ttm) REVERT: 0 544 TYR cc_start: 0.8236 (t80) cc_final: 0.7988 (t80) REVERT: 0 732 ASP cc_start: 0.7771 (t0) cc_final: 0.7418 (t0) REVERT: 1 1 MET cc_start: 0.5078 (ppp) cc_final: 0.4516 (ppp) REVERT: 1 192 MET cc_start: 0.8191 (tpt) cc_final: 0.7834 (tpp) REVERT: 1 469 MET cc_start: 0.6822 (ttm) cc_final: 0.6568 (ttm) REVERT: 1 616 LEU cc_start: 0.8710 (mp) cc_final: 0.8502 (mp) REVERT: 2 36 TYR cc_start: 0.7384 (t80) cc_final: 0.7175 (t80) REVERT: 2 108 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7906 (mm) REVERT: 2 223 HIS cc_start: 0.8233 (m90) cc_final: 0.7561 (m-70) REVERT: 2 355 LEU cc_start: 0.9208 (pt) cc_final: 0.8462 (mt) REVERT: 3 25 ASP cc_start: 0.8097 (m-30) cc_final: 0.7696 (t0) REVERT: 3 28 PHE cc_start: 0.8716 (m-80) cc_final: 0.8090 (m-80) REVERT: 3 45 ARG cc_start: 0.8222 (tmm-80) cc_final: 0.7766 (tmm-80) REVERT: 3 80 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8642 (ttpt) REVERT: 3 106 TYR cc_start: 0.8031 (t80) cc_final: 0.7793 (t80) REVERT: 4 36 LEU cc_start: 0.8291 (mt) cc_final: 0.7995 (mt) REVERT: 4 116 ARG cc_start: 0.7615 (mmm160) cc_final: 0.6995 (mmm160) REVERT: 4 146 ARG cc_start: 0.6617 (mtm110) cc_final: 0.6230 (ptp90) REVERT: 4 226 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7711 (tp40) REVERT: 4 228 THR cc_start: 0.8536 (p) cc_final: 0.8291 (t) REVERT: 4 255 ASP cc_start: 0.8386 (t0) cc_final: 0.8109 (t0) REVERT: 5 52 HIS cc_start: 0.8716 (p-80) cc_final: 0.8171 (p-80) REVERT: 5 53 GLU cc_start: 0.9293 (tp30) cc_final: 0.9060 (mm-30) REVERT: 5 66 MET cc_start: 0.7921 (tpp) cc_final: 0.7612 (tpp) REVERT: 6 188 ASN cc_start: 0.7929 (t0) cc_final: 0.7022 (t0) REVERT: 6 191 ASP cc_start: 0.7840 (m-30) cc_final: 0.7506 (m-30) REVERT: 6 450 ASN cc_start: 0.7943 (p0) cc_final: 0.7522 (p0) REVERT: 7 459 MET cc_start: 0.8508 (mtt) cc_final: 0.7365 (ttm) REVERT: 7 464 ARG cc_start: 0.4750 (OUTLIER) cc_final: 0.4150 (ptp-170) REVERT: 7 474 MET cc_start: 0.8835 (tpp) cc_final: 0.8266 (mmm) REVERT: 7 561 MET cc_start: 0.6828 (ttt) cc_final: 0.6324 (tmm) REVERT: 7 716 MET cc_start: 0.9214 (mmm) cc_final: 0.8867 (mmp) REVERT: A 41 MET cc_start: 0.7920 (mmm) cc_final: 0.7666 (mmm) REVERT: A 177 ASP cc_start: 0.7602 (t0) cc_final: 0.7367 (t0) REVERT: A 414 ASP cc_start: 0.8023 (t0) cc_final: 0.7757 (t0) REVERT: A 731 ARG cc_start: 0.7335 (mtm-85) cc_final: 0.7030 (mtm-85) REVERT: A 949 ASP cc_start: 0.7788 (t0) cc_final: 0.7436 (t0) REVERT: A 1038 THR cc_start: 0.8182 (m) cc_final: 0.7859 (p) REVERT: A 1135 ARG cc_start: 0.8098 (ttt180) cc_final: 0.7783 (ttt-90) REVERT: A 1140 HIS cc_start: 0.8170 (t-170) cc_final: 0.7906 (t-90) REVERT: A 1304 TRP cc_start: 0.7811 (m100) cc_final: 0.7588 (m100) REVERT: A 1448 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6636 (tm-30) REVERT: B 177 LYS cc_start: 0.8760 (mttt) cc_final: 0.8541 (mtmt) REVERT: B 277 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8088 (ptpt) REVERT: B 373 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.8010 (mtt-85) REVERT: B 391 ASP cc_start: 0.7434 (m-30) cc_final: 0.6900 (t0) REVERT: B 440 HIS cc_start: 0.7988 (m90) cc_final: 0.7335 (m-70) REVERT: B 873 THR cc_start: 0.8506 (p) cc_final: 0.8230 (t) REVERT: B 935 ARG cc_start: 0.7617 (ptm160) cc_final: 0.7097 (ttt90) REVERT: B 1190 ASP cc_start: 0.7510 (t0) cc_final: 0.7090 (t0) REVERT: C 193 TYR cc_start: 0.9099 (p90) cc_final: 0.8858 (p90) REVERT: D 48 ILE cc_start: 0.8537 (mm) cc_final: 0.8334 (mt) REVERT: D 71 LYS cc_start: 0.7775 (mttt) cc_final: 0.6849 (mmtm) REVERT: D 155 ARG cc_start: 0.8008 (mmt90) cc_final: 0.7197 (mmt90) REVERT: E 16 PHE cc_start: 0.8438 (t80) cc_final: 0.7967 (t80) REVERT: E 40 GLU cc_start: 0.8193 (pm20) cc_final: 0.7842 (pm20) REVERT: E 41 ASP cc_start: 0.8480 (m-30) cc_final: 0.7653 (m-30) REVERT: E 93 MET cc_start: 0.6730 (mmt) cc_final: 0.6502 (mmp) REVERT: E 107 THR cc_start: 0.8248 (m) cc_final: 0.7882 (p) REVERT: E 132 ILE cc_start: 0.9165 (mm) cc_final: 0.8830 (tp) REVERT: F 76 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8216 (tttp) REVERT: F 110 ASP cc_start: 0.7919 (p0) cc_final: 0.7608 (p0) REVERT: G 44 TYR cc_start: 0.8530 (m-80) cc_final: 0.8283 (m-80) REVERT: G 50 ASP cc_start: 0.8344 (t0) cc_final: 0.8078 (t70) REVERT: G 53 ASN cc_start: 0.7445 (m110) cc_final: 0.6667 (t0) REVERT: G 71 ASN cc_start: 0.8867 (t0) cc_final: 0.8640 (t0) REVERT: G 113 HIS cc_start: 0.7613 (m-70) cc_final: 0.7200 (m-70) REVERT: G 126 ASN cc_start: 0.7411 (t0) cc_final: 0.7185 (t0) REVERT: G 140 LYS cc_start: 0.8840 (tttt) cc_final: 0.8407 (mtmt) REVERT: I 11 ASN cc_start: 0.8764 (t0) cc_final: 0.8295 (t0) REVERT: I 15 TYR cc_start: 0.7671 (m-80) cc_final: 0.7327 (m-80) REVERT: I 99 LEU cc_start: 0.8731 (mt) cc_final: 0.8475 (mp) REVERT: J 49 MET cc_start: 0.9191 (tpp) cc_final: 0.8977 (tpp) REVERT: L 39 SER cc_start: 0.8844 (m) cc_final: 0.8450 (p) REVERT: M 33 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7665 (mmtp) REVERT: M 168 MET cc_start: 0.7471 (tpp) cc_final: 0.7199 (tpt) REVERT: M 214 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7962 (mm) REVERT: M 250 MET cc_start: 0.7116 (tmm) cc_final: 0.6741 (tpp) REVERT: M 300 GLN cc_start: 0.8050 (tp40) cc_final: 0.7715 (tp40) REVERT: O 68 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7437 (mt0) REVERT: O 158 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8331 (mm-40) REVERT: O 179 HIS cc_start: 0.7564 (m90) cc_final: 0.7230 (m90) REVERT: O 222 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6909 (pt0) REVERT: Q 128 ASN cc_start: 0.7493 (t0) cc_final: 0.6999 (t0) REVERT: R 111 ASN cc_start: 0.5188 (OUTLIER) cc_final: 0.4940 (t0) REVERT: R 123 GLU cc_start: 0.5372 (tt0) cc_final: 0.5108 (mp0) REVERT: R 229 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6654 (t0) REVERT: R 334 ASP cc_start: 0.7603 (m-30) cc_final: 0.7264 (p0) REVERT: U 38 LEU cc_start: 0.8406 (tp) cc_final: 0.8192 (pp) REVERT: U 242 ASN cc_start: 0.7424 (m-40) cc_final: 0.6627 (m-40) REVERT: U 276 PHE cc_start: 0.8110 (p90) cc_final: 0.7622 (p90) REVERT: U 280 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7822 (tp40) REVERT: V 44 PHE cc_start: 0.8571 (t80) cc_final: 0.8368 (t80) REVERT: V 62 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8530 (t) REVERT: V 112 ARG cc_start: 0.8186 (ttt-90) cc_final: 0.7707 (ttt-90) REVERT: W 187 LYS cc_start: 0.8491 (mttt) cc_final: 0.8216 (tmtt) REVERT: X 227 ASP cc_start: 0.7394 (t0) cc_final: 0.6822 (t0) outliers start: 167 outliers final: 105 residues processed: 1228 average time/residue: 0.7544 time to fit residues: 1569.3248 Evaluate side-chains 1166 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1051 time to evaluate : 6.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 7 ASP Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 250 LEU Chi-restraints excluded: chain 0 residue 354 GLU Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 619 THR Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 280 GLU Chi-restraints excluded: chain 1 residue 364 ILE Chi-restraints excluded: chain 1 residue 505 THR Chi-restraints excluded: chain 1 residue 633 TYR Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 76 VAL Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 3 residue 93 ASN Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 121 VAL Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 226 GLN Chi-restraints excluded: chain 4 residue 275 SER Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 294 CYS Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 238 SER Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 347 TYR Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 760 LEU Chi-restraints excluded: chain 7 residue 833 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 102 LYS Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 263 CYS Chi-restraints excluded: chain O residue 223 ILE Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain Q residue 329 THR Chi-restraints excluded: chain Q residue 360 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 229 ASN Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain U residue 247 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 193 ARG Chi-restraints excluded: chain W residue 218 THR Chi-restraints excluded: chain W residue 353 ASN Chi-restraints excluded: chain X residue 193 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 799 optimal weight: 10.0000 chunk 608 optimal weight: 20.0000 chunk 420 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 386 optimal weight: 0.7980 chunk 543 optimal weight: 1.9990 chunk 812 optimal weight: 20.0000 chunk 860 optimal weight: 4.9990 chunk 424 optimal weight: 1.9990 chunk 770 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 182 GLN ** 1 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 303 ASN ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 642 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN A1048 ASN B 415 GLN B 592 ASN B 887 HIS B 951 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 HIS Q 150 GLN R 111 ASN X 279 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 75541 Z= 0.226 Angle : 0.545 13.507 102537 Z= 0.285 Chirality : 0.042 0.193 11587 Planarity : 0.004 0.061 12694 Dihedral : 12.380 139.137 11139 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.95 % Allowed : 11.49 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.09), residues: 8762 helix: 1.49 (0.09), residues: 3639 sheet: 0.07 (0.14), residues: 1316 loop : -0.29 (0.10), residues: 3807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP 7 133 HIS 0.006 0.001 HIS 2 85 PHE 0.025 0.001 PHE A 219 TYR 0.023 0.001 TYR 7 581 ARG 0.010 0.000 ARG I 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1107 time to evaluate : 6.814 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 7 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: 0 41 GLU cc_start: 0.7634 (tt0) cc_final: 0.7385 (tt0) REVERT: 0 76 MET cc_start: 0.7969 (ttp) cc_final: 0.7649 (ttt) REVERT: 0 78 GLU cc_start: 0.7876 (mp0) cc_final: 0.7328 (mp0) REVERT: 0 134 ARG cc_start: 0.8744 (mtt90) cc_final: 0.8116 (mtt90) REVERT: 0 180 LYS cc_start: 0.7513 (tttt) cc_final: 0.7243 (tttt) REVERT: 0 250 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7780 (mm) REVERT: 0 438 THR cc_start: 0.8927 (p) cc_final: 0.8662 (t) REVERT: 0 481 LYS cc_start: 0.8667 (ptpt) cc_final: 0.8315 (ptmm) REVERT: 0 521 ASN cc_start: 0.8204 (m-40) cc_final: 0.7980 (m-40) REVERT: 0 525 MET cc_start: 0.7902 (ttm) cc_final: 0.7668 (ttm) REVERT: 0 544 TYR cc_start: 0.8048 (t80) cc_final: 0.7794 (t80) REVERT: 1 1 MET cc_start: 0.5295 (ppp) cc_final: 0.4911 (ppp) REVERT: 1 97 MET cc_start: 0.8693 (ttp) cc_final: 0.8240 (ttt) REVERT: 1 182 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6254 (mm110) REVERT: 1 192 MET cc_start: 0.8147 (tpt) cc_final: 0.7790 (tpp) REVERT: 1 349 VAL cc_start: 0.8589 (t) cc_final: 0.8220 (m) REVERT: 1 608 MET cc_start: 0.8137 (tpp) cc_final: 0.7637 (tpp) REVERT: 2 97 MET cc_start: 0.6635 (mmm) cc_final: 0.6370 (mmp) REVERT: 2 108 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7772 (mm) REVERT: 2 223 HIS cc_start: 0.8188 (m90) cc_final: 0.7521 (m-70) REVERT: 2 355 LEU cc_start: 0.9232 (pt) cc_final: 0.8530 (mt) REVERT: 3 25 ASP cc_start: 0.8055 (m-30) cc_final: 0.7645 (t0) REVERT: 3 28 PHE cc_start: 0.8725 (m-80) cc_final: 0.8116 (m-80) REVERT: 3 80 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8648 (ttpt) REVERT: 4 36 LEU cc_start: 0.8245 (mt) cc_final: 0.7895 (mt) REVERT: 4 139 GLN cc_start: 0.8567 (pp30) cc_final: 0.8323 (pt0) REVERT: 4 146 ARG cc_start: 0.6910 (mtm110) cc_final: 0.6492 (ptp-110) REVERT: 4 226 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7642 (tp40) REVERT: 4 228 THR cc_start: 0.8485 (p) cc_final: 0.8246 (t) REVERT: 4 271 ASP cc_start: 0.5848 (p0) cc_final: 0.5643 (p0) REVERT: 5 51 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8451 (mmtm) REVERT: 5 52 HIS cc_start: 0.8622 (p-80) cc_final: 0.8150 (p-80) REVERT: 5 53 GLU cc_start: 0.9302 (tp30) cc_final: 0.9058 (mm-30) REVERT: 5 66 MET cc_start: 0.7886 (tpp) cc_final: 0.7562 (tpp) REVERT: 6 216 MET cc_start: 0.8414 (ttm) cc_final: 0.8199 (ttp) REVERT: 6 450 ASN cc_start: 0.8020 (p0) cc_final: 0.7529 (p0) REVERT: 7 244 MET cc_start: 0.8784 (mmm) cc_final: 0.8258 (ptt) REVERT: 7 459 MET cc_start: 0.8558 (mtt) cc_final: 0.7459 (ttm) REVERT: 7 464 ARG cc_start: 0.5084 (OUTLIER) cc_final: 0.4411 (ptp-170) REVERT: 7 474 MET cc_start: 0.8867 (tpp) cc_final: 0.8306 (mmm) REVERT: 7 716 MET cc_start: 0.9225 (mmm) cc_final: 0.8882 (mmp) REVERT: 7 721 LYS cc_start: 0.9279 (tttt) cc_final: 0.9075 (pttp) REVERT: A 41 MET cc_start: 0.7928 (mmm) cc_final: 0.7688 (mmm) REVERT: A 175 ARG cc_start: 0.7305 (mtm-85) cc_final: 0.7102 (mtm110) REVERT: A 949 ASP cc_start: 0.7787 (t0) cc_final: 0.7481 (t0) REVERT: A 1038 THR cc_start: 0.8138 (m) cc_final: 0.7864 (p) REVERT: A 1135 ARG cc_start: 0.8083 (ttt180) cc_final: 0.7748 (ttt-90) REVERT: A 1304 TRP cc_start: 0.7807 (m100) cc_final: 0.7502 (m100) REVERT: B 177 LYS cc_start: 0.8804 (mttt) cc_final: 0.8567 (mtmt) REVERT: B 277 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8048 (ptpt) REVERT: B 312 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7500 (tp30) REVERT: B 331 LEU cc_start: 0.8923 (mt) cc_final: 0.8715 (mp) REVERT: B 332 ASP cc_start: 0.8261 (m-30) cc_final: 0.7567 (t70) REVERT: B 373 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7876 (mtt-85) REVERT: B 391 ASP cc_start: 0.7402 (m-30) cc_final: 0.6890 (t0) REVERT: B 440 HIS cc_start: 0.7932 (m90) cc_final: 0.7255 (m-70) REVERT: B 591 ARG cc_start: 0.7537 (tpp80) cc_final: 0.7265 (mmt90) REVERT: B 873 THR cc_start: 0.8446 (p) cc_final: 0.8185 (t) REVERT: B 935 ARG cc_start: 0.7606 (ptm160) cc_final: 0.7089 (ttt90) REVERT: B 1190 ASP cc_start: 0.7517 (t0) cc_final: 0.7088 (t0) REVERT: C 155 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8744 (pp) REVERT: C 193 TYR cc_start: 0.9101 (p90) cc_final: 0.8900 (p90) REVERT: D 37 GLN cc_start: 0.7447 (mt0) cc_final: 0.7107 (mt0) REVERT: D 48 ILE cc_start: 0.8525 (mm) cc_final: 0.8313 (mt) REVERT: D 71 LYS cc_start: 0.7822 (mttt) cc_final: 0.7040 (mmtm) REVERT: E 16 PHE cc_start: 0.8425 (t80) cc_final: 0.7938 (t80) REVERT: E 40 GLU cc_start: 0.8185 (pm20) cc_final: 0.7819 (pm20) REVERT: E 41 ASP cc_start: 0.8477 (m-30) cc_final: 0.7620 (m-30) REVERT: E 61 GLN cc_start: 0.8226 (tt0) cc_final: 0.7831 (tm-30) REVERT: E 93 MET cc_start: 0.6688 (mmt) cc_final: 0.6463 (mmp) REVERT: E 107 THR cc_start: 0.8279 (m) cc_final: 0.7967 (p) REVERT: E 132 ILE cc_start: 0.9183 (mm) cc_final: 0.8829 (tp) REVERT: F 76 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8198 (tttp) REVERT: F 110 ASP cc_start: 0.7926 (p0) cc_final: 0.7656 (p0) REVERT: G 50 ASP cc_start: 0.8336 (t0) cc_final: 0.8086 (t70) REVERT: G 53 ASN cc_start: 0.7367 (m110) cc_final: 0.6694 (t0) REVERT: G 114 LEU cc_start: 0.8647 (mt) cc_final: 0.8376 (tp) REVERT: G 140 LYS cc_start: 0.8831 (tttt) cc_final: 0.8390 (mtmt) REVERT: I 12 ASN cc_start: 0.8155 (t0) cc_final: 0.7918 (t0) REVERT: I 15 TYR cc_start: 0.7672 (m-80) cc_final: 0.7317 (m-10) REVERT: I 17 ARG cc_start: 0.6700 (ttm-80) cc_final: 0.6244 (ttm-80) REVERT: I 28 GLU cc_start: 0.7210 (tt0) cc_final: 0.6257 (tp30) REVERT: L 30 ILE cc_start: 0.9032 (tt) cc_final: 0.8708 (tp) REVERT: L 39 SER cc_start: 0.8788 (m) cc_final: 0.8420 (p) REVERT: M 33 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7646 (mmtp) REVERT: M 250 MET cc_start: 0.7073 (tmm) cc_final: 0.6736 (tpp) REVERT: M 300 GLN cc_start: 0.8028 (tp40) cc_final: 0.7671 (tp-100) REVERT: O 68 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7430 (mt0) REVERT: O 158 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8310 (mm-40) REVERT: O 179 HIS cc_start: 0.7513 (m90) cc_final: 0.7158 (m90) REVERT: O 188 GLU cc_start: 0.8206 (tt0) cc_final: 0.7959 (tt0) REVERT: O 197 MET cc_start: 0.7320 (mtp) cc_final: 0.7085 (mtp) REVERT: Q 128 ASN cc_start: 0.7490 (t0) cc_final: 0.6989 (t0) REVERT: R 111 ASN cc_start: 0.4997 (OUTLIER) cc_final: 0.4674 (t0) REVERT: R 229 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6667 (t0) REVERT: R 334 ASP cc_start: 0.7498 (m-30) cc_final: 0.7180 (p0) REVERT: U 38 LEU cc_start: 0.8493 (tp) cc_final: 0.8198 (pp) REVERT: U 242 ASN cc_start: 0.7269 (m-40) cc_final: 0.6333 (m-40) REVERT: U 250 LYS cc_start: 0.8480 (tptp) cc_final: 0.8259 (tptp) REVERT: U 276 PHE cc_start: 0.8125 (p90) cc_final: 0.7640 (p90) REVERT: U 280 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7855 (tp40) REVERT: V 78 PHE cc_start: 0.8460 (m-80) cc_final: 0.8228 (m-80) REVERT: W 187 LYS cc_start: 0.8476 (mttt) cc_final: 0.8189 (tmtt) REVERT: X 227 ASP cc_start: 0.7332 (t0) cc_final: 0.6771 (t0) outliers start: 155 outliers final: 100 residues processed: 1199 average time/residue: 0.8437 time to fit residues: 1732.1798 Evaluate side-chains 1161 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1052 time to evaluate : 7.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 7 ASP Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 250 LEU Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 619 THR Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 182 GLN Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 633 TYR Chi-restraints excluded: chain 2 residue 5 SER Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 76 VAL Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 3 residue 93 ASN Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 294 CYS Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 347 TYR Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 464 ARG Chi-restraints excluded: chain 7 residue 760 LEU Chi-restraints excluded: chain 7 residue 833 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 263 CYS Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 223 ILE Chi-restraints excluded: chain Q residue 329 THR Chi-restraints excluded: chain Q residue 360 THR Chi-restraints excluded: chain Q residue 407 ASP Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 229 ASN Chi-restraints excluded: chain R residue 313 TRP Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain U residue 247 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 193 ARG Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 267 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 716 optimal weight: 1.9990 chunk 488 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 640 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 734 optimal weight: 3.9990 chunk 594 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 439 optimal weight: 2.9990 chunk 772 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 427 ASN 1 38 HIS 1 359 GLN 1 468 GLN ** 1 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 93 ASN 4 142 GLN 4 161 ASN 4 303 ASN ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN A 118 HIS A 124 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN B 887 HIS ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN J 53 HIS K 110 ASN M 251 GLN Q 117 HIS Q 150 GLN W 178 GLN W 353 ASN X 279 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 75541 Z= 0.360 Angle : 0.579 10.839 102537 Z= 0.302 Chirality : 0.043 0.206 11587 Planarity : 0.004 0.068 12694 Dihedral : 12.367 118.376 11139 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.35 % Allowed : 12.17 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 8762 helix: 1.44 (0.09), residues: 3646 sheet: -0.03 (0.14), residues: 1295 loop : -0.34 (0.10), residues: 3821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP 7 133 HIS 0.006 0.001 HIS B1104 PHE 0.029 0.002 PHE A 219 TYR 0.024 0.002 TYR G 51 ARG 0.010 0.000 ARG 0 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1080 time to evaluate : 9.609 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 7 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: 0 41 GLU cc_start: 0.7656 (tt0) cc_final: 0.7381 (tt0) REVERT: 0 76 MET cc_start: 0.7999 (ttp) cc_final: 0.7677 (ttt) REVERT: 0 134 ARG cc_start: 0.8778 (mtt90) cc_final: 0.8128 (mtt90) REVERT: 0 180 LYS cc_start: 0.7533 (tttt) cc_final: 0.7333 (tttt) REVERT: 0 250 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7867 (mm) REVERT: 0 525 MET cc_start: 0.7972 (ttm) cc_final: 0.7706 (ttm) REVERT: 0 544 TYR cc_start: 0.8229 (t80) cc_final: 0.7992 (t80) REVERT: 1 192 MET cc_start: 0.8197 (tpt) cc_final: 0.7867 (tpp) REVERT: 1 349 VAL cc_start: 0.8588 (t) cc_final: 0.8227 (m) REVERT: 1 469 MET cc_start: 0.6896 (ttm) cc_final: 0.6567 (ttm) REVERT: 1 608 MET cc_start: 0.8154 (tpp) cc_final: 0.7636 (tpp) REVERT: 2 97 MET cc_start: 0.6912 (mmm) cc_final: 0.6644 (mmp) REVERT: 2 108 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7717 (mm) REVERT: 2 223 HIS cc_start: 0.8229 (m90) cc_final: 0.7373 (m90) REVERT: 2 355 LEU cc_start: 0.9227 (pt) cc_final: 0.8529 (mt) REVERT: 3 28 PHE cc_start: 0.8753 (m-80) cc_final: 0.8140 (m-80) REVERT: 3 80 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8664 (ttpt) REVERT: 4 36 LEU cc_start: 0.8296 (mt) cc_final: 0.7950 (mt) REVERT: 4 116 ARG cc_start: 0.7763 (mmm160) cc_final: 0.7341 (mmm160) REVERT: 4 127 GLU cc_start: 0.8679 (tt0) cc_final: 0.8469 (mt-10) REVERT: 4 146 ARG cc_start: 0.6685 (mtm110) cc_final: 0.6409 (ptp90) REVERT: 4 228 THR cc_start: 0.8504 (p) cc_final: 0.8271 (t) REVERT: 4 271 ASP cc_start: 0.6267 (p0) cc_final: 0.6001 (p0) REVERT: 5 52 HIS cc_start: 0.8653 (p-80) cc_final: 0.8033 (p-80) REVERT: 5 53 GLU cc_start: 0.9277 (tp30) cc_final: 0.9001 (mm-30) REVERT: 6 194 ASP cc_start: 0.7363 (m-30) cc_final: 0.7109 (t0) REVERT: 6 380 TYR cc_start: 0.8103 (m-80) cc_final: 0.7894 (m-80) REVERT: 7 133 TRP cc_start: 0.8265 (m100) cc_final: 0.7610 (m100) REVERT: 7 459 MET cc_start: 0.8588 (mtt) cc_final: 0.7488 (ttm) REVERT: 7 474 MET cc_start: 0.8883 (tpp) cc_final: 0.8426 (mmm) REVERT: 7 561 MET cc_start: 0.6798 (ttt) cc_final: 0.6024 (tmm) REVERT: 7 716 MET cc_start: 0.9279 (mmm) cc_final: 0.8911 (mmp) REVERT: 7 721 LYS cc_start: 0.9293 (tttt) cc_final: 0.9084 (pttp) REVERT: A 41 MET cc_start: 0.7935 (mmm) cc_final: 0.7699 (mmm) REVERT: A 709 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8420 (p) REVERT: A 949 ASP cc_start: 0.7801 (t0) cc_final: 0.7503 (t0) REVERT: A 1038 THR cc_start: 0.8161 (m) cc_final: 0.7883 (p) REVERT: A 1135 ARG cc_start: 0.8056 (ttt180) cc_final: 0.7758 (ttt-90) REVERT: A 1415 SER cc_start: 0.8899 (t) cc_final: 0.8625 (p) REVERT: A 1448 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6596 (tm-30) REVERT: B 177 LYS cc_start: 0.8797 (mttt) cc_final: 0.8566 (mtmt) REVERT: B 234 ILE cc_start: 0.8893 (mt) cc_final: 0.8662 (mt) REVERT: B 277 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8140 (ptpt) REVERT: B 312 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7523 (tp30) REVERT: B 315 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8143 (tttt) REVERT: B 332 ASP cc_start: 0.8383 (m-30) cc_final: 0.7708 (t0) REVERT: B 373 ARG cc_start: 0.8194 (mtt-85) cc_final: 0.7792 (mtt-85) REVERT: B 391 ASP cc_start: 0.7380 (m-30) cc_final: 0.6881 (t0) REVERT: B 440 HIS cc_start: 0.7921 (m90) cc_final: 0.7229 (m-70) REVERT: B 873 THR cc_start: 0.8473 (p) cc_final: 0.8211 (t) REVERT: B 935 ARG cc_start: 0.7683 (ptm160) cc_final: 0.7135 (ttt90) REVERT: B 1190 ASP cc_start: 0.7499 (t0) cc_final: 0.7170 (t0) REVERT: C 34 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7576 (ttp80) REVERT: C 155 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8782 (pp) REVERT: C 193 TYR cc_start: 0.9114 (p90) cc_final: 0.8910 (p90) REVERT: D 48 ILE cc_start: 0.8544 (mm) cc_final: 0.8311 (mt) REVERT: D 71 LYS cc_start: 0.7794 (mttt) cc_final: 0.6964 (mmtm) REVERT: D 155 ARG cc_start: 0.7983 (mmt90) cc_final: 0.7617 (mmm160) REVERT: E 16 PHE cc_start: 0.8485 (t80) cc_final: 0.7960 (t80) REVERT: E 40 GLU cc_start: 0.8195 (pm20) cc_final: 0.7837 (pm20) REVERT: E 41 ASP cc_start: 0.8478 (m-30) cc_final: 0.7578 (m-30) REVERT: E 93 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6501 (mmp) REVERT: E 132 ILE cc_start: 0.9245 (mm) cc_final: 0.8814 (tp) REVERT: F 76 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8288 (tttp) REVERT: F 110 ASP cc_start: 0.7790 (p0) cc_final: 0.7472 (p0) REVERT: G 50 ASP cc_start: 0.8326 (t0) cc_final: 0.7809 (t0) REVERT: G 53 ASN cc_start: 0.7555 (m110) cc_final: 0.6667 (t0) REVERT: G 114 LEU cc_start: 0.8661 (mt) cc_final: 0.8409 (tp) REVERT: G 140 LYS cc_start: 0.8797 (tttt) cc_final: 0.8376 (mtmt) REVERT: H 52 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8258 (mm-40) REVERT: I 5 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.4301 (ttp-110) REVERT: I 12 ASN cc_start: 0.8215 (t0) cc_final: 0.7961 (t0) REVERT: I 15 TYR cc_start: 0.7766 (m-80) cc_final: 0.7519 (m-80) REVERT: I 28 GLU cc_start: 0.7241 (tt0) cc_final: 0.6265 (tp30) REVERT: L 39 SER cc_start: 0.8814 (m) cc_final: 0.8447 (p) REVERT: L 62 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8106 (mmmt) REVERT: M 33 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7653 (mmtp) REVERT: M 214 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7963 (mm) REVERT: M 250 MET cc_start: 0.7143 (tmm) cc_final: 0.6778 (tpp) REVERT: M 300 GLN cc_start: 0.7988 (tp40) cc_final: 0.7637 (tp-100) REVERT: O 158 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8312 (mm-40) REVERT: O 179 HIS cc_start: 0.7441 (m90) cc_final: 0.7086 (m90) REVERT: Q 128 ASN cc_start: 0.7485 (t0) cc_final: 0.6973 (t0) REVERT: Q 425 MET cc_start: 0.5826 (tpp) cc_final: 0.5263 (tpp) REVERT: R 229 ASN cc_start: 0.7299 (m110) cc_final: 0.6686 (t0) REVERT: R 239 GLN cc_start: 0.8070 (mt0) cc_final: 0.7663 (mt0) REVERT: R 313 TRP cc_start: 0.1359 (OUTLIER) cc_final: 0.1064 (m-90) REVERT: R 334 ASP cc_start: 0.7498 (m-30) cc_final: 0.7160 (p0) REVERT: U 38 LEU cc_start: 0.8519 (tp) cc_final: 0.8239 (pp) REVERT: U 242 ASN cc_start: 0.7191 (m-40) cc_final: 0.6428 (m-40) REVERT: U 276 PHE cc_start: 0.8152 (p90) cc_final: 0.7739 (p90) REVERT: V 78 PHE cc_start: 0.8425 (m-80) cc_final: 0.8224 (m-80) REVERT: W 187 LYS cc_start: 0.8510 (mttt) cc_final: 0.8252 (tmtt) REVERT: X 227 ASP cc_start: 0.7379 (t0) cc_final: 0.6784 (t0) outliers start: 187 outliers final: 126 residues processed: 1195 average time/residue: 0.8490 time to fit residues: 1732.1002 Evaluate side-chains 1181 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1043 time to evaluate : 6.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 7 ASP Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 250 LEU Chi-restraints excluded: chain 0 residue 352 ILE Chi-restraints excluded: chain 0 residue 463 ILE Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 538 VAL Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 619 THR Chi-restraints excluded: chain 0 residue 669 VAL Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 364 ILE Chi-restraints excluded: chain 1 residue 505 THR Chi-restraints excluded: chain 1 residue 633 TYR Chi-restraints excluded: chain 2 residue 5 SER Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 2 residue 360 LEU Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 76 VAL Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 3 residue 93 ASN Chi-restraints excluded: chain 3 residue 120 LEU Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 191 PHE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 294 CYS Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 347 TYR Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 760 LEU Chi-restraints excluded: chain 7 residue 833 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 251 GLN Chi-restraints excluded: chain M residue 263 CYS Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 223 ILE Chi-restraints excluded: chain Q residue 329 THR Chi-restraints excluded: chain Q residue 360 THR Chi-restraints excluded: chain Q residue 407 ASP Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 313 TRP Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain U residue 247 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 116 ASN Chi-restraints excluded: chain W residue 193 ARG Chi-restraints excluded: chain W residue 218 THR Chi-restraints excluded: chain W residue 353 ASN Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 279 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 289 optimal weight: 1.9990 chunk 774 optimal weight: 6.9990 chunk 170 optimal weight: 40.0000 chunk 505 optimal weight: 0.0870 chunk 212 optimal weight: 0.0270 chunk 861 optimal weight: 6.9990 chunk 714 optimal weight: 10.0000 chunk 398 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 284 optimal weight: 40.0000 chunk 452 optimal weight: 0.8980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 403 HIS ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 93 ASN ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 22 GLN ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 HIS 5 64 ASN 7 567 GLN 7 685 GLN A 118 HIS A 427 GLN A 451 HIS A 517 ASN A 640 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 GLN B 325 GLN B 592 ASN B 951 GLN G 96 GLN G 113 HIS K 110 ASN Q 117 HIS Q 150 GLN W 133 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 75541 Z= 0.163 Angle : 0.521 9.420 102537 Z= 0.273 Chirality : 0.041 0.161 11587 Planarity : 0.004 0.061 12694 Dihedral : 12.275 105.402 11139 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.77 % Allowed : 13.23 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 8762 helix: 1.62 (0.09), residues: 3646 sheet: 0.06 (0.14), residues: 1282 loop : -0.29 (0.10), residues: 3834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 7 133 HIS 0.007 0.001 HIS 2 85 PHE 0.023 0.001 PHE A 219 TYR 0.041 0.001 TYR O 224 ARG 0.012 0.000 ARG 0 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1120 time to evaluate : 6.648 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: 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: 0 76 MET cc_start: 0.7906 (ttp) cc_final: 0.7596 (ttt) REVERT: 0 134 ARG cc_start: 0.8776 (mtt90) cc_final: 0.8108 (mtt90) REVERT: 0 180 LYS cc_start: 0.7490 (tttt) cc_final: 0.7233 (tttt) REVERT: 0 250 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7802 (mm) REVERT: 0 438 THR cc_start: 0.8915 (p) cc_final: 0.8650 (t) REVERT: 0 521 ASN cc_start: 0.8164 (m-40) cc_final: 0.7950 (m-40) REVERT: 0 525 MET cc_start: 0.7880 (ttm) cc_final: 0.7634 (ttm) REVERT: 0 544 TYR cc_start: 0.7909 (t80) cc_final: 0.7657 (t80) REVERT: 0 643 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7742 (ttm170) REVERT: 0 659 MET cc_start: 0.8801 (mmt) cc_final: 0.8176 (mmt) REVERT: 0 741 TYR cc_start: 0.7971 (t80) cc_final: 0.7755 (t80) REVERT: 1 1 MET cc_start: 0.5142 (ppp) cc_final: 0.4538 (ppp) REVERT: 1 97 MET cc_start: 0.8634 (ttp) cc_final: 0.8232 (ttt) REVERT: 1 192 MET cc_start: 0.8239 (tpt) cc_final: 0.7898 (tpp) REVERT: 1 349 VAL cc_start: 0.8451 (t) cc_final: 0.8117 (m) REVERT: 1 608 MET cc_start: 0.8110 (tpp) cc_final: 0.7705 (tpp) REVERT: 2 97 MET cc_start: 0.7007 (mmm) cc_final: 0.6759 (mmp) REVERT: 2 108 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7711 (mm) REVERT: 2 216 MET cc_start: 0.6395 (ppp) cc_final: 0.5910 (pmm) REVERT: 2 223 HIS cc_start: 0.8204 (m90) cc_final: 0.7172 (m90) REVERT: 2 227 MET cc_start: 0.8168 (tmm) cc_final: 0.7352 (ptp) REVERT: 2 355 LEU cc_start: 0.9206 (pt) cc_final: 0.8762 (mt) REVERT: 3 28 PHE cc_start: 0.8727 (m-80) cc_final: 0.8142 (m-80) REVERT: 3 80 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8663 (ttpt) REVERT: 4 36 LEU cc_start: 0.8329 (mt) cc_final: 0.7972 (mt) REVERT: 4 116 ARG cc_start: 0.7745 (mmm160) cc_final: 0.7335 (mmm160) REVERT: 4 127 GLU cc_start: 0.8656 (tt0) cc_final: 0.8443 (mt-10) REVERT: 4 139 GLN cc_start: 0.8663 (pp30) cc_final: 0.8228 (pt0) REVERT: 4 226 GLN cc_start: 0.7961 (tp-100) cc_final: 0.7527 (tp40) REVERT: 4 228 THR cc_start: 0.8407 (p) cc_final: 0.8139 (t) REVERT: 4 271 ASP cc_start: 0.6080 (p0) cc_final: 0.5763 (p0) REVERT: 4 303 ASN cc_start: 0.7802 (t0) cc_final: 0.7577 (t0) REVERT: 5 52 HIS cc_start: 0.8780 (p90) cc_final: 0.7920 (p-80) REVERT: 5 53 GLU cc_start: 0.9302 (tp30) cc_final: 0.9044 (mm-30) REVERT: 6 194 ASP cc_start: 0.7279 (m-30) cc_final: 0.7045 (t0) REVERT: 6 380 TYR cc_start: 0.8077 (m-80) cc_final: 0.7877 (m-80) REVERT: 7 244 MET cc_start: 0.8752 (mmm) cc_final: 0.8269 (ptt) REVERT: 7 459 MET cc_start: 0.8566 (mtt) cc_final: 0.8066 (mtm) REVERT: 7 474 MET cc_start: 0.8975 (tpp) cc_final: 0.8505 (mmm) REVERT: 7 561 MET cc_start: 0.6872 (ttt) cc_final: 0.6180 (tmm) REVERT: 7 716 MET cc_start: 0.9287 (mmm) cc_final: 0.8946 (mmp) REVERT: 7 721 LYS cc_start: 0.9280 (tttt) cc_final: 0.9072 (pttp) REVERT: A 41 MET cc_start: 0.7905 (mmm) cc_final: 0.7661 (mmm) REVERT: A 100 LYS cc_start: 0.8737 (tttt) cc_final: 0.8393 (ttpp) REVERT: A 205 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7060 (mm-30) REVERT: A 517 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8772 (p0) REVERT: A 709 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8307 (p) REVERT: A 949 ASP cc_start: 0.7754 (t0) cc_final: 0.7460 (t0) REVERT: A 1038 THR cc_start: 0.7998 (m) cc_final: 0.7724 (p) REVERT: A 1135 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7635 (ttt-90) REVERT: A 1143 LEU cc_start: 0.8715 (mm) cc_final: 0.8476 (mm) REVERT: A 1304 TRP cc_start: 0.7808 (m100) cc_final: 0.7304 (m100) REVERT: B 234 ILE cc_start: 0.8874 (mt) cc_final: 0.8654 (mt) REVERT: B 277 LYS cc_start: 0.8400 (ttpt) cc_final: 0.8092 (ptpt) REVERT: B 312 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7375 (tp30) REVERT: B 332 ASP cc_start: 0.8426 (m-30) cc_final: 0.7763 (t0) REVERT: B 373 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7838 (mtt-85) REVERT: B 391 ASP cc_start: 0.7346 (m-30) cc_final: 0.6839 (t0) REVERT: B 433 GLN cc_start: 0.7943 (mt0) cc_final: 0.7678 (tt0) REVERT: B 440 HIS cc_start: 0.7885 (m90) cc_final: 0.7270 (m-70) REVERT: B 561 TRP cc_start: 0.8072 (m100) cc_final: 0.7864 (t-100) REVERT: B 873 THR cc_start: 0.8398 (p) cc_final: 0.8182 (t) REVERT: B 878 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7975 (mm-40) REVERT: B 935 ARG cc_start: 0.7641 (ptm160) cc_final: 0.7118 (ttt90) REVERT: B 1190 ASP cc_start: 0.7517 (t0) cc_final: 0.7085 (t0) REVERT: C 155 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8742 (pp) REVERT: D 37 GLN cc_start: 0.7313 (mt0) cc_final: 0.7067 (mt0) REVERT: D 48 ILE cc_start: 0.8538 (mm) cc_final: 0.8324 (mt) REVERT: D 71 LYS cc_start: 0.7739 (mttt) cc_final: 0.6963 (mmtm) REVERT: D 155 ARG cc_start: 0.7982 (mmt90) cc_final: 0.7601 (mmm160) REVERT: E 16 PHE cc_start: 0.8379 (t80) cc_final: 0.7893 (t80) REVERT: E 40 GLU cc_start: 0.8180 (pm20) cc_final: 0.7813 (pm20) REVERT: E 41 ASP cc_start: 0.8476 (m-30) cc_final: 0.7597 (m-30) REVERT: E 61 GLN cc_start: 0.8181 (tt0) cc_final: 0.7803 (tm-30) REVERT: E 93 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.6437 (mmp) REVERT: E 104 ASN cc_start: 0.7194 (t0) cc_final: 0.6984 (t0) REVERT: E 107 THR cc_start: 0.8280 (m) cc_final: 0.7911 (p) REVERT: E 121 MET cc_start: 0.7949 (tpt) cc_final: 0.7560 (tpt) REVERT: E 132 ILE cc_start: 0.9302 (mm) cc_final: 0.8861 (tp) REVERT: F 76 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8282 (tttp) REVERT: F 110 ASP cc_start: 0.7895 (p0) cc_final: 0.7620 (p0) REVERT: G 50 ASP cc_start: 0.8358 (t0) cc_final: 0.7893 (t0) REVERT: G 53 ASN cc_start: 0.7422 (m110) cc_final: 0.6636 (t0) REVERT: G 114 LEU cc_start: 0.8709 (mt) cc_final: 0.8503 (tp) REVERT: G 140 LYS cc_start: 0.8741 (tttt) cc_final: 0.8342 (mtmt) REVERT: H 52 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8203 (mm-40) REVERT: I 12 ASN cc_start: 0.8114 (m-40) cc_final: 0.7841 (t0) REVERT: I 28 GLU cc_start: 0.7167 (tt0) cc_final: 0.6237 (tp30) REVERT: K 54 ARG cc_start: 0.7497 (mmm160) cc_final: 0.7229 (mmm160) REVERT: L 30 ILE cc_start: 0.9019 (tt) cc_final: 0.8745 (tp) REVERT: L 39 SER cc_start: 0.8756 (m) cc_final: 0.8420 (p) REVERT: L 62 LYS cc_start: 0.8325 (mmmt) cc_final: 0.8114 (mmmt) REVERT: M 33 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7638 (mmtp) REVERT: M 214 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7913 (mm) REVERT: M 250 MET cc_start: 0.6975 (tmm) cc_final: 0.6600 (tpp) REVERT: M 300 GLN cc_start: 0.7961 (tp40) cc_final: 0.7613 (tp40) REVERT: O 68 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7493 (mt0) REVERT: O 158 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8271 (mm-40) REVERT: O 179 HIS cc_start: 0.7388 (m90) cc_final: 0.7001 (m90) REVERT: O 188 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: O 221 GLU cc_start: 0.8047 (pm20) cc_final: 0.7793 (tp30) REVERT: Q 117 HIS cc_start: 0.8174 (m-70) cc_final: 0.7965 (m170) REVERT: Q 128 ASN cc_start: 0.7564 (t0) cc_final: 0.7065 (t0) REVERT: Q 425 MET cc_start: 0.5918 (tpp) cc_final: 0.5306 (tpp) REVERT: R 229 ASN cc_start: 0.7324 (OUTLIER) cc_final: 0.6703 (t0) REVERT: R 239 GLN cc_start: 0.8005 (mt0) cc_final: 0.7617 (mt0) REVERT: R 313 TRP cc_start: 0.1186 (OUTLIER) cc_final: 0.0932 (m-90) REVERT: R 334 ASP cc_start: 0.7413 (m-30) cc_final: 0.7089 (p0) REVERT: U 38 LEU cc_start: 0.8572 (tp) cc_final: 0.8295 (pp) REVERT: U 242 ASN cc_start: 0.7141 (m-40) cc_final: 0.6379 (m-40) REVERT: U 244 MET cc_start: 0.7429 (tmm) cc_final: 0.7167 (tmm) REVERT: U 250 LYS cc_start: 0.8449 (tptp) cc_final: 0.8206 (tptp) REVERT: U 276 PHE cc_start: 0.8139 (p90) cc_final: 0.7823 (p90) REVERT: W 187 LYS cc_start: 0.8474 (mttt) cc_final: 0.8228 (tmtt) REVERT: X 208 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8454 (mtmm) REVERT: X 227 ASP cc_start: 0.7216 (t0) cc_final: 0.6661 (t0) REVERT: X 317 MET cc_start: 0.5983 (mmp) cc_final: 0.5571 (mmt) outliers start: 141 outliers final: 82 residues processed: 1206 average time/residue: 0.7252 time to fit residues: 1481.8454 Evaluate side-chains 1142 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1049 time to evaluate : 6.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 250 LEU Chi-restraints excluded: chain 0 residue 352 ILE Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 485 MET Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 619 THR Chi-restraints excluded: chain 0 residue 669 VAL Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 633 TYR Chi-restraints excluded: chain 2 residue 5 SER Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 3 residue 29 LEU Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 76 VAL Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 3 residue 93 ASN Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 191 PHE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 294 CYS Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 760 LEU Chi-restraints excluded: chain 7 residue 833 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 263 CYS Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 188 GLU Chi-restraints excluded: chain Q residue 329 THR Chi-restraints excluded: chain Q residue 360 THR Chi-restraints excluded: chain Q residue 406 ILE Chi-restraints excluded: chain Q residue 407 ASP Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 229 ASN Chi-restraints excluded: chain R residue 313 TRP Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain U residue 247 LEU Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 116 ASN Chi-restraints excluded: chain W residue 193 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 830 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 490 optimal weight: 6.9990 chunk 628 optimal weight: 10.0000 chunk 487 optimal weight: 0.5980 chunk 724 optimal weight: 0.9980 chunk 480 optimal weight: 0.5980 chunk 857 optimal weight: 7.9990 chunk 536 optimal weight: 0.7980 chunk 522 optimal weight: 3.9990 chunk 396 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 93 ASN ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN A 118 HIS A 124 GLN A 427 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 HIS A 640 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 GLN B 513 GLN G 97 HIS ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 HIS ** W 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 279 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 75541 Z= 0.239 Angle : 0.542 12.779 102537 Z= 0.281 Chirality : 0.042 0.231 11587 Planarity : 0.004 0.061 12694 Dihedral : 12.252 93.028 11139 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.86 % Allowed : 13.71 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 8762 helix: 1.60 (0.09), residues: 3655 sheet: 0.07 (0.14), residues: 1266 loop : -0.28 (0.10), residues: 3841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP 7 133 HIS 0.006 0.001 HIS A 109 PHE 0.033 0.001 PHE R 307 TYR 0.025 0.001 TYR G 51 ARG 0.013 0.000 ARG 4 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1072 time to evaluate : 6.705 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 76 MET cc_start: 0.7891 (ttp) cc_final: 0.7584 (ttt) REVERT: 0 134 ARG cc_start: 0.8789 (mtt90) cc_final: 0.8105 (mtt90) REVERT: 0 180 LYS cc_start: 0.7521 (tttt) cc_final: 0.7282 (tttt) REVERT: 0 250 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7844 (mm) REVERT: 0 438 THR cc_start: 0.8911 (p) cc_final: 0.8653 (t) REVERT: 0 521 ASN cc_start: 0.8256 (m-40) cc_final: 0.8038 (m-40) REVERT: 0 525 MET cc_start: 0.7861 (ttm) cc_final: 0.7623 (ttm) REVERT: 0 544 TYR cc_start: 0.8040 (t80) cc_final: 0.7800 (t80) REVERT: 0 741 TYR cc_start: 0.8048 (t80) cc_final: 0.7749 (t80) REVERT: 1 1 MET cc_start: 0.5340 (ppp) cc_final: 0.4783 (ppp) REVERT: 1 97 MET cc_start: 0.8650 (ttp) cc_final: 0.8236 (ttt) REVERT: 1 192 MET cc_start: 0.8206 (tpt) cc_final: 0.7848 (tpp) REVERT: 1 349 VAL cc_start: 0.8467 (t) cc_final: 0.8131 (m) REVERT: 2 108 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7724 (mm) REVERT: 2 216 MET cc_start: 0.6275 (ppp) cc_final: 0.5664 (pmm) REVERT: 2 223 HIS cc_start: 0.8240 (m90) cc_final: 0.7335 (m90) REVERT: 2 355 LEU cc_start: 0.9409 (pt) cc_final: 0.8828 (mt) REVERT: 3 28 PHE cc_start: 0.8768 (m-80) cc_final: 0.8204 (m-80) REVERT: 3 80 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8674 (ttpt) REVERT: 3 83 ASP cc_start: 0.7722 (t0) cc_final: 0.7517 (m-30) REVERT: 4 36 LEU cc_start: 0.8304 (mt) cc_final: 0.7977 (mt) REVERT: 4 116 ARG cc_start: 0.7760 (mmm160) cc_final: 0.7282 (mmm160) REVERT: 4 127 GLU cc_start: 0.8669 (tt0) cc_final: 0.8442 (mt-10) REVERT: 4 139 GLN cc_start: 0.8577 (pp30) cc_final: 0.8255 (pt0) REVERT: 4 146 ARG cc_start: 0.6445 (mtm110) cc_final: 0.5637 (ptp90) REVERT: 4 228 THR cc_start: 0.8424 (p) cc_final: 0.8188 (t) REVERT: 4 271 ASP cc_start: 0.6245 (p0) cc_final: 0.5990 (p0) REVERT: 5 52 HIS cc_start: 0.8652 (p90) cc_final: 0.7656 (p-80) REVERT: 5 53 GLU cc_start: 0.9308 (tp30) cc_final: 0.9027 (mm-30) REVERT: 6 380 TYR cc_start: 0.8084 (m-80) cc_final: 0.7877 (m-80) REVERT: 7 133 TRP cc_start: 0.8082 (m100) cc_final: 0.7626 (m100) REVERT: 7 244 MET cc_start: 0.8723 (mmm) cc_final: 0.8234 (ptt) REVERT: 7 459 MET cc_start: 0.8579 (mtt) cc_final: 0.8069 (mtm) REVERT: 7 474 MET cc_start: 0.8986 (tpp) cc_final: 0.8524 (mmm) REVERT: 7 561 MET cc_start: 0.6953 (ttt) cc_final: 0.6383 (tmm) REVERT: 7 721 LYS cc_start: 0.9280 (tttt) cc_final: 0.9064 (pttp) REVERT: A 41 MET cc_start: 0.7906 (mmm) cc_final: 0.7677 (mmm) REVERT: A 100 LYS cc_start: 0.8758 (tttt) cc_final: 0.8396 (ttpp) REVERT: A 501 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8280 (mp) REVERT: A 949 ASP cc_start: 0.7780 (t0) cc_final: 0.7528 (t0) REVERT: A 1038 THR cc_start: 0.8007 (m) cc_final: 0.7754 (p) REVERT: A 1052 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7048 (mt0) REVERT: A 1135 ARG cc_start: 0.8069 (ttt180) cc_final: 0.7660 (ttt-90) REVERT: A 1143 LEU cc_start: 0.8707 (mm) cc_final: 0.8452 (mm) REVERT: A 1304 TRP cc_start: 0.7830 (m100) cc_final: 0.7319 (m100) REVERT: A 1448 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6578 (tm-30) REVERT: B 234 ILE cc_start: 0.8880 (mt) cc_final: 0.8655 (mt) REVERT: B 277 LYS cc_start: 0.8422 (ttpt) cc_final: 0.8127 (ptpt) REVERT: B 312 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7426 (tp30) REVERT: B 373 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7859 (mtt-85) REVERT: B 391 ASP cc_start: 0.7326 (m-30) cc_final: 0.6839 (t0) REVERT: B 398 ARG cc_start: 0.7763 (ptp-170) cc_final: 0.7363 (ptp-170) REVERT: B 440 HIS cc_start: 0.7879 (m90) cc_final: 0.7255 (m-70) REVERT: B 873 THR cc_start: 0.8436 (p) cc_final: 0.8209 (t) REVERT: B 935 ARG cc_start: 0.7661 (ptm160) cc_final: 0.7123 (ttt90) REVERT: B 1190 ASP cc_start: 0.7493 (t0) cc_final: 0.7158 (t0) REVERT: C 155 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8764 (pp) REVERT: D 37 GLN cc_start: 0.7346 (mt0) cc_final: 0.7101 (mt0) REVERT: D 48 ILE cc_start: 0.8558 (mm) cc_final: 0.8335 (mt) REVERT: D 155 ARG cc_start: 0.8009 (mmt90) cc_final: 0.7653 (mmm160) REVERT: E 16 PHE cc_start: 0.8403 (t80) cc_final: 0.7894 (t80) REVERT: E 40 GLU cc_start: 0.8177 (pm20) cc_final: 0.7822 (pm20) REVERT: E 41 ASP cc_start: 0.8488 (m-30) cc_final: 0.7577 (m-30) REVERT: E 61 GLN cc_start: 0.8202 (tt0) cc_final: 0.7795 (tm-30) REVERT: E 93 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6449 (mmp) REVERT: E 107 THR cc_start: 0.8276 (m) cc_final: 0.7953 (p) REVERT: E 121 MET cc_start: 0.7959 (tpt) cc_final: 0.7496 (tpt) REVERT: E 132 ILE cc_start: 0.9312 (mm) cc_final: 0.8865 (tp) REVERT: F 76 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8308 (tttp) REVERT: F 110 ASP cc_start: 0.7847 (p0) cc_final: 0.7544 (p0) REVERT: G 50 ASP cc_start: 0.8359 (t0) cc_final: 0.7899 (t0) REVERT: G 114 LEU cc_start: 0.8728 (mt) cc_final: 0.8501 (tp) REVERT: G 140 LYS cc_start: 0.8752 (tttt) cc_final: 0.8345 (mtmt) REVERT: H 52 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8183 (mm-40) REVERT: I 28 GLU cc_start: 0.7195 (tt0) cc_final: 0.6270 (tp30) REVERT: L 30 ILE cc_start: 0.8999 (tt) cc_final: 0.8736 (tp) REVERT: L 39 SER cc_start: 0.8753 (m) cc_final: 0.8406 (p) REVERT: M 33 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7644 (mmtp) REVERT: M 214 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7891 (mm) REVERT: M 250 MET cc_start: 0.7073 (tmm) cc_final: 0.6687 (tpp) REVERT: M 300 GLN cc_start: 0.7962 (tp40) cc_final: 0.7609 (tp40) REVERT: M 320 ARG cc_start: 0.8383 (ptp90) cc_final: 0.8102 (ptt180) REVERT: O 158 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8171 (mm-40) REVERT: O 179 HIS cc_start: 0.7435 (m90) cc_final: 0.7047 (m90) REVERT: Q 128 ASN cc_start: 0.7564 (t0) cc_final: 0.7067 (t0) REVERT: Q 425 MET cc_start: 0.6044 (tpp) cc_final: 0.5453 (tpp) REVERT: R 229 ASN cc_start: 0.7323 (OUTLIER) cc_final: 0.6699 (t0) REVERT: R 239 GLN cc_start: 0.8016 (mt0) cc_final: 0.7680 (mt0) REVERT: R 313 TRP cc_start: 0.1146 (OUTLIER) cc_final: 0.0871 (m-90) REVERT: R 334 ASP cc_start: 0.7403 (m-30) cc_final: 0.7047 (p0) REVERT: U 38 LEU cc_start: 0.8574 (tp) cc_final: 0.8296 (pp) REVERT: U 242 ASN cc_start: 0.7084 (m-40) cc_final: 0.6265 (m-40) REVERT: U 244 MET cc_start: 0.7313 (tmm) cc_final: 0.6894 (tmm) REVERT: U 250 LYS cc_start: 0.8412 (tptp) cc_final: 0.8153 (tptp) REVERT: U 276 PHE cc_start: 0.8110 (p90) cc_final: 0.7853 (p90) REVERT: V 112 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7781 (ttp80) REVERT: W 187 LYS cc_start: 0.8466 (mttt) cc_final: 0.8242 (tmtt) REVERT: X 227 ASP cc_start: 0.7258 (t0) cc_final: 0.6713 (t0) REVERT: X 317 MET cc_start: 0.6005 (mmp) cc_final: 0.5581 (mmt) outliers start: 148 outliers final: 102 residues processed: 1165 average time/residue: 0.7295 time to fit residues: 1438.0771 Evaluate side-chains 1149 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1037 time to evaluate : 6.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 250 LEU Chi-restraints excluded: chain 0 residue 352 ILE Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 485 MET Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 619 THR Chi-restraints excluded: chain 0 residue 669 VAL Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 633 TYR Chi-restraints excluded: chain 2 residue 5 SER Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 2 residue 360 LEU Chi-restraints excluded: chain 3 residue 29 LEU Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 3 residue 120 LEU Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 191 PHE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 294 CYS Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 760 LEU Chi-restraints excluded: chain 7 residue 833 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1052 GLN Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 263 CYS Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 329 THR Chi-restraints excluded: chain Q residue 360 THR Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 229 ASN Chi-restraints excluded: chain R residue 313 TRP Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 116 ASN Chi-restraints excluded: chain W residue 193 ARG Chi-restraints excluded: chain X residue 193 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 530 optimal weight: 0.6980 chunk 342 optimal weight: 3.9990 chunk 512 optimal weight: 0.9980 chunk 258 optimal weight: 30.0000 chunk 168 optimal weight: 8.9990 chunk 166 optimal weight: 50.0000 chunk 545 optimal weight: 0.5980 chunk 584 optimal weight: 2.9990 chunk 424 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 674 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 395 GLN ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 93 ASN ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS A 427 GLN A 517 ASN A 640 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN K 110 ASN ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 HIS R 328 HIS W 120 ASN ** W 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 279 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 75541 Z= 0.222 Angle : 0.543 10.955 102537 Z= 0.281 Chirality : 0.042 0.181 11587 Planarity : 0.004 0.061 12694 Dihedral : 12.238 77.110 11139 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.89 % Allowed : 13.94 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 8762 helix: 1.60 (0.09), residues: 3664 sheet: 0.05 (0.14), residues: 1281 loop : -0.27 (0.10), residues: 3817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP 7 133 HIS 0.006 0.001 HIS 2 85 PHE 0.025 0.001 PHE A 219 TYR 0.027 0.001 TYR G 51 ARG 0.013 0.000 ARG 0 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1075 time to evaluate : 6.667 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: 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: 0 76 MET cc_start: 0.7869 (ttp) cc_final: 0.7569 (ttt) REVERT: 0 134 ARG cc_start: 0.8792 (mtt90) cc_final: 0.8112 (mtt90) REVERT: 0 180 LYS cc_start: 0.7524 (tttt) cc_final: 0.7284 (tttt) REVERT: 0 250 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7868 (mm) REVERT: 0 438 THR cc_start: 0.8907 (p) cc_final: 0.8649 (t) REVERT: 0 525 MET cc_start: 0.7860 (ttm) cc_final: 0.7616 (ttm) REVERT: 0 544 TYR cc_start: 0.8043 (t80) cc_final: 0.7810 (t80) REVERT: 0 643 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7757 (ttm170) REVERT: 1 1 MET cc_start: 0.5306 (ppp) cc_final: 0.4867 (ppp) REVERT: 1 97 MET cc_start: 0.8704 (ttp) cc_final: 0.8230 (ttt) REVERT: 1 192 MET cc_start: 0.8233 (tpt) cc_final: 0.7869 (tpp) REVERT: 1 349 VAL cc_start: 0.8436 (t) cc_final: 0.8098 (m) REVERT: 1 439 ARG cc_start: 0.6742 (tpt170) cc_final: 0.6513 (ptt180) REVERT: 1 608 MET cc_start: 0.8075 (tpp) cc_final: 0.7621 (tpp) REVERT: 2 97 MET cc_start: 0.6758 (mmm) cc_final: 0.5999 (mmm) REVERT: 2 108 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7721 (mm) REVERT: 2 216 MET cc_start: 0.6199 (ppp) cc_final: 0.5653 (pmm) REVERT: 2 223 HIS cc_start: 0.8239 (m90) cc_final: 0.7294 (m-70) REVERT: 2 227 MET cc_start: 0.8171 (tmm) cc_final: 0.7339 (ptp) REVERT: 2 355 LEU cc_start: 0.9408 (pt) cc_final: 0.8830 (mt) REVERT: 3 28 PHE cc_start: 0.8775 (m-80) cc_final: 0.8212 (m-80) REVERT: 3 80 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8647 (ttpt) REVERT: 3 83 ASP cc_start: 0.7693 (t0) cc_final: 0.7490 (m-30) REVERT: 4 36 LEU cc_start: 0.8340 (mt) cc_final: 0.7996 (mt) REVERT: 4 116 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7306 (mmm160) REVERT: 4 119 ARG cc_start: 0.8495 (ttp80) cc_final: 0.8164 (ttp80) REVERT: 4 127 GLU cc_start: 0.8671 (tt0) cc_final: 0.8428 (mt-10) REVERT: 4 139 GLN cc_start: 0.8587 (pp30) cc_final: 0.8290 (pt0) REVERT: 4 146 ARG cc_start: 0.6488 (mtm110) cc_final: 0.5765 (ptp90) REVERT: 4 226 GLN cc_start: 0.7827 (tp-100) cc_final: 0.7534 (tp40) REVERT: 4 228 THR cc_start: 0.8357 (p) cc_final: 0.8124 (t) REVERT: 4 322 ARG cc_start: 0.7758 (tpp-160) cc_final: 0.7547 (tpp-160) REVERT: 5 53 GLU cc_start: 0.9315 (tp30) cc_final: 0.9005 (tp30) REVERT: 7 133 TRP cc_start: 0.8115 (m100) cc_final: 0.7883 (m100) REVERT: 7 244 MET cc_start: 0.8715 (mmm) cc_final: 0.8228 (ptt) REVERT: 7 459 MET cc_start: 0.8556 (mtt) cc_final: 0.8090 (mtm) REVERT: 7 474 MET cc_start: 0.8988 (tpp) cc_final: 0.8531 (mmm) REVERT: 7 561 MET cc_start: 0.6935 (ttt) cc_final: 0.6405 (tmm) REVERT: 7 721 LYS cc_start: 0.9269 (tttt) cc_final: 0.9048 (pttp) REVERT: A 41 MET cc_start: 0.7902 (mmm) cc_final: 0.7664 (mmm) REVERT: A 100 LYS cc_start: 0.8747 (tttt) cc_final: 0.8396 (ttpp) REVERT: A 501 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8283 (mp) REVERT: A 517 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8744 (p0) REVERT: A 685 GLU cc_start: 0.7340 (tp30) cc_final: 0.7126 (tp30) REVERT: A 949 ASP cc_start: 0.7759 (t0) cc_final: 0.7511 (t0) REVERT: A 1038 THR cc_start: 0.7992 (m) cc_final: 0.7730 (p) REVERT: A 1135 ARG cc_start: 0.8039 (ttt180) cc_final: 0.7623 (ttt-90) REVERT: A 1143 LEU cc_start: 0.8697 (mm) cc_final: 0.8443 (mm) REVERT: B 234 ILE cc_start: 0.8890 (mt) cc_final: 0.8632 (mt) REVERT: B 277 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8043 (ptpt) REVERT: B 312 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7382 (tp30) REVERT: B 373 ARG cc_start: 0.8186 (mtt-85) cc_final: 0.7851 (mtt-85) REVERT: B 398 ARG cc_start: 0.7808 (ptp-170) cc_final: 0.7445 (ptp-170) REVERT: B 430 ARG cc_start: 0.6958 (ttm170) cc_final: 0.6744 (ttm170) REVERT: B 873 THR cc_start: 0.8457 (p) cc_final: 0.8230 (t) REVERT: B 878 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7746 (mm-40) REVERT: B 935 ARG cc_start: 0.7698 (ptm160) cc_final: 0.7178 (ttt90) REVERT: B 1190 ASP cc_start: 0.7502 (t0) cc_final: 0.7155 (t0) REVERT: C 34 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7742 (ttp80) REVERT: C 155 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8762 (pp) REVERT: D 37 GLN cc_start: 0.7335 (mt0) cc_final: 0.7098 (mt0) REVERT: D 48 ILE cc_start: 0.8557 (mm) cc_final: 0.8339 (mt) REVERT: D 155 ARG cc_start: 0.8007 (mmt90) cc_final: 0.7644 (mmm160) REVERT: E 16 PHE cc_start: 0.8396 (t80) cc_final: 0.7890 (t80) REVERT: E 40 GLU cc_start: 0.8180 (pm20) cc_final: 0.7827 (pm20) REVERT: E 41 ASP cc_start: 0.8492 (m-30) cc_final: 0.7575 (m-30) REVERT: E 61 GLN cc_start: 0.8125 (tt0) cc_final: 0.7737 (tm-30) REVERT: E 93 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6436 (mmp) REVERT: E 107 THR cc_start: 0.8283 (m) cc_final: 0.7975 (p) REVERT: E 132 ILE cc_start: 0.9321 (mm) cc_final: 0.8822 (tp) REVERT: F 76 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8329 (tttp) REVERT: F 110 ASP cc_start: 0.7760 (p0) cc_final: 0.7470 (p0) REVERT: G 50 ASP cc_start: 0.8375 (t0) cc_final: 0.8099 (t0) REVERT: G 53 ASN cc_start: 0.7580 (m110) cc_final: 0.6719 (t0) REVERT: G 114 LEU cc_start: 0.8719 (mt) cc_final: 0.8518 (tp) REVERT: G 140 LYS cc_start: 0.8752 (tttt) cc_final: 0.8340 (mtmt) REVERT: H 52 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8190 (mm-40) REVERT: I 28 GLU cc_start: 0.7198 (tt0) cc_final: 0.6224 (tp30) REVERT: L 30 ILE cc_start: 0.8985 (tt) cc_final: 0.8732 (tp) REVERT: L 39 SER cc_start: 0.8756 (m) cc_final: 0.8412 (p) REVERT: L 62 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8127 (mmmt) REVERT: M 33 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7654 (mmtp) REVERT: M 214 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7903 (mm) REVERT: M 250 MET cc_start: 0.7085 (tmm) cc_final: 0.6708 (tpp) REVERT: M 300 GLN cc_start: 0.7967 (tp40) cc_final: 0.7612 (tp40) REVERT: M 320 ARG cc_start: 0.8396 (ptp90) cc_final: 0.8123 (ptt180) REVERT: O 68 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7360 (mt0) REVERT: O 158 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8223 (mt0) REVERT: O 179 HIS cc_start: 0.7434 (m90) cc_final: 0.7047 (m90) REVERT: O 221 GLU cc_start: 0.8240 (pm20) cc_final: 0.7928 (tm-30) REVERT: Q 128 ASN cc_start: 0.7365 (t0) cc_final: 0.6914 (t0) REVERT: Q 425 MET cc_start: 0.6135 (tpp) cc_final: 0.5568 (tpp) REVERT: R 229 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.6745 (t0) REVERT: R 239 GLN cc_start: 0.7982 (mt0) cc_final: 0.7652 (mt0) REVERT: R 270 MET cc_start: 0.8137 (mmm) cc_final: 0.7802 (mmm) REVERT: R 313 TRP cc_start: 0.0798 (OUTLIER) cc_final: 0.0550 (m-90) REVERT: R 334 ASP cc_start: 0.7390 (m-30) cc_final: 0.6964 (p0) REVERT: U 38 LEU cc_start: 0.8574 (tp) cc_final: 0.8293 (pp) REVERT: U 244 MET cc_start: 0.7257 (tmm) cc_final: 0.6894 (tmm) REVERT: U 250 LYS cc_start: 0.8440 (tptp) cc_final: 0.8157 (tptp) REVERT: U 276 PHE cc_start: 0.8107 (p90) cc_final: 0.7863 (p90) REVERT: V 76 TRP cc_start: 0.8793 (m100) cc_final: 0.8517 (m100) REVERT: V 112 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7796 (ttp80) REVERT: W 187 LYS cc_start: 0.8471 (mttt) cc_final: 0.8237 (tmtt) REVERT: X 208 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8318 (ptpp) REVERT: X 227 ASP cc_start: 0.7245 (t0) cc_final: 0.6703 (t0) REVERT: X 317 MET cc_start: 0.5969 (mmp) cc_final: 0.5504 (mmt) outliers start: 150 outliers final: 114 residues processed: 1170 average time/residue: 0.7585 time to fit residues: 1508.7432 Evaluate side-chains 1170 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1045 time to evaluate : 6.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 250 LEU Chi-restraints excluded: chain 0 residue 352 ILE Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 669 VAL Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 633 TYR Chi-restraints excluded: chain 2 residue 5 SER Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 2 residue 166 LEU Chi-restraints excluded: chain 2 residue 360 LEU Chi-restraints excluded: chain 3 residue 29 LEU Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 3 residue 93 ASN Chi-restraints excluded: chain 3 residue 120 LEU Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 191 PHE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 275 SER Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 294 CYS Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 760 LEU Chi-restraints excluded: chain 7 residue 833 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 102 LYS Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 263 CYS Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain Q residue 329 THR Chi-restraints excluded: chain Q residue 360 THR Chi-restraints excluded: chain Q residue 406 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 229 ASN Chi-restraints excluded: chain R residue 313 TRP Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain U residue 247 LEU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 116 ASN Chi-restraints excluded: chain W residue 193 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 780 optimal weight: 7.9990 chunk 821 optimal weight: 5.9990 chunk 749 optimal weight: 4.9990 chunk 799 optimal weight: 9.9990 chunk 481 optimal weight: 5.9990 chunk 348 optimal weight: 1.9990 chunk 627 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 722 optimal weight: 0.9980 chunk 756 optimal weight: 5.9990 chunk 796 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 62 HIS ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 93 ASN ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 449 HIS ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A 587 HIS A 640 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 HIS ** W 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 279 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 75541 Z= 0.361 Angle : 0.598 11.614 102537 Z= 0.308 Chirality : 0.044 0.208 11587 Planarity : 0.004 0.062 12694 Dihedral : 12.289 75.562 11139 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.96 % Allowed : 14.36 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.09), residues: 8762 helix: 1.52 (0.09), residues: 3661 sheet: -0.04 (0.14), residues: 1275 loop : -0.31 (0.10), residues: 3826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP 7 133 HIS 0.008 0.001 HIS A 587 PHE 0.029 0.002 PHE A 219 TYR 0.029 0.002 TYR G 51 ARG 0.010 0.001 ARG 4 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1050 time to evaluate : 6.616 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.7745 (tt0) cc_final: 0.7410 (tt0) REVERT: 0 76 MET cc_start: 0.7922 (ttp) cc_final: 0.7628 (ttt) REVERT: 0 134 ARG cc_start: 0.8800 (mtt90) cc_final: 0.8119 (mtt90) REVERT: 0 180 LYS cc_start: 0.7515 (tttt) cc_final: 0.7307 (tttt) REVERT: 0 250 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7947 (mm) REVERT: 0 525 MET cc_start: 0.7944 (ttm) cc_final: 0.7665 (ttm) REVERT: 0 544 TYR cc_start: 0.8243 (t80) cc_final: 0.8018 (t80) REVERT: 0 643 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7731 (ttm170) REVERT: 1 1 MET cc_start: 0.5412 (ppp) cc_final: 0.4972 (ppp) REVERT: 1 97 MET cc_start: 0.8765 (ttp) cc_final: 0.8343 (ttt) REVERT: 1 192 MET cc_start: 0.8228 (tpt) cc_final: 0.7849 (tpp) REVERT: 1 349 VAL cc_start: 0.8484 (t) cc_final: 0.8135 (m) REVERT: 1 608 MET cc_start: 0.8105 (tpp) cc_final: 0.7648 (tpp) REVERT: 2 108 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7735 (mm) REVERT: 2 216 MET cc_start: 0.6204 (ppp) cc_final: 0.5703 (pmm) REVERT: 2 223 HIS cc_start: 0.8269 (m90) cc_final: 0.7300 (m-70) REVERT: 2 227 MET cc_start: 0.8163 (tmm) cc_final: 0.7358 (ptp) REVERT: 2 355 LEU cc_start: 0.9384 (pt) cc_final: 0.8804 (mt) REVERT: 3 28 PHE cc_start: 0.8776 (m-80) cc_final: 0.8188 (m-80) REVERT: 3 35 TYR cc_start: 0.8711 (m-80) cc_final: 0.8272 (m-80) REVERT: 3 80 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8675 (ttpt) REVERT: 4 36 LEU cc_start: 0.8384 (mt) cc_final: 0.8013 (mt) REVERT: 4 37 TRP cc_start: 0.7394 (m100) cc_final: 0.7131 (m100) REVERT: 4 116 ARG cc_start: 0.7741 (mmm160) cc_final: 0.7235 (mmm160) REVERT: 4 127 GLU cc_start: 0.8667 (tt0) cc_final: 0.8433 (mt-10) REVERT: 4 139 GLN cc_start: 0.8578 (pp30) cc_final: 0.8281 (pt0) REVERT: 4 146 ARG cc_start: 0.6525 (mtm110) cc_final: 0.5804 (ptp90) REVERT: 4 228 THR cc_start: 0.8381 (p) cc_final: 0.8139 (t) REVERT: 5 53 GLU cc_start: 0.9374 (tp30) cc_final: 0.9010 (tp30) REVERT: 6 194 ASP cc_start: 0.7296 (m-30) cc_final: 0.7066 (t0) REVERT: 7 459 MET cc_start: 0.8554 (mtt) cc_final: 0.8094 (mtm) REVERT: 7 474 MET cc_start: 0.8999 (tpp) cc_final: 0.8551 (mmm) REVERT: 7 561 MET cc_start: 0.6985 (ttt) cc_final: 0.6430 (tmm) REVERT: A 41 MET cc_start: 0.7914 (mmm) cc_final: 0.7577 (mmm) REVERT: A 501 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8238 (mp) REVERT: A 949 ASP cc_start: 0.7784 (t0) cc_final: 0.7528 (t0) REVERT: A 1038 THR cc_start: 0.7964 (m) cc_final: 0.7762 (p) REVERT: A 1135 ARG cc_start: 0.7997 (ttt180) cc_final: 0.7638 (ttt-90) REVERT: A 1143 LEU cc_start: 0.8744 (mm) cc_final: 0.8486 (mm) REVERT: A 1415 SER cc_start: 0.8912 (t) cc_final: 0.8640 (p) REVERT: B 234 ILE cc_start: 0.8902 (mt) cc_final: 0.8633 (mt) REVERT: B 277 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8110 (ptpt) REVERT: B 312 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7521 (tp30) REVERT: B 398 ARG cc_start: 0.7814 (ptp-170) cc_final: 0.7476 (ptp-170) REVERT: B 873 THR cc_start: 0.8505 (p) cc_final: 0.8249 (t) REVERT: B 935 ARG cc_start: 0.7719 (ptm160) cc_final: 0.7163 (ttt90) REVERT: B 1190 ASP cc_start: 0.7531 (t0) cc_final: 0.7192 (t0) REVERT: C 34 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8018 (ptm-80) REVERT: C 155 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8784 (pp) REVERT: D 14 ARG cc_start: 0.6361 (pmt170) cc_final: 0.1516 (pmt170) REVERT: D 37 GLN cc_start: 0.7391 (mt0) cc_final: 0.7120 (mt0) REVERT: D 48 ILE cc_start: 0.8560 (mm) cc_final: 0.8338 (mt) REVERT: D 155 ARG cc_start: 0.8010 (mmt90) cc_final: 0.7596 (mmm160) REVERT: E 16 PHE cc_start: 0.8458 (t80) cc_final: 0.7923 (t80) REVERT: E 40 GLU cc_start: 0.8203 (pm20) cc_final: 0.7851 (pm20) REVERT: E 41 ASP cc_start: 0.8496 (m-30) cc_final: 0.7567 (m-30) REVERT: E 121 MET cc_start: 0.7958 (tpt) cc_final: 0.7481 (tpt) REVERT: E 132 ILE cc_start: 0.9326 (mm) cc_final: 0.8803 (tp) REVERT: F 76 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8305 (tttp) REVERT: F 110 ASP cc_start: 0.7824 (p0) cc_final: 0.7513 (p0) REVERT: G 50 ASP cc_start: 0.8327 (t0) cc_final: 0.8040 (t0) REVERT: G 53 ASN cc_start: 0.7540 (m110) cc_final: 0.6672 (t0) REVERT: G 114 LEU cc_start: 0.8739 (mt) cc_final: 0.8506 (tp) REVERT: G 130 TYR cc_start: 0.7009 (m-80) cc_final: 0.6683 (m-80) REVERT: G 140 LYS cc_start: 0.8765 (tttt) cc_final: 0.8360 (mtmt) REVERT: I 28 GLU cc_start: 0.7267 (tt0) cc_final: 0.6294 (tp30) REVERT: J 62 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8419 (mmm-85) REVERT: L 39 SER cc_start: 0.8775 (m) cc_final: 0.8415 (p) REVERT: L 62 LYS cc_start: 0.8490 (mmmt) cc_final: 0.8192 (mmmt) REVERT: M 33 LYS cc_start: 0.8023 (mmmt) cc_final: 0.7658 (mmtp) REVERT: M 214 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7968 (mm) REVERT: M 250 MET cc_start: 0.7133 (tmm) cc_final: 0.6738 (tpp) REVERT: M 300 GLN cc_start: 0.7972 (tp40) cc_final: 0.7639 (tp-100) REVERT: M 320 ARG cc_start: 0.8418 (ptp90) cc_final: 0.8110 (ptt180) REVERT: O 158 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8194 (mt0) REVERT: Q 128 ASN cc_start: 0.7410 (t0) cc_final: 0.6956 (t0) REVERT: Q 152 THR cc_start: 0.7031 (OUTLIER) cc_final: 0.6414 (p) REVERT: Q 425 MET cc_start: 0.6102 (tpp) cc_final: 0.5540 (tpp) REVERT: R 229 ASN cc_start: 0.7376 (m110) cc_final: 0.6798 (t0) REVERT: R 239 GLN cc_start: 0.7992 (mt0) cc_final: 0.7672 (mt0) REVERT: R 270 MET cc_start: 0.8181 (mmm) cc_final: 0.7846 (mmm) REVERT: R 313 TRP cc_start: 0.0345 (OUTLIER) cc_final: 0.0040 (m-90) REVERT: R 334 ASP cc_start: 0.7305 (m-30) cc_final: 0.6880 (p0) REVERT: U 38 LEU cc_start: 0.8558 (tp) cc_final: 0.8283 (pp) REVERT: U 244 MET cc_start: 0.7232 (tmm) cc_final: 0.6988 (tmm) REVERT: U 250 LYS cc_start: 0.8470 (tptp) cc_final: 0.8152 (tptp) REVERT: U 276 PHE cc_start: 0.8049 (p90) cc_final: 0.7816 (p90) REVERT: V 76 TRP cc_start: 0.8799 (m100) cc_final: 0.8565 (m100) REVERT: W 187 LYS cc_start: 0.8519 (mttt) cc_final: 0.8285 (tmtt) REVERT: X 208 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8346 (ptpp) REVERT: X 227 ASP cc_start: 0.7303 (t0) cc_final: 0.6763 (t0) REVERT: X 317 MET cc_start: 0.5989 (mmp) cc_final: 0.5499 (mmt) outliers start: 156 outliers final: 121 residues processed: 1147 average time/residue: 0.7300 time to fit residues: 1415.4270 Evaluate side-chains 1158 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1028 time to evaluate : 6.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 250 LEU Chi-restraints excluded: chain 0 residue 352 ILE Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 463 ILE Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 669 VAL Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 364 ILE Chi-restraints excluded: chain 1 residue 633 TYR Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 2 residue 166 LEU Chi-restraints excluded: chain 2 residue 191 PHE Chi-restraints excluded: chain 2 residue 360 LEU Chi-restraints excluded: chain 3 residue 29 LEU Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 3 residue 93 ASN Chi-restraints excluded: chain 3 residue 120 LEU Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 191 PHE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 275 SER Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 294 CYS Chi-restraints excluded: chain 5 residue 52 HIS Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 760 LEU Chi-restraints excluded: chain 7 residue 833 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 263 CYS Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 188 GLU Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain Q residue 329 THR Chi-restraints excluded: chain Q residue 360 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 313 TRP Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 116 ASN Chi-restraints excluded: chain W residue 193 ARG Chi-restraints excluded: chain W residue 218 THR Chi-restraints excluded: chain X residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 524 optimal weight: 0.0870 chunk 845 optimal weight: 5.9990 chunk 515 optimal weight: 0.0980 chunk 401 optimal weight: 0.8980 chunk 587 optimal weight: 0.9990 chunk 886 optimal weight: 0.9990 chunk 816 optimal weight: 6.9990 chunk 706 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 545 optimal weight: 0.0040 chunk 432 optimal weight: 9.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 226 GLN ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS A 640 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS K 110 ASN ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 HIS U 272 ASN ** W 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 279 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 75541 Z= 0.156 Angle : 0.551 13.374 102537 Z= 0.284 Chirality : 0.041 0.209 11587 Planarity : 0.004 0.060 12694 Dihedral : 12.220 74.429 11139 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.37 % Allowed : 15.40 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.09), residues: 8762 helix: 1.62 (0.09), residues: 3668 sheet: 0.02 (0.14), residues: 1287 loop : -0.26 (0.10), residues: 3807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.001 TRP 7 133 HIS 0.006 0.001 HIS 2 85 PHE 0.047 0.001 PHE 0 396 TYR 0.026 0.001 TYR G 51 ARG 0.009 0.000 ARG 4 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1094 time to evaluate : 6.626 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 76 MET cc_start: 0.7798 (ttp) cc_final: 0.7481 (ttt) REVERT: 0 134 ARG cc_start: 0.8780 (mtt90) cc_final: 0.8504 (ttm-80) REVERT: 0 180 LYS cc_start: 0.7508 (tttt) cc_final: 0.7228 (tttt) REVERT: 0 250 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7808 (mm) REVERT: 0 438 THR cc_start: 0.8918 (p) cc_final: 0.8651 (t) REVERT: 0 544 TYR cc_start: 0.7914 (t80) cc_final: 0.7687 (t80) REVERT: 0 643 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7717 (ttm170) REVERT: 1 1 MET cc_start: 0.5404 (ppp) cc_final: 0.4877 (ppp) REVERT: 1 3 HIS cc_start: 0.7924 (m-70) cc_final: 0.7676 (m-70) REVERT: 1 97 MET cc_start: 0.8733 (ttp) cc_final: 0.8316 (ttt) REVERT: 1 192 MET cc_start: 0.8297 (tpt) cc_final: 0.7947 (tpp) REVERT: 1 349 VAL cc_start: 0.8465 (t) cc_final: 0.8139 (m) REVERT: 1 439 ARG cc_start: 0.6718 (tpt170) cc_final: 0.6498 (ptt180) REVERT: 1 608 MET cc_start: 0.7978 (tpp) cc_final: 0.7482 (tpp) REVERT: 2 97 MET cc_start: 0.6769 (mmm) cc_final: 0.6333 (mmm) REVERT: 2 108 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7734 (mm) REVERT: 2 216 MET cc_start: 0.6405 (ppp) cc_final: 0.5862 (pmm) REVERT: 2 223 HIS cc_start: 0.8274 (m90) cc_final: 0.7312 (m-70) REVERT: 2 227 MET cc_start: 0.8155 (tmm) cc_final: 0.7359 (ptp) REVERT: 2 355 LEU cc_start: 0.9419 (pt) cc_final: 0.8870 (mt) REVERT: 3 28 PHE cc_start: 0.8783 (m-80) cc_final: 0.8185 (m-80) REVERT: 4 36 LEU cc_start: 0.8335 (mt) cc_final: 0.7963 (mt) REVERT: 4 37 TRP cc_start: 0.7336 (m100) cc_final: 0.7080 (m100) REVERT: 4 116 ARG cc_start: 0.7705 (mmm160) cc_final: 0.7253 (mmm160) REVERT: 4 127 GLU cc_start: 0.8648 (tt0) cc_final: 0.8406 (mt-10) REVERT: 4 146 ARG cc_start: 0.6420 (mtm110) cc_final: 0.5702 (ptp90) REVERT: 4 228 THR cc_start: 0.8320 (p) cc_final: 0.8093 (t) REVERT: 4 294 CYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6677 (m) REVERT: 5 53 GLU cc_start: 0.9353 (tp30) cc_final: 0.8957 (tp30) REVERT: 7 133 TRP cc_start: 0.7910 (m100) cc_final: 0.7606 (m100) REVERT: 7 244 MET cc_start: 0.8551 (mmm) cc_final: 0.8094 (ptt) REVERT: 7 474 MET cc_start: 0.8958 (tpp) cc_final: 0.8539 (mmm) REVERT: 7 561 MET cc_start: 0.6976 (ttt) cc_final: 0.6492 (tmm) REVERT: 7 721 LYS cc_start: 0.9234 (tttt) cc_final: 0.8986 (ptmm) REVERT: A 41 MET cc_start: 0.7899 (mmm) cc_final: 0.7559 (mmm) REVERT: A 100 LYS cc_start: 0.8640 (tttt) cc_final: 0.8218 (ttpt) REVERT: A 205 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7063 (mm-30) REVERT: A 685 GLU cc_start: 0.7364 (tp30) cc_final: 0.7158 (tp30) REVERT: A 949 ASP cc_start: 0.7660 (t0) cc_final: 0.7415 (t0) REVERT: A 1135 ARG cc_start: 0.7920 (ttt180) cc_final: 0.7610 (ttt-90) REVERT: A 1143 LEU cc_start: 0.8719 (mm) cc_final: 0.8476 (mm) REVERT: B 173 MET cc_start: 0.9240 (ttm) cc_final: 0.8748 (ttm) REVERT: B 234 ILE cc_start: 0.8870 (mt) cc_final: 0.8633 (mt) REVERT: B 277 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8048 (ptpt) REVERT: B 312 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7342 (tp30) REVERT: B 373 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7680 (mtt-85) REVERT: B 391 ASP cc_start: 0.7248 (m-30) cc_final: 0.6945 (m-30) REVERT: B 398 ARG cc_start: 0.7826 (ptp-170) cc_final: 0.7463 (ptp-170) REVERT: B 591 ARG cc_start: 0.7508 (tpp80) cc_final: 0.6967 (mtm-85) REVERT: B 878 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7760 (mm-40) REVERT: B 935 ARG cc_start: 0.7730 (ptm160) cc_final: 0.7231 (ttt90) REVERT: B 1190 ASP cc_start: 0.7483 (t0) cc_final: 0.7126 (t0) REVERT: C 155 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8742 (pp) REVERT: D 37 GLN cc_start: 0.7241 (mt0) cc_final: 0.6989 (mt0) REVERT: D 48 ILE cc_start: 0.8544 (mm) cc_final: 0.8340 (mt) REVERT: D 155 ARG cc_start: 0.7971 (mmt90) cc_final: 0.7562 (mmm160) REVERT: E 16 PHE cc_start: 0.8350 (t80) cc_final: 0.7837 (t80) REVERT: E 40 GLU cc_start: 0.8187 (pm20) cc_final: 0.7869 (pm20) REVERT: E 41 ASP cc_start: 0.8485 (m-30) cc_final: 0.7627 (m-30) REVERT: E 61 GLN cc_start: 0.8115 (tt0) cc_final: 0.7750 (tm-30) REVERT: E 107 THR cc_start: 0.8290 (m) cc_final: 0.7992 (p) REVERT: E 121 MET cc_start: 0.7932 (tpt) cc_final: 0.7456 (tpt) REVERT: E 132 ILE cc_start: 0.9325 (mm) cc_final: 0.8800 (tp) REVERT: F 76 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8299 (tttp) REVERT: F 110 ASP cc_start: 0.7754 (p0) cc_final: 0.7472 (p0) REVERT: G 50 ASP cc_start: 0.8344 (t0) cc_final: 0.8100 (t0) REVERT: G 53 ASN cc_start: 0.7471 (m110) cc_final: 0.6743 (t0) REVERT: G 140 LYS cc_start: 0.8745 (tttt) cc_final: 0.8318 (mtmt) REVERT: H 95 TYR cc_start: 0.8237 (t80) cc_final: 0.8002 (t80) REVERT: H 136 LYS cc_start: 0.7730 (tptt) cc_final: 0.7484 (tppt) REVERT: I 28 GLU cc_start: 0.7255 (tt0) cc_final: 0.6238 (tp30) REVERT: J 62 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8425 (mmm-85) REVERT: K 8 GLU cc_start: 0.7648 (tp30) cc_final: 0.7283 (tm-30) REVERT: L 39 SER cc_start: 0.8725 (m) cc_final: 0.8404 (p) REVERT: L 62 LYS cc_start: 0.8372 (mmmt) cc_final: 0.8118 (mmmt) REVERT: M 33 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7641 (mmtp) REVERT: M 214 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7901 (mm) REVERT: M 250 MET cc_start: 0.7013 (tmm) cc_final: 0.6627 (tpp) REVERT: M 300 GLN cc_start: 0.7941 (tp40) cc_final: 0.7599 (tp40) REVERT: M 320 ARG cc_start: 0.8392 (ptp90) cc_final: 0.8110 (ptt180) REVERT: Q 128 ASN cc_start: 0.7325 (t0) cc_final: 0.6892 (t0) REVERT: Q 152 THR cc_start: 0.6951 (OUTLIER) cc_final: 0.6342 (p) REVERT: Q 425 MET cc_start: 0.6173 (tpp) cc_final: 0.5558 (tpp) REVERT: R 229 ASN cc_start: 0.7464 (m110) cc_final: 0.6854 (t0) REVERT: R 270 MET cc_start: 0.8121 (mmm) cc_final: 0.7815 (mmm) REVERT: R 313 TRP cc_start: 0.0519 (OUTLIER) cc_final: 0.0292 (m-90) REVERT: U 38 LEU cc_start: 0.8567 (tp) cc_final: 0.8303 (pp) REVERT: U 244 MET cc_start: 0.7165 (tmm) cc_final: 0.6934 (tmm) REVERT: U 250 LYS cc_start: 0.8466 (tptp) cc_final: 0.8168 (tptp) REVERT: U 255 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7718 (ttmm) REVERT: U 271 ARG cc_start: 0.8524 (mpp-170) cc_final: 0.8241 (mpp-170) REVERT: U 276 PHE cc_start: 0.8044 (p90) cc_final: 0.7823 (p90) REVERT: V 71 PHE cc_start: 0.7662 (t80) cc_final: 0.7356 (t80) REVERT: V 112 ARG cc_start: 0.8017 (ttt-90) cc_final: 0.7748 (ttp80) REVERT: X 227 ASP cc_start: 0.7195 (t0) cc_final: 0.6695 (t0) REVERT: X 317 MET cc_start: 0.5972 (mmp) cc_final: 0.5472 (mmt) outliers start: 109 outliers final: 74 residues processed: 1158 average time/residue: 0.7780 time to fit residues: 1531.0282 Evaluate side-chains 1119 residues out of total 7950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1038 time to evaluate : 6.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 90 MET Chi-restraints excluded: chain 0 residue 250 LEU Chi-restraints excluded: chain 0 residue 352 ILE Chi-restraints excluded: chain 0 residue 388 LEU Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 633 TYR Chi-restraints excluded: chain 2 residue 5 SER Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 2 residue 360 LEU Chi-restraints excluded: chain 3 residue 29 LEU Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 93 ASN Chi-restraints excluded: chain 3 residue 120 LEU Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 191 PHE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 275 SER Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 294 CYS Chi-restraints excluded: chain 5 residue 52 HIS Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 760 LEU Chi-restraints excluded: chain 7 residue 833 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 263 CYS Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain Q residue 329 THR Chi-restraints excluded: chain Q residue 360 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 313 TRP Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain W residue 116 ASN Chi-restraints excluded: chain W residue 193 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 560 optimal weight: 0.9990 chunk 752 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 651 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 707 optimal weight: 0.0270 chunk 295 optimal weight: 6.9990 chunk 726 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 66 ASN ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 226 GLN ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 HIS A 640 GLN ** A1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 GLN A1278 ASN B 887 HIS B 951 GLN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 279 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.185706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121013 restraints weight = 111812.568| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.91 r_work: 0.3056 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 75541 Z= 0.281 Angle : 0.578 11.800 102537 Z= 0.298 Chirality : 0.042 0.185 11587 Planarity : 0.004 0.068 12694 Dihedral : 12.240 73.900 11139 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.36 % Allowed : 15.66 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.09), residues: 8762 helix: 1.59 (0.09), residues: 3670 sheet: -0.02 (0.14), residues: 1279 loop : -0.29 (0.10), residues: 3813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.001 TRP 7 133 HIS 0.006 0.001 HIS A 587 PHE 0.039 0.002 PHE I 27 TYR 0.028 0.001 TYR 4 130 ARG 0.015 0.000 ARG 0 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25652.94 seconds wall clock time: 440 minutes 17.28 seconds (26417.28 seconds total)