####################################################### # # # 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 T0534TS042_1_3-D2 # Molecule2: number of CA atoms 176 ( 1347), selected 20 , name T0534-D2.pdb # PARAMETERS: -3 -ie -o1 -sda -d:4 -swap T0534TS042_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: 17 150 - 166 4.59 7.57 LONGEST_CONTINUOUS_SEGMENT: 17 151 - 167 4.98 7.71 LCS_AVERAGE: 9.15 LCS - RMSD CUTOFF 2.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 9 151 - 159 1.28 12.36 LCS_AVERAGE: 3.30 LCS - RMSD CUTOFF 1.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 8 151 - 158 0.92 12.65 LCS_AVERAGE: 2.87 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 3 3 17 3 3 5 5 7 8 9 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT N 151 N 151 8 9 17 5 5 8 9 9 9 9 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT I 152 I 152 8 9 17 5 5 8 9 9 9 9 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT Y 153 Y 153 8 9 17 5 5 8 9 9 9 9 10 11 12 14 15 16 17 17 17 18 19 20 20 LCS_GDT S 154 S 154 8 9 17 5 5 8 9 9 9 9 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT I 155 I 155 8 9 17 5 5 8 9 9 9 9 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT R 156 R 156 8 9 17 4 5 8 9 9 9 9 10 11 12 14 15 16 17 17 17 18 19 20 20 LCS_GDT N 157 N 157 8 9 17 4 5 8 9 9 9 9 10 10 11 14 15 16 17 17 17 18 19 20 20 LCS_GDT A 158 A 158 8 9 17 4 5 8 9 9 9 9 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT Y 159 Y 159 6 9 17 3 3 5 9 9 9 9 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT Y 160 Y 160 3 4 17 3 3 3 5 6 8 9 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT G 161 G 161 3 4 17 3 3 5 5 5 6 8 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT S 162 S 162 4 4 17 3 4 4 4 5 6 8 9 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT L 163 L 163 4 4 17 3 4 4 4 7 7 8 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT D 164 D 164 4 4 17 3 4 4 5 7 8 9 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT G 165 G 165 4 4 17 3 4 4 5 7 8 9 10 11 13 14 15 16 17 17 17 18 19 20 20 LCS_GDT N 166 N 166 3 4 17 3 3 3 3 4 4 5 9 11 11 14 15 16 17 17 17 18 19 20 20 LCS_GDT I 167 I 167 3 4 17 3 3 3 3 4 4 5 5 6 7 9 9 12 14 14 16 16 18 20 20 LCS_GDT Q 255 Q 255 0 0 8 0 0 0 0 0 4 4 4 6 7 9 11 12 14 14 16 17 19 20 20 LCS_GDT Y 256 Y 256 0 0 8 0 0 0 3 3 4 4 4 6 7 9 11 12 14 14 16 18 19 20 20 LCS_AVERAGE LCS_A: 5.10 ( 2.87 3.30 9.15 ) 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 5 8 9 9 9 9 10 11 13 14 15 16 17 17 17 18 19 20 20 GDT PERCENT_AT 2.84 2.84 4.55 5.11 5.11 5.11 5.11 5.68 6.25 7.39 7.95 8.52 9.09 9.66 9.66 9.66 10.23 10.80 11.36 11.36 GDT RMS_LOCAL 0.26 0.26 0.92 1.28 1.28 1.28 1.28 2.20 2.95 3.54 3.85 4.10 4.29 4.59 4.59 4.59 5.81 6.40 6.67 6.67 GDT RMS_ALL_AT 13.41 13.41 12.65 12.36 12.36 12.36 12.36 11.49 7.74 7.75 7.68 7.61 7.70 7.57 7.57 7.57 7.02 6.72 6.67 6.67 # Checking swapping # Molecule1 Molecule2 DISTANCE Mis MC All Dist_max GDC_mc GDC_all LGA N 150 N 150 9.568 3 0.621 0.605 11.338 6.905 3.452 LGA N 151 N 151 2.355 3 0.582 0.549 5.138 63.452 39.821 LGA I 152 I 152 0.400 3 0.064 0.069 0.956 92.857 57.738 LGA Y 153 Y 153 1.692 7 0.023 0.025 2.333 77.143 31.111 LGA S 154 S 154 0.837 1 0.104 0.106 1.257 85.952 73.968 LGA I 155 I 155 1.885 3 0.140 0.150 2.287 70.952 43.571 LGA R 156 R 156 2.793 6 0.091 0.102 3.137 60.952 26.710 LGA N 157 N 157 1.593 3 0.162 0.172 1.807 75.000 46.607 LGA A 158 A 158 0.735 0 0.585 0.581 2.745 82.143 82.000 LGA Y 159 Y 159 1.859 7 0.634 0.613 4.481 71.071 26.786 LGA Y 160 Y 160 4.594 7 0.177 0.191 8.676 24.405 9.563 LGA G 161 G 161 9.656 0 0.371 0.371 13.328 2.619 2.619 LGA S 162 S 162 12.000 1 0.597 0.591 12.000 0.000 0.000 LGA L 163 L 163 12.509 3 0.136 0.144 14.668 0.000 0.000 LGA D 164 D 164 17.281 3 0.170 0.176 19.028 0.000 0.000 LGA G 165 G 165 16.812 0 0.140 0.140 18.047 0.000 0.000 LGA N 166 N 166 17.595 3 0.512 0.499 18.496 0.000 0.000 LGA I 167 I 167 15.852 3 0.613 0.552 19.903 0.000 0.000 LGA Q 255 Q 255 23.847 4 0.004 0.011 23.847 0.000 0.000 LGA Y 256 Y 256 19.887 7 0.049 0.059 21.161 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): 6.671 6.426 6.777 4.054 2.522 #CA N1 N2 DIST N RMSD GDT_TS LGA_S3 LGA_Q SUMMARY(GDT) 20 176 4.0 10 2.20 5.824 5.419 0.435 LGA_LOCAL RMSD: 2.197 Number of atoms: 10 under DIST: 4.00 LGA_ASGN_ATOMS RMSD: 11.489 Number of assigned atoms: 20 Std_ASGN_ATOMS RMSD: 6.671 Standard rmsd on all 20 assigned CA atoms Unitary ROTATION matrix and the SHIFT vector superimpose molecules (1=>2) X_new = -0.704007 * X + -0.108200 * Y + 0.701903 * Z + -19.100117 Y_new = -0.700578 * X + 0.267886 * Y + -0.661383 * Z + 10.909938 Z_new = -0.116468 * X + -0.957356 * Y + -0.264396 * Z + 76.892174 Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ: Phi Theta Psi [DEG: Phi Theta Psi ] XYZ: -2.358636 0.116733 -1.840253 [DEG: -135.1399 6.6883 -105.4387 ] ZXZ: 0.815111 1.838374 -3.020531 [DEG: 46.7024 105.3310 -173.0637 ] # 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: T0534TS042_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 T0534TS042_1_3-D2.lga REMARK #CA N1 N2 DIST N RMSD LGA_S3 RMSD_global REMARK SUMMARY: 20 176 4.0 10 2.20 5.419 6.67 REMARK ---------------------------------------------------------- MOLECULE T0534TS042_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 -19.100 10.910 76.892 1.00 0.00 N ATOM 2 CA ASN 150 -20.127 9.888 76.722 1.00 0.00 C ATOM 3 C ASN 150 -20.668 9.883 75.299 1.00 0.00 C ATOM 4 O ASN 150 -20.528 10.863 74.567 1.00 0.00 O ATOM 5 CB ASN 150 -21.261 10.071 77.714 1.00 0.00 C ATOM 6 CEN ASN 150 -21.526 9.729 78.670 1.00 0.00 C ATOM 7 H ASN 150 -19.228 11.640 77.563 1.00 0.00 H ATOM 8 N ASN 151 -21.288 8.773 74.911 1.00 0.00 N ATOM 9 CA ASN 151 -21.739 8.589 73.537 1.00 0.00 C ATOM 10 C ASN 151 -23.027 9.357 73.272 1.00 0.00 C ATOM 11 O ASN 151 -24.108 8.937 73.684 1.00 0.00 O ATOM 12 CB ASN 151 -21.928 7.119 73.209 1.00 0.00 C ATOM 13 CEN ASN 151 -21.369 6.332 72.797 1.00 0.00 C ATOM 14 H ASN 151 -21.450 8.039 75.586 1.00 0.00 H ATOM 15 N ILE 152 -22.905 10.486 72.583 1.00 0.00 N ATOM 16 CA ILE 152 -24.036 11.383 72.375 1.00 0.00 C ATOM 17 C ILE 152 -25.009 10.815 71.350 1.00 0.00 C ATOM 18 O ILE 152 -26.210 10.725 71.602 1.00 0.00 O ATOM 19 CB ILE 152 -23.575 12.777 71.913 1.00 0.00 C ATOM 20 CEN ILE 152 -23.225 13.756 72.243 1.00 0.00 C ATOM 21 H ILE 152 -22.007 10.730 72.192 1.00 0.00 H ATOM 22 N TYR 153 -24.483 10.431 70.192 1.00 0.00 N ATOM 23 CA TYR 153 -25.308 9.901 69.113 1.00 0.00 C ATOM 24 C TYR 153 -26.015 8.621 69.538 1.00 0.00 C ATOM 25 O TYR 153 -27.043 8.249 68.972 1.00 0.00 O ATOM 26 CB TYR 153 -24.459 9.643 67.866 1.00 0.00 C ATOM 27 CEN TYR 153 -24.071 10.377 66.323 1.00 0.00 C ATOM 28 H TYR 153 -23.485 10.510 70.054 1.00 0.00 H ATOM 29 N SER 154 -25.457 7.948 70.540 1.00 0.00 N ATOM 30 CA SER 154 -26.025 6.700 71.034 1.00 0.00 C ATOM 31 C SER 154 -27.309 6.950 71.814 1.00 0.00 C ATOM 32 O SER 154 -28.144 6.056 71.958 1.00 0.00 O ATOM 33 CB SER 154 -25.014 5.973 71.900 1.00 0.00 C ATOM 34 CEN SER 154 -24.609 5.901 72.256 1.00 0.00 C ATOM 35 H SER 154 -24.618 8.311 70.968 1.00 0.00 H ATOM 36 N ILE 155 -27.462 8.171 72.316 1.00 0.00 N ATOM 37 CA ILE 155 -28.624 8.527 73.124 1.00 0.00 C ATOM 38 C ILE 155 -29.906 8.460 72.303 1.00 0.00 C ATOM 39 O ILE 155 -31.002 8.362 72.855 1.00 0.00 O ATOM 40 CB ILE 155 -28.482 9.937 73.724 1.00 0.00 C ATOM 41 CEN ILE 155 -28.082 10.517 74.557 1.00 0.00 C ATOM 42 H ILE 155 -26.757 8.870 72.133 1.00 0.00 H ATOM 43 N ARG 156 -29.762 8.515 70.984 1.00 0.00 N ATOM 44 CA ARG 156 -30.910 8.467 70.085 1.00 0.00 C ATOM 45 C ARG 156 -31.648 7.141 70.204 1.00 0.00 C ATOM 46 O ARG 156 -32.871 7.087 70.085 1.00 0.00 O ATOM 47 CB ARG 156 -30.523 8.763 68.644 1.00 0.00 C ATOM 48 CEN ARG 156 -30.142 10.004 66.530 1.00 0.00 C ATOM 49 H ARG 156 -28.834 8.591 70.593 1.00 0.00 H ATOM 50 N ASN 157 -30.897 6.070 70.440 1.00 0.00 N ATOM 51 CA ASN 157 -31.477 4.739 70.570 1.00 0.00 C ATOM 52 C ASN 157 -31.860 4.444 72.015 1.00 0.00 C ATOM 53 O ASN 157 -32.605 3.504 72.289 1.00 0.00 O ATOM 54 CB ASN 157 -30.537 3.670 70.046 1.00 0.00 C ATOM 55 CEN ASN 157 -30.356 3.158 69.148 1.00 0.00 C ATOM 56 H ASN 157 -29.897 6.182 70.530 1.00 0.00 H ATOM 57 N ALA 158 -31.345 5.252 72.935 1.00 0.00 N ATOM 58 CA ALA 158 -31.643 5.088 74.351 1.00 0.00 C ATOM 59 C ALA 158 -33.004 5.679 74.700 1.00 0.00 C ATOM 60 O ALA 158 -33.608 6.387 73.894 1.00 0.00 O ATOM 61 CB ALA 158 -30.553 5.725 75.200 1.00 0.00 C ATOM 62 CEN ALA 158 -30.553 5.726 75.200 1.00 0.00 C ATOM 63 H ALA 158 -30.730 6.000 72.644 1.00 0.00 H ATOM 64 N TYR 159 -33.481 5.384 75.904 1.00 0.00 N ATOM 65 CA TYR 159 -34.762 5.901 76.369 1.00 0.00 C ATOM 66 C TYR 159 -34.643 7.357 76.800 1.00 0.00 C ATOM 67 O TYR 159 -33.549 7.846 77.079 1.00 0.00 O ATOM 68 CB TYR 159 -35.295 5.053 77.524 1.00 0.00 C ATOM 69 CEN TYR 159 -36.446 3.769 77.836 1.00 0.00 C ATOM 70 H TYR 159 -32.942 4.784 76.513 1.00 0.00 H ATOM 71 N TYR 160 -35.778 8.047 76.855 1.00 0.00 N ATOM 72 CA TYR 160 -35.805 9.447 77.265 1.00 0.00 C ATOM 73 C TYR 160 -35.152 9.635 78.627 1.00 0.00 C ATOM 74 O TYR 160 -34.362 10.558 78.827 1.00 0.00 O ATOM 75 CB TYR 160 -37.243 9.968 77.295 1.00 0.00 C ATOM 76 CEN TYR 160 -38.356 10.912 76.326 1.00 0.00 C ATOM 77 H TYR 160 -36.644 7.590 76.607 1.00 0.00 H ATOM 78 N GLY 161 -35.486 8.754 79.565 1.00 0.00 N ATOM 79 CA GLY 161 -34.919 8.810 80.906 1.00 0.00 C ATOM 80 C GLY 161 -33.430 8.491 80.889 1.00 0.00 C ATOM 81 O GLY 161 -32.644 9.109 81.606 1.00 0.00 O ATOM 82 CEN GLY 161 -34.919 8.810 80.906 1.00 0.00 C ATOM 83 H GLY 161 -36.151 8.026 79.341 1.00 0.00 H ATOM 84 N SER 162 -33.049 7.519 80.065 1.00 0.00 N ATOM 85 CA SER 162 -31.647 7.146 79.920 1.00 0.00 C ATOM 86 C SER 162 -30.856 8.240 79.215 1.00 0.00 C ATOM 87 O SER 162 -29.715 8.526 79.578 1.00 0.00 O ATOM 88 CB SER 162 -31.532 5.838 79.159 1.00 0.00 C ATOM 89 CEN SER 162 -31.647 5.450 78.797 1.00 0.00 C ATOM 90 H SER 162 -33.748 7.027 79.527 1.00 0.00 H ATOM 91 N LEU 163 -31.468 8.850 78.206 1.00 0.00 N ATOM 92 CA LEU 163 -30.828 9.926 77.458 1.00 0.00 C ATOM 93 C LEU 163 -30.545 11.126 78.352 1.00 0.00 C ATOM 94 O LEU 163 -29.514 11.784 78.216 1.00 0.00 O ATOM 95 CB LEU 163 -31.704 10.339 76.268 1.00 0.00 C ATOM 96 CEN LEU 163 -31.607 10.069 74.755 1.00 0.00 C ATOM 97 H LEU 163 -32.402 8.561 77.950 1.00 0.00 H ATOM 98 N ASP 164 -31.468 11.406 79.266 1.00 0.00 N ATOM 99 CA ASP 164 -31.300 12.504 80.212 1.00 0.00 C ATOM 100 C ASP 164 -30.081 12.284 81.099 1.00 0.00 C ATOM 101 O ASP 164 -29.465 13.240 81.570 1.00 0.00 O ATOM 102 CB ASP 164 -32.556 12.665 81.074 1.00 0.00 C ATOM 103 CEN ASP 164 -33.405 13.225 81.123 1.00 0.00 C ATOM 104 H ASP 164 -32.308 10.846 79.306 1.00 0.00 H ATOM 105 N GLY 165 -29.739 11.021 81.323 1.00 0.00 N ATOM 106 CA GLY 165 -28.615 10.673 82.184 1.00 0.00 C ATOM 107 C GLY 165 -27.287 11.029 81.528 1.00 0.00 C ATOM 108 O GLY 165 -26.274 11.199 82.206 1.00 0.00 O ATOM 109 CEN GLY 165 -28.614 10.673 82.184 1.00 0.00 C ATOM 110 H GLY 165 -30.270 10.281 80.885 1.00 0.00 H ATOM 111 N ASN 166 -27.299 11.143 80.204 1.00 0.00 N ATOM 112 CA ASN 166 -26.089 11.451 79.450 1.00 0.00 C ATOM 113 C ASN 166 -26.220 12.781 78.720 1.00 0.00 C ATOM 114 O ASN 166 -25.576 13.003 77.695 1.00 0.00 O ATOM 115 CB ASN 166 -25.747 10.345 78.470 1.00 0.00 C ATOM 116 CEN ASN 166 -25.161 9.475 78.446 1.00 0.00 C ATOM 117 H ASN 166 -28.168 11.010 79.706 1.00 0.00 H ATOM 118 N ILE 167 -27.060 13.663 79.252 1.00 0.00 N ATOM 119 CA ILE 167 -27.221 15.001 78.695 1.00 0.00 C ATOM 120 C ILE 167 -25.969 15.841 78.909 1.00 0.00 C ATOM 121 O ILE 167 -25.831 16.923 78.339 1.00 0.00 O ATOM 122 CB ILE 167 -28.429 15.727 79.311 1.00 0.00 C ATOM 123 CEN ILE 167 -29.507 15.881 79.247 1.00 0.00 C ATOM 124 H ILE 167 -27.600 13.400 80.064 1.00 0.00 H ATOM 125 N GLN 255 -25.059 15.338 79.735 1.00 0.00 N ATOM 126 CA GLN 255 -23.729 15.923 79.859 1.00 0.00 C ATOM 127 C GLN 255 -22.988 15.894 78.529 1.00 0.00 C ATOM 128 O GLN 255 -22.302 16.849 78.169 1.00 0.00 O ATOM 129 CB GLN 255 -22.914 15.180 80.921 1.00 0.00 C ATOM 130 CEN GLN 255 -22.355 15.230 82.575 1.00 0.00 C ATOM 131 H GLN 255 -25.294 14.529 80.293 1.00 0.00 H ATOM 132 N TYR 256 -23.132 14.792 77.802 1.00 0.00 N ATOM 133 CA TYR 256 -22.419 14.606 76.544 1.00 0.00 C ATOM 134 C TYR 256 -22.888 15.603 75.491 1.00 0.00 C ATOM 135 O TYR 256 -22.081 16.160 74.748 1.00 0.00 O ATOM 136 CB TYR 256 -22.604 13.175 76.030 1.00 0.00 C ATOM 137 CEN TYR 256 -21.758 11.642 75.978 1.00 0.00 C ATOM 138 H TYR 256 -23.751 14.063 78.129 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