####################################################### # # # LGA # # --------------- # # # # Local-Global Alignment # # A Method for Finding 3-D Similarities # # in Protein Structures # # # # ------------ 05/2009 # # # # Adam Zemla (adamz@llnl.gov) # # Lawrence Livermore National Laboratory, CA # # # ####################################################### # Molecule1: number of CA atoms 20 ( 138), selected 20 , name T0534TS316_1_3-D2 # Molecule2: number of CA atoms 176 ( 1347), selected 20 , name T0534-D2.pdb # PARAMETERS: -3 -ie -o1 -sda -d:4 -swap T0534TS316_1_3-D2.lga # FIXED Atom-Atom correspondence # GDT and LCS analysis LCS - RMSD CUTOFF 5.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 18 150 - 167 4.14 7.34 LCS_AVERAGE: 9.66 LCS - RMSD CUTOFF 2.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 8 150 - 157 1.13 11.40 LCS_AVERAGE: 3.18 LCS - RMSD CUTOFF 1.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 7 150 - 156 0.56 11.36 LCS_AVERAGE: 2.70 LCS_GDT MOLECULE-1 MOLECULE-2 LCS_DETAILS GDT_DETAILS TOTAL NUMBER OF RESIDUE PAIRS: 20 LCS_GDT RESIDUE RESIDUE SEGMENT_SIZE GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair LCS_GDT NAME NUMBER NAME NUMBER 1.0 2.0 5.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0 8.5 9.0 9.5 10.0 LCS_GDT N 150 N 150 7 8 18 5 7 7 7 8 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT N 151 N 151 7 8 18 5 7 7 7 8 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT I 152 I 152 7 8 18 5 7 7 7 8 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT Y 153 Y 153 7 8 18 5 7 7 7 8 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT S 154 S 154 7 8 18 5 7 7 7 8 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT I 155 I 155 7 8 18 5 7 7 7 8 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT R 156 R 156 7 8 18 5 7 7 7 8 8 10 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT N 157 N 157 6 8 18 4 5 6 7 8 8 9 10 10 12 17 17 17 18 18 18 18 18 18 18 LCS_GDT A 158 A 158 5 6 18 4 5 5 5 6 8 10 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT Y 159 Y 159 5 6 18 4 5 5 6 7 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT Y 160 Y 160 5 6 18 4 5 5 5 6 7 8 9 13 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT G 161 G 161 3 6 18 3 3 3 4 6 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT S 162 S 162 4 4 18 3 4 4 4 6 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT L 163 L 163 4 4 18 3 4 4 4 6 7 8 11 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT D 164 D 164 4 4 18 3 4 4 4 5 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT G 165 G 165 4 4 18 3 4 5 6 7 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT N 166 N 166 3 4 18 3 3 4 4 5 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 LCS_GDT I 167 I 167 3 4 18 3 3 4 4 4 4 7 9 10 11 14 14 17 18 18 18 18 18 18 18 LCS_GDT Q 255 Q 255 0 0 8 0 0 0 0 0 0 2 2 4 4 8 10 12 13 13 15 17 17 17 18 LCS_GDT Y 256 Y 256 0 0 8 0 0 0 1 1 1 2 3 5 6 8 10 12 13 13 15 17 17 17 18 LCS_AVERAGE LCS_A: 5.18 ( 2.70 3.18 9.66 ) GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds) GDT DIST_CUTOFF 0.50 1.00 1.50 2.00 2.50 3.00 3.50 4.00 4.50 5.00 5.50 6.00 6.50 7.00 7.50 8.00 8.50 9.00 9.50 10.00 GDT NUMBER_AT 5 7 7 7 8 8 11 14 14 15 17 17 17 18 18 18 18 18 18 18 GDT PERCENT_AT 2.84 3.98 3.98 3.98 4.55 4.55 6.25 7.95 7.95 8.52 9.66 9.66 9.66 10.23 10.23 10.23 10.23 10.23 10.23 10.23 GDT RMS_LOCAL 0.23 0.56 0.56 0.56 1.13 1.13 2.73 3.05 3.05 3.20 3.67 3.67 3.67 4.14 4.14 4.14 4.14 4.14 4.14 4.14 GDT RMS_ALL_AT 10.90 11.36 11.36 11.36 11.40 11.40 7.51 7.54 7.54 7.58 7.59 7.59 7.59 7.34 7.34 7.34 7.34 7.34 7.34 7.34 # Checking swapping # Molecule1 Molecule2 DISTANCE Mis MC All Dist_max GDC_mc GDC_all LGA N 150 N 150 3.078 3 0.060 0.066 3.975 55.833 35.060 LGA N 151 N 151 2.944 3 0.049 0.054 3.837 61.190 36.012 LGA I 152 I 152 2.494 3 0.035 0.043 3.640 69.048 39.940 LGA Y 153 Y 153 2.500 7 0.049 0.060 3.141 66.786 26.429 LGA S 154 S 154 1.048 1 0.029 0.029 3.154 71.667 59.921 LGA I 155 I 155 2.618 3 0.056 0.063 4.338 54.286 35.238 LGA R 156 R 156 4.126 6 0.574 0.571 5.611 36.786 16.753 LGA N 157 N 157 6.757 3 0.141 0.150 8.668 20.595 10.655 LGA A 158 A 158 3.844 0 0.064 0.068 5.193 54.524 48.857 LGA Y 159 Y 159 1.706 7 0.274 0.277 4.214 62.143 26.111 LGA Y 160 Y 160 5.056 7 0.183 0.197 6.539 31.190 11.508 LGA G 161 G 161 3.705 0 0.363 0.363 4.498 45.119 45.119 LGA S 162 S 162 3.331 1 0.571 0.576 4.704 47.857 39.127 LGA L 163 L 163 6.031 3 0.158 0.167 8.118 26.548 13.869 LGA D 164 D 164 3.474 3 0.256 0.266 5.274 57.738 32.143 LGA G 165 G 165 3.078 0 0.222 0.222 4.244 56.429 56.429 LGA N 166 N 166 3.223 3 0.512 0.499 6.766 39.405 25.119 LGA I 167 I 167 9.264 3 0.631 0.577 12.659 2.857 1.429 LGA Q 255 Q 255 20.401 4 0.015 0.022 20.756 0.000 0.000 LGA Y 256 Y 256 19.920 7 0.109 0.121 21.137 0.000 0.000 # RMSD_GDC results: CA MC common percent ALL common percent GDC_mc GDC_all NUMBER_OF_ATOMS_AA: 20 80 80 100.00 165 98 59.39 176 SUMMARY(RMSD_GDC): 6.768 6.740 6.900 4.886 3.180 #CA N1 N2 DIST N RMSD GDT_TS LGA_S3 LGA_Q SUMMARY(GDT) 20 176 4.0 14 3.05 6.534 5.755 0.445 LGA_LOCAL RMSD: 3.048 Number of atoms: 14 under DIST: 4.00 LGA_ASGN_ATOMS RMSD: 7.538 Number of assigned atoms: 20 Std_ASGN_ATOMS RMSD: 6.768 Standard rmsd on all 20 assigned CA atoms Unitary ROTATION matrix and the SHIFT vector superimpose molecules (1=>2) X_new = 0.070888 * X + 0.352891 * Y + -0.932975 * Z + -25.622400 Y_new = -0.956848 * X + 0.288308 * Y + 0.036348 * Z + 10.456043 Z_new = 0.281811 * X + 0.890139 * Y + 0.358100 * Z + 65.933823 Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ: Phi Theta Psi [DEG: Phi Theta Psi ] XYZ: -1.496846 -0.285681 1.188311 [DEG: -85.7630 -16.3683 68.0852 ] ZXZ: -1.609736 1.204564 0.306609 [DEG: -92.2311 69.0164 17.5674 ] # END of job REMARK ---------------------------------------------------------- REMARK Citing LGA: REMARK Zemla A., LGA - a Method for Finding 3D Similarities in REMARK Protein Structures, Nucleic Acids Research, 2003, V. 31, REMARK No. 13, pp. 3370-3374. REMARK ---------------------------------------------------------- REMARK Superimposed MOLECULES (1=>2) Output: 1 molecule REMARK 1: T0534TS316_1_3-D2 REMARK 2: T0534-D2.pdb REMARK GDT and LCS analysis REMARK FIXED Atom-Atom correspondence REMARK LGA parameters: -3 -ie -o1 -sda -d:4 -swap T0534TS316_1_3-D2.lga REMARK #CA N1 N2 DIST N RMSD LGA_S3 RMSD_global REMARK SUMMARY: 20 176 4.0 14 3.05 5.755 6.77 REMARK ---------------------------------------------------------- MOLECULE T0534TS316_1_3-D2 REMARK This file has been preprocessed by preprocess_pdbv2.1.00.100503REMARK PARENT number 3 REMARK PFRMAT TS REMARK TARGET T0534 REMARK PARENT N/A ATOM 1 N ASN 150 -25.622 10.456 65.934 1.00 0.00 N ATOM 2 CA ASN 150 -25.519 9.061 66.345 1.00 0.00 C ATOM 3 C ASN 150 -24.979 8.943 67.764 1.00 0.00 C ATOM 4 O ASN 150 -25.231 7.956 68.454 1.00 0.00 O ATOM 5 CB ASN 150 -24.654 8.263 65.386 1.00 0.00 C ATOM 6 CEN ASN 150 -24.778 7.672 64.528 1.00 0.00 C ATOM 7 H ASN 150 -25.111 10.782 65.139 1.00 0.00 H ATOM 8 N ASN 151 -24.234 9.956 68.194 1.00 0.00 N ATOM 9 CA ASN 151 -23.548 9.911 69.479 1.00 0.00 C ATOM 10 C ASN 151 -24.525 10.100 70.633 1.00 0.00 C ATOM 11 O ASN 151 -24.369 9.498 71.696 1.00 0.00 O ATOM 12 CB ASN 151 -22.442 10.947 69.555 1.00 0.00 C ATOM 13 CEN ASN 151 -21.411 11.006 69.364 1.00 0.00 C ATOM 14 H ASN 151 -24.142 10.779 67.616 1.00 0.00 H ATOM 15 N ILE 152 -25.533 10.938 70.417 1.00 0.00 N ATOM 16 CA ILE 152 -26.576 11.154 71.412 1.00 0.00 C ATOM 17 C ILE 152 -27.391 9.887 71.640 1.00 0.00 C ATOM 18 O ILE 152 -27.662 9.509 72.780 1.00 0.00 O ATOM 19 CB ILE 152 -27.524 12.295 70.998 1.00 0.00 C ATOM 20 CEN ILE 152 -27.682 13.373 71.014 1.00 0.00 C ATOM 21 H ILE 152 -25.577 11.438 69.541 1.00 0.00 H ATOM 22 N TYR 153 -27.778 9.234 70.550 1.00 0.00 N ATOM 23 CA TYR 153 -28.488 7.964 70.630 1.00 0.00 C ATOM 24 C TYR 153 -27.645 6.904 71.327 1.00 0.00 C ATOM 25 O TYR 153 -28.166 6.072 72.070 1.00 0.00 O ATOM 26 CB TYR 153 -28.884 7.483 69.231 1.00 0.00 C ATOM 27 CEN TYR 153 -30.271 7.440 68.163 1.00 0.00 C ATOM 28 H TYR 153 -27.576 9.629 69.642 1.00 0.00 H ATOM 29 N SER 154 -26.339 6.940 71.083 1.00 0.00 N ATOM 30 CA SER 154 -25.418 5.997 71.706 1.00 0.00 C ATOM 31 C SER 154 -25.284 6.263 73.201 1.00 0.00 C ATOM 32 O SER 154 -25.190 5.332 74.001 1.00 0.00 O ATOM 33 CB SER 154 -24.061 6.071 71.033 1.00 0.00 C ATOM 34 CEN SER 154 -23.630 6.286 70.782 1.00 0.00 C ATOM 35 H SER 154 -25.976 7.637 70.451 1.00 0.00 H ATOM 36 N ILE 155 -25.276 7.539 73.571 1.00 0.00 N ATOM 37 CA ILE 155 -25.173 7.930 74.971 1.00 0.00 C ATOM 38 C ILE 155 -26.449 7.597 75.732 1.00 0.00 C ATOM 39 O ILE 155 -26.403 7.201 76.896 1.00 0.00 O ATOM 40 CB ILE 155 -24.875 9.433 75.118 1.00 0.00 C ATOM 41 CEN ILE 155 -24.090 10.189 75.145 1.00 0.00 C ATOM 42 H ILE 155 -25.344 8.257 72.863 1.00 0.00 H ATOM 43 N ARG 156 -27.588 7.761 75.068 1.00 0.00 N ATOM 44 CA ARG 156 -28.881 7.493 75.685 1.00 0.00 C ATOM 45 C ARG 156 -29.028 6.018 76.037 1.00 0.00 C ATOM 46 O ARG 156 -28.642 5.144 75.261 1.00 0.00 O ATOM 47 CB ARG 156 -30.039 7.980 74.827 1.00 0.00 C ATOM 48 CEN ARG 156 -31.848 9.426 73.938 1.00 0.00 C ATOM 49 H ARG 156 -27.557 8.080 74.110 1.00 0.00 H ATOM 50 N ASN 157 -29.591 5.748 77.209 1.00 0.00 N ATOM 51 CA ASN 157 -29.802 4.378 77.660 1.00 0.00 C ATOM 52 C ASN 157 -31.286 4.066 77.799 1.00 0.00 C ATOM 53 O ASN 157 -31.687 2.902 77.821 1.00 0.00 O ATOM 54 CB ASN 157 -29.085 4.109 78.971 1.00 0.00 C ATOM 55 CEN ASN 157 -28.158 3.737 79.292 1.00 0.00 C ATOM 56 H ASN 157 -29.880 6.512 77.805 1.00 0.00 H ATOM 57 N ALA 158 -32.099 5.113 77.893 1.00 0.00 N ATOM 58 CA ALA 158 -33.539 4.951 78.062 1.00 0.00 C ATOM 59 C ALA 158 -34.287 5.306 76.784 1.00 0.00 C ATOM 60 O ALA 158 -35.352 4.756 76.504 1.00 0.00 O ATOM 61 CB ALA 158 -34.033 5.801 79.223 1.00 0.00 C ATOM 62 CEN ALA 158 -34.034 5.801 79.222 1.00 0.00 C ATOM 63 H ALA 158 -31.711 6.043 77.846 1.00 0.00 H ATOM 64 N TYR 159 -33.724 6.228 76.011 1.00 0.00 N ATOM 65 CA TYR 159 -34.366 6.700 74.790 1.00 0.00 C ATOM 66 C TYR 159 -33.424 6.596 73.597 1.00 0.00 C ATOM 67 O TYR 159 -33.620 7.260 72.580 1.00 0.00 O ATOM 68 CB TYR 159 -34.839 8.145 74.959 1.00 0.00 C ATOM 69 CEN TYR 159 -36.298 9.055 75.297 1.00 0.00 C ATOM 70 H TYR 159 -32.827 6.611 76.276 1.00 0.00 H ATOM 71 N TYR 160 -32.402 5.758 73.728 1.00 0.00 N ATOM 72 CA TYR 160 -31.416 5.580 72.668 1.00 0.00 C ATOM 73 C TYR 160 -32.089 5.287 71.333 1.00 0.00 C ATOM 74 O TYR 160 -31.737 5.871 70.309 1.00 0.00 O ATOM 75 CB TYR 160 -30.445 4.452 73.024 1.00 0.00 C ATOM 76 CEN TYR 160 -28.831 4.214 73.664 1.00 0.00 C ATOM 77 H TYR 160 -32.305 5.231 74.584 1.00 0.00 H ATOM 78 N GLY 161 -33.059 4.380 71.352 1.00 0.00 N ATOM 79 CA GLY 161 -33.774 3.997 70.141 1.00 0.00 C ATOM 80 C GLY 161 -34.627 5.146 69.618 1.00 0.00 C ATOM 81 O GLY 161 -34.742 5.344 68.409 1.00 0.00 O ATOM 82 CEN GLY 161 -33.774 3.997 70.140 1.00 0.00 C ATOM 83 H GLY 161 -33.309 3.944 72.229 1.00 0.00 H ATOM 84 N SER 162 -35.222 5.899 70.536 1.00 0.00 N ATOM 85 CA SER 162 -36.075 7.022 70.169 1.00 0.00 C ATOM 86 C SER 162 -35.270 8.133 69.508 1.00 0.00 C ATOM 87 O SER 162 -35.670 8.674 68.477 1.00 0.00 O ATOM 88 CB SER 162 -36.798 7.552 71.393 1.00 0.00 C ATOM 89 CEN SER 162 -36.884 7.688 71.912 1.00 0.00 C ATOM 90 H SER 162 -35.081 5.688 71.513 1.00 0.00 H ATOM 91 N LEU 163 -34.132 8.469 70.106 1.00 0.00 N ATOM 92 CA LEU 163 -33.267 9.516 69.576 1.00 0.00 C ATOM 93 C LEU 163 -32.859 9.218 68.139 1.00 0.00 C ATOM 94 O LEU 163 -32.839 10.110 67.292 1.00 0.00 O ATOM 95 CB LEU 163 -32.024 9.675 70.462 1.00 0.00 C ATOM 96 CEN LEU 163 -31.614 10.730 71.507 1.00 0.00 C ATOM 97 H LEU 163 -33.860 7.986 70.951 1.00 0.00 H ATOM 98 N ASP 164 -32.534 7.958 67.871 1.00 0.00 N ATOM 99 CA ASP 164 -32.126 7.540 66.535 1.00 0.00 C ATOM 100 C ASP 164 -33.256 7.724 65.531 1.00 0.00 C ATOM 101 O ASP 164 -33.047 8.236 64.432 1.00 0.00 O ATOM 102 CB ASP 164 -31.666 6.079 66.547 1.00 0.00 C ATOM 103 CEN ASP 164 -30.812 5.527 66.592 1.00 0.00 C ATOM 104 H ASP 164 -32.570 7.272 68.612 1.00 0.00 H ATOM 105 N GLY 165 -34.458 7.304 65.916 1.00 0.00 N ATOM 106 CA GLY 165 -35.623 7.419 65.048 1.00 0.00 C ATOM 107 C GLY 165 -35.975 8.878 64.790 1.00 0.00 C ATOM 108 O GLY 165 -36.368 9.244 63.682 1.00 0.00 O ATOM 109 CEN GLY 165 -35.624 7.418 65.048 1.00 0.00 C ATOM 110 H GLY 165 -34.564 6.895 66.833 1.00 0.00 H ATOM 111 N ASN 166 -35.834 9.707 65.817 1.00 0.00 N ATOM 112 CA ASN 166 -36.151 11.126 65.707 1.00 0.00 C ATOM 113 C ASN 166 -34.913 11.986 65.931 1.00 0.00 C ATOM 114 O ASN 166 -35.015 13.138 66.352 1.00 0.00 O ATOM 115 CB ASN 166 -37.249 11.526 66.675 1.00 0.00 C ATOM 116 CEN ASN 166 -38.296 11.616 66.676 1.00 0.00 C ATOM 117 H ASN 166 -35.497 9.346 66.699 1.00 0.00 H ATOM 118 N ILE 167 -33.745 11.419 65.647 1.00 0.00 N ATOM 119 CA ILE 167 -32.492 12.157 65.745 1.00 0.00 C ATOM 120 C ILE 167 -32.545 13.442 64.928 1.00 0.00 C ATOM 121 O ILE 167 -31.926 14.443 65.289 1.00 0.00 O ATOM 122 CB ILE 167 -31.298 11.308 65.271 1.00 0.00 C ATOM 123 CEN ILE 167 -30.556 10.568 65.571 1.00 0.00 C ATOM 124 H ILE 167 -33.726 10.452 65.357 1.00 0.00 H ATOM 125 N GLN 255 -33.287 13.407 63.826 1.00 0.00 N ATOM 126 CA GLN 255 -33.378 14.552 62.928 1.00 0.00 C ATOM 127 C GLN 255 -34.003 15.752 63.627 1.00 0.00 C ATOM 128 O GLN 255 -33.611 16.895 63.388 1.00 0.00 O ATOM 129 CB GLN 255 -34.198 14.193 61.686 1.00 0.00 C ATOM 130 CEN GLN 255 -34.100 13.734 60.004 1.00 0.00 C ATOM 131 H GLN 255 -33.800 12.566 63.605 1.00 0.00 H ATOM 132 N TYR 256 -34.976 15.487 64.492 1.00 0.00 N ATOM 133 CA TYR 256 -35.688 16.548 65.193 1.00 0.00 C ATOM 134 C TYR 256 -34.900 17.033 66.403 1.00 0.00 C ATOM 135 O TYR 256 -35.000 18.197 66.794 1.00 0.00 O ATOM 136 CB TYR 256 -37.074 16.065 65.628 1.00 0.00 C ATOM 137 CEN TYR 256 -38.752 16.165 65.136 1.00 0.00 C ATOM 138 H TYR 256 -35.228 14.525 64.669 1.00 0.00 H TER END ########################## # # # ACE results: # # # ########################## WARNING!!! Different chains are predicted. Only first chain will be considered. Number of atoms possible to evaluate: 0 ERROR! The set of atoms possible to evaluate is empty-> END of the results output