####################################################### # # # 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 ( 80), selected 20 , name T0624AL285_1-D1 # Molecule2: number of CA atoms 69 ( 570), selected 20 , name T0624-D1.pdb # PARAMETERS: -3 -ie -o1 -sda -d:4 -swap T0624AL285_1-D1.lga # FIXED Atom-Atom correspondence # GDT and LCS analysis LCS - RMSD CUTOFF 5.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 17 27 - 43 4.94 7.07 LCS_AVERAGE: 24.35 LCS - RMSD CUTOFF 2.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 12 31 - 42 1.84 9.63 LCS_AVERAGE: 13.62 LCS - RMSD CUTOFF 1.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 10 32 - 41 0.99 10.12 LCS_AVERAGE: 10.36 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 F 27 F 27 3 5 17 0 3 3 4 5 6 6 7 7 9 12 13 16 17 17 18 18 19 19 19 LCS_GDT Y 28 Y 28 3 5 17 3 3 3 4 5 6 6 7 7 9 10 10 11 12 17 18 18 19 19 19 LCS_GDT G 29 G 29 4 5 17 3 3 4 4 5 6 6 6 7 10 12 13 16 17 17 18 18 19 19 19 LCS_GDT G 30 G 30 4 5 17 3 3 4 4 5 9 10 10 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT L 31 L 31 4 12 17 3 3 4 4 5 6 9 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT H 32 H 32 10 12 17 5 8 9 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT C 33 C 33 10 12 17 5 8 9 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT G 34 G 34 10 12 17 5 8 9 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT E 35 E 35 10 12 17 5 8 9 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT C 36 C 36 10 12 17 5 8 9 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT F 37 F 37 10 12 17 3 6 8 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT D 38 D 38 10 12 17 5 8 9 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT V 39 V 39 10 12 17 5 8 9 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT K 40 K 40 10 12 17 5 8 9 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT V 41 V 41 10 12 17 4 8 9 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT K 42 K 42 5 12 17 4 4 5 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT D 43 D 43 5 6 17 4 4 5 5 7 10 12 12 13 14 14 14 16 17 17 18 18 19 19 19 LCS_GDT V 44 V 44 5 6 16 4 4 5 5 5 5 7 9 10 12 13 14 15 17 17 18 18 19 19 19 LCS_GDT W 45 W 45 5 6 16 4 4 5 5 5 5 5 6 6 7 8 9 11 13 14 15 17 19 19 19 LCS_GDT V 46 V 46 5 6 15 3 3 5 5 5 5 5 6 6 6 8 8 11 11 11 12 15 15 15 15 LCS_AVERAGE LCS_A: 16.11 ( 10.36 13.62 24.35 ) 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 8 9 10 11 11 12 12 13 14 14 14 16 17 17 18 18 19 19 19 GDT PERCENT_AT 7.25 11.59 13.04 14.49 15.94 15.94 17.39 17.39 18.84 20.29 20.29 20.29 23.19 24.64 24.64 26.09 26.09 27.54 27.54 27.54 GDT RMS_LOCAL 0.32 0.54 0.76 0.99 1.27 1.27 2.01 2.01 2.36 2.90 2.90 2.90 4.55 4.89 4.89 5.19 5.19 5.68 5.68 5.68 GDT RMS_ALL_AT 10.42 10.33 10.26 10.12 9.97 9.97 9.85 9.85 9.40 8.54 8.54 8.54 7.19 6.88 6.88 6.80 6.80 6.63 6.63 6.63 # Checking swapping # Molecule1 Molecule2 DISTANCE Mis MC All Dist_max GDC_mc GDC_all LGA F 27 F 27 22.758 7 0.662 0.662 23.796 0.000 0.000 LGA Y 28 Y 28 20.723 8 0.645 0.645 21.015 0.000 0.000 LGA G 29 G 29 16.283 0 0.281 0.281 17.899 0.000 0.000 LGA G 30 G 30 9.656 0 0.135 0.135 12.367 3.690 3.690 LGA L 31 L 31 5.371 4 0.618 0.618 6.571 36.667 18.333 LGA H 32 H 32 1.547 6 0.668 0.668 2.465 75.119 30.048 LGA C 33 C 33 0.295 2 0.036 0.036 0.763 95.238 63.492 LGA G 34 G 34 1.023 0 0.066 0.066 1.406 85.952 85.952 LGA E 35 E 35 0.428 5 0.044 0.044 0.635 97.619 43.386 LGA C 36 C 36 0.402 2 0.058 0.058 0.877 95.238 63.492 LGA F 37 F 37 1.650 7 0.217 0.217 1.650 86.190 31.342 LGA D 38 D 38 1.152 4 0.107 0.107 1.152 85.952 42.976 LGA V 39 V 39 1.732 3 0.024 0.024 2.452 70.952 40.544 LGA K 40 K 40 2.600 5 0.010 0.010 2.680 60.952 27.090 LGA V 41 V 41 1.910 3 0.144 0.144 2.867 66.905 38.231 LGA K 42 K 42 2.068 5 0.462 0.462 2.528 69.048 30.688 LGA D 43 D 43 4.768 4 0.110 0.110 9.332 25.000 12.500 LGA V 44 V 44 10.132 3 0.109 0.109 10.384 2.500 1.429 LGA W 45 W 45 13.632 10 0.154 0.154 16.955 0.000 0.000 LGA V 46 V 46 16.436 3 0.025 0.025 18.237 0.000 0.000 # RMSD_GDC results: CA MC common percent ALL common percent GDC_mc GDC_all NUMBER_OF_ATOMS_AA: 20 80 80 100.00 161 80 49.69 69 SUMMARY(RMSD_GDC): 6.543 6.562 6.562 13.870 7.727 #CA N1 N2 DIST N RMSD GDT_TS LGA_S3 LGA_Q SUMMARY(GDT) 20 69 4.0 12 2.01 17.391 16.621 0.570 LGA_LOCAL RMSD: 2.007 Number of atoms: 12 under DIST: 4.00 LGA_ASGN_ATOMS RMSD: 9.853 Number of assigned atoms: 20 Std_ASGN_ATOMS RMSD: 6.543 Standard rmsd on all 20 assigned CA atoms Unitary ROTATION matrix and the SHIFT vector superimpose molecules (1=>2) X_new = 0.375858 * X + -0.883822 * Y + -0.278548 * Z + 61.298004 Y_new = 0.919301 * X + 0.317770 * Y + 0.232183 * Z + -5.676261 Z_new = -0.116694 * X + -0.343337 * Y + 0.931935 * Z + -21.304958 Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ: Phi Theta Psi [DEG: Phi Theta Psi ] XYZ: 1.182683 0.116961 -0.352984 [DEG: 67.7627 6.7014 -20.2245 ] ZXZ: -2.265661 0.371085 -2.813959 [DEG: -129.8128 21.2616 -161.2280 ] # 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: T0624AL285_1-D1 REMARK 2: T0624-D1.pdb REMARK GDT and LCS analysis REMARK FIXED Atom-Atom correspondence REMARK LGA parameters: -3 -ie -o1 -sda -d:4 -swap T0624AL285_1-D1.lga REMARK #CA N1 N2 DIST N RMSD LGA_S3 RMSD_global REMARK SUMMARY: 20 69 4.0 12 2.01 16.621 6.54 REMARK ---------------------------------------------------------- MOLECULE T0624AL285_1-D1 REMARK This file has been preprocessed by preprocess_pdbv2.1.00.100503REMARK Aligment from pdb entry: 1wc2A ATOM 1 N PHE 27 10.738 36.115 13.573 1.00 0.00 N ATOM 2 CA PHE 27 11.642 37.021 14.268 1.00 0.00 C ATOM 3 C PHE 27 11.923 36.658 15.720 1.00 0.00 C ATOM 4 O PHE 27 12.570 37.434 16.430 1.00 0.00 O ATOM 5 N TYR 28 11.450 35.487 16.158 1.00 0.00 N ATOM 6 CA TYR 28 11.507 35.051 17.557 1.00 0.00 C ATOM 7 C TYR 28 11.483 33.525 17.555 1.00 0.00 C ATOM 8 O TYR 28 10.651 32.923 16.871 1.00 0.00 O ATOM 9 N GLY 29 12.396 32.901 18.296 1.00 0.00 N ATOM 10 CA GLY 29 12.436 31.437 18.413 1.00 0.00 C ATOM 11 C GLY 29 12.457 30.757 17.042 1.00 0.00 C ATOM 12 O GLY 29 11.695 29.834 16.749 1.00 0.00 O ATOM 13 N GLY 30 13.389 31.197 16.209 1.00 0.00 N ATOM 14 CA GLY 30 13.592 30.590 14.910 1.00 0.00 C ATOM 15 C GLY 30 14.085 29.153 14.997 1.00 0.00 C ATOM 16 O GLY 30 14.670 28.730 15.993 1.00 0.00 O ATOM 17 N LEU 31 13.882 28.428 13.904 1.00 0.00 N ATOM 18 CA LEU 31 14.357 27.045 13.722 1.00 0.00 C ATOM 19 C LEU 31 15.766 26.805 14.243 1.00 0.00 C ATOM 20 O LEU 31 16.038 25.767 14.863 1.00 0.00 O ATOM 21 N HIS 32 16.679 27.719 13.923 1.00 0.00 N ATOM 22 CA HIS 32 18.093 27.498 14.181 1.00 0.00 C ATOM 23 C HIS 32 18.633 28.224 15.411 1.00 0.00 C ATOM 24 O HIS 32 19.837 28.245 15.623 1.00 0.00 O ATOM 25 N CYS 33 17.744 28.758 16.250 1.00 0.00 N ATOM 26 CA CYS 33 18.165 29.218 17.577 1.00 0.00 C ATOM 27 C CYS 33 18.870 28.087 18.335 1.00 0.00 C ATOM 28 O CYS 33 18.368 26.967 18.390 1.00 0.00 O ATOM 29 N GLY 34 20.005 28.405 18.940 1.00 0.00 N ATOM 30 CA GLY 34 20.759 27.447 19.744 1.00 0.00 C ATOM 31 C GLY 34 21.664 26.498 18.972 1.00 0.00 C ATOM 32 O GLY 34 22.384 25.695 19.586 1.00 0.00 O ATOM 33 N GLU 35 21.632 26.557 17.639 1.00 0.00 N ATOM 34 CA GLU 35 22.457 25.672 16.827 1.00 0.00 C ATOM 35 C GLU 35 23.878 26.222 16.800 1.00 0.00 C ATOM 36 O GLU 35 24.082 27.438 16.710 1.00 0.00 O ATOM 37 N CYS 36 24.861 25.322 16.869 1.00 0.00 N ATOM 38 CA CYS 36 26.265 25.707 16.757 1.00 0.00 C ATOM 39 C CYS 36 26.808 25.451 15.352 1.00 0.00 C ATOM 40 O CYS 36 26.561 24.388 14.749 1.00 0.00 O ATOM 41 N PHE 37 27.539 26.446 14.860 1.00 0.00 N ATOM 42 CA PHE 37 28.135 26.462 13.532 1.00 0.00 C ATOM 43 C PHE 37 29.647 26.632 13.676 1.00 0.00 C ATOM 44 O PHE 37 30.116 27.623 14.233 1.00 0.00 O ATOM 45 N ASP 38 30.402 25.658 13.171 1.00 0.00 N ATOM 46 CA ASP 38 31.856 25.723 13.131 1.00 0.00 C ATOM 47 C ASP 38 32.298 26.403 11.842 1.00 0.00 C ATOM 48 O ASP 38 31.948 25.948 10.742 1.00 0.00 O ATOM 49 N VAL 39 33.028 27.507 11.979 1.00 0.00 N ATOM 50 CA VAL 39 33.540 28.275 10.853 1.00 0.00 C ATOM 51 C VAL 39 35.024 28.006 10.683 1.00 0.00 C ATOM 52 O VAL 39 35.762 28.002 11.670 1.00 0.00 O ATOM 53 N LYS 40 35.457 27.794 9.442 1.00 0.00 N ATOM 54 CA LYS 40 36.866 27.624 9.094 1.00 0.00 C ATOM 55 C LYS 40 37.259 28.706 8.093 1.00 0.00 C ATOM 56 O LYS 40 36.592 28.881 7.072 1.00 0.00 O ATOM 57 N VAL 41 38.342 29.440 8.360 1.00 0.00 N ATOM 58 CA VAL 41 38.736 30.526 7.464 1.00 0.00 C ATOM 59 C VAL 41 39.291 29.974 6.156 1.00 0.00 C ATOM 60 O VAL 41 40.014 28.968 6.141 1.00 0.00 O ATOM 61 N LYS 42 38.930 30.609 5.047 1.00 0.00 N ATOM 62 CA LYS 42 39.499 30.268 3.747 1.00 0.00 C ATOM 63 C LYS 42 40.839 30.962 3.502 1.00 0.00 C ATOM 64 O LYS 42 41.596 30.539 2.626 1.00 0.00 O ATOM 65 N ASP 43 41.110 32.027 4.257 1.00 0.00 N ATOM 66 CA ASP 43 42.199 32.945 3.977 1.00 0.00 C ATOM 67 C ASP 43 41.735 34.228 3.288 1.00 0.00 C ATOM 68 O ASP 43 42.495 35.203 3.231 1.00 0.00 O ATOM 69 N VAL 44 40.515 34.234 2.743 1.00 0.00 N ATOM 70 CA VAL 44 39.971 35.387 2.036 1.00 0.00 C ATOM 71 C VAL 44 39.087 36.285 2.886 1.00 0.00 C ATOM 72 O VAL 44 38.908 36.073 4.083 1.00 0.00 O ATOM 73 N TRP 45 38.535 37.296 2.228 1.00 0.00 N ATOM 74 CA TRP 45 37.694 38.315 2.842 1.00 0.00 C ATOM 75 C TRP 45 37.084 39.140 1.699 1.00 0.00 C ATOM 76 O TRP 45 37.605 39.148 0.586 1.00 0.00 O ATOM 77 N VAL 46 35.982 39.830 1.962 1.00 0.00 N ATOM 78 CA VAL 46 35.373 40.699 0.962 1.00 0.00 C ATOM 79 C VAL 46 36.189 41.989 0.868 1.00 0.00 C ATOM 80 O VAL 46 36.384 42.647 1.895 1.00 0.00 O END ########################## # # # ACE results: # # # ########################## Number of atoms possible to evaluate: 80 MEASURES: ANGLES RMS : model <-> target (MC: PHI+PSI) DIHED RMS: ARMSMC PC NP PP TN ALL . . . . . . . . . . 76.42 44.7 38 27.9 136 ARMSMC SECONDARY STRUCTURE . . 35.09 52.9 17 23.6 72 ARMSMC SURFACE . . . . . . . . 74.73 44.4 27 27.6 98 ARMSMC BURIED . . . . . . . . 80.41 45.5 11 28.9 38 ARMSMC (SC: CHI1) DIHED RMS: ARMSSC PC NP PP TN ALL . . . . . . . . . . 0.00 0.0 0 0.0 61 ARMSSC1 RELIABLE SIDE CHAINS . 0.00 0.0 0 0.0 53 ARMSSC1 SECONDARY STRUCTURE . . 0.00 0.0 0 0.0 35 ARMSSC1 SURFACE . . . . . . . . 0.00 0.0 0 0.0 44 ARMSSC1 BURIED . . . . . . . . 0.00 0.0 0 0.0 17 ARMSSC1 (SC: CHI2) DIHED RMS: ARMSSC PC NP PP TN ALL . . . . . . . . . . 0.00 0.0 0 0.0 46 ARMSSC2 RELIABLE SIDE CHAINS . 0.00 0.0 0 0.0 37 ARMSSC2 SECONDARY STRUCTURE . . 0.00 0.0 0 0.0 26 ARMSSC2 SURFACE . . . . . . . . 0.00 0.0 0 0.0 33 ARMSSC2 BURIED . . . . . . . . 0.00 0.0 0 0.0 13 ARMSSC2 (SC: CHI3) DIHED RMS: ARMSSC PC NP PP TN ALL . . . . . . . . . . 0.00 0.0 0 0.0 16 ARMSSC3 RELIABLE SIDE CHAINS . 0.00 0.0 0 0.0 16 ARMSSC3 SECONDARY STRUCTURE . . 0.00 0.0 0 0.0 9 ARMSSC3 SURFACE . . . . . . . . 0.00 0.0 0 0.0 15 ARMSSC3 BURIED . . . . . . . . 0.00 0.0 0 0.0 1 ARMSSC3 (SC: CHI4) DIHED RMS: ARMSSC PC NP PP TN ALL . . . . . . . . . . 0.00 0.0 0 0.0 9 ARMSSC4 RELIABLE SIDE CHAINS . 0.00 0.0 0 0.0 9 ARMSSC4 SECONDARY STRUCTURE . . 0.00 0.0 0 0.0 6 ARMSSC4 SURFACE . . . . . . . . 0.00 0.0 0 0.0 9 ARMSSC4 BURIED . . . . . . . . 0.00 0.0 0 0.0 0 ARMSSC4 COORDINATES RMS : model <-> target TEST (CA) RMS = 6.54 (Number of atoms: 20) (CA) RMS: CRMSCA NP PP TN ALL . . . . . . . . . . 6.54 20 29.0 69 CRMSCA CRN = ALL/NP . . . . . 0.3271 CRMSCA SECONDARY STRUCTURE . . 7.50 9 25.0 36 CRMSCA SURFACE . . . . . . . . 6.17 14 28.0 50 CRMSCA BURIED . . . . . . . . 7.34 6 31.6 19 CRMSCA (MC) RMS: CRMSMC NP PP TN ALL . . . . . . . . . . 6.57 80 23.7 337 CRMSMC SECONDARY STRUCTURE . . 7.82 36 20.1 179 CRMSMC SURFACE . . . . . . . . 6.12 56 23.0 244 CRMSMC BURIED . . . . . . . . 7.51 24 25.8 93 CRMSMC (SC) RMS: CRMSSC NP PP TN ALL . . . . . . . . . . 0.00 0 0.0 294 CRMSSC RELIABLE SIDE CHAINS . 0.00 0 0.0 258 CRMSSC SECONDARY STRUCTURE . . 0.00 0 0.0 180 CRMSSC SURFACE . . . . . . . . 0.00 0 0.0 216 CRMSSC BURIED . . . . . . . . 0.00 0 0.0 78 CRMSSC (ALL) RMS: CRMSALL NP PP TN ALL . . . . . . . . . . 6.57 80 14.0 570 CRMSALL SECONDARY STRUCTURE . . 7.82 36 11.1 324 CRMSALL SURFACE . . . . . . . . 6.12 56 13.5 416 CRMSALL BURIED . . . . . . . . 7.51 24 15.6 154 CRMSALL Accuracy of estimates of atomic coordinate errors: model <-> target (CA) ERRORS: |D-E| |D-E|/|D+E| SR(D,E) NP PP TN ALL . . . . . . . . . . 5.990 1.000 0.500 20 29.0 69 ERRCA SECONDARY STRUCTURE . . 6.694 1.000 0.500 9 25.0 36 ERRCA SURFACE . . . . . . . . 5.995 1.000 0.500 14 28.0 50 ERRCA BURIED . . . . . . . . 5.976 1.000 0.500 6 31.6 19 ERRCA (MC) ERRORS: |D-E| |D-E|/|D+E| SR(D,E) NP PP TN ALL . . . . . . . . . . 5.916 1.000 0.500 80 23.7 337 ERRMC SECONDARY STRUCTURE . . 6.887 1.000 0.500 36 20.1 179 ERRMC SURFACE . . . . . . . . 5.858 1.000 0.500 56 23.0 244 ERRMC BURIED . . . . . . . . 6.050 1.000 0.500 24 25.8 93 ERRMC (SC) ERRORS: |D-E| |D-E|/|D+E| SR(D,E) NP PP TN ALL . . . . . . . . . . 0.000 0.000 0.000 0 0.0 294 ERRSC RELIABLE SIDE CHAINS . 0.000 0.000 0.000 0 0.0 258 ERRSC SECONDARY STRUCTURE . . 0.000 0.000 0.000 0 0.0 180 ERRSC SURFACE . . . . . . . . 0.000 0.000 0.000 0 0.0 216 ERRSC BURIED . . . . . . . . 0.000 0.000 0.000 0 0.0 78 ERRSC (ALL) ERRORS: |D-E| |D-E|/|D+E| SR(D,E) NP PP TN ALL . . . . . . . . . . 5.916 1.000 0.500 80 14.0 570 ERRALL SECONDARY STRUCTURE . . 6.887 1.000 0.500 36 11.1 324 ERRALL SURFACE . . . . . . . . 5.858 1.000 0.500 56 13.5 416 ERRALL BURIED . . . . . . . . 6.050 1.000 0.500 24 15.6 154 ERRALL DISTANCES: Percent of total atoms where distance (target <-> model) in global superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms D < 1 D < 2 D < 3 D < 5 D < 10 NP TN CA (N) 0 1 1 7 19 20 69 DISTCA CA (P) 0.00 1.45 1.45 10.14 27.54 69 DISTCA CA (RMS) 0.00 1.79 1.79 4.04 5.77 DISTCA ALL (N) 0 1 5 31 74 80 570 DISTALL ALL (P) 0.00 0.18 0.88 5.44 12.98 570 DISTALL ALL (RMS) 0.00 1.79 2.33 3.93 5.43 DISTALL END of the results output