
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   19 (  147),  selected   19 , name T0295TS193_2_2-D1
# Molecule2: number of CA atoms  180 ( 1390),  selected   19 , name T0295_D1.pdb
# PARAMETERS: T0295TS193_2_2-D1.T0295_D1.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       162 - 174         4.45    12.68
  LONGEST_CONTINUOUS_SEGMENT:    13       163 - 175         4.81    10.80
  LCS_AVERAGE:      6.96

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       166 - 173         1.84    13.16
  LCS_AVERAGE:      3.65

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       175 - 180         0.75    19.87
  LCS_AVERAGE:      2.66

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:  180
LCS_GDT     P     162     P     162      4    5   13     3    4    4    5    5    6    6    7    9    9   11   12   12   12   13   14   14   14   14   14 
LCS_GDT     P     163     P     163      4    5   13     3    4    4    5    5    6    7    9   10   10   11   12   12   12   13   14   14   14   14   14 
LCS_GDT     K     164     K     164      4    5   13     3    4    4    5    5    6    6    9   10   11   11   12   12   12   13   14   14   14   14   14 
LCS_GDT     V     165     V     165      4    5   13     3    4    4    5    5    6    6    9   10   11   11   12   12   12   13   14   14   14   14   14 
LCS_GDT     D     166     D     166      3    8   13     3    4    5    6    7    8    8    9   10   11   11   12   12   12   13   14   14   14   14   15 
LCS_GDT     S     167     S     167      5    8   13     5    5    5    6    7    8    8    9   10   11   11   12   12   12   13   14   14   14   14   15 
LCS_GDT     V     168     V     168      5    8   13     5    5    5    6    7    8    8    9   10   11   11   12   12   12   13   14   14   14   14   15 
LCS_GDT     I     169     I     169      5    8   13     5    5    5    6    7    8    8    9   10   11   11   12   12   12   13   14   14   14   14   15 
LCS_GDT     V     170     V     170      5    8   13     5    5    5    6    7    8    8    9   10   11   11   12   12   12   13   14   14   14   14   15 
LCS_GDT     K     171     K     171      5    8   13     5    5    5    6    7    8    8    9   10   11   11   12   12   12   13   14   14   14   14   15 
LCS_GDT     L     172     L     172      3    8   13     3    4    5    6    7    8    8    9   10   11   11   12   12   12   13   14   14   14   14   15 
LCS_GDT     I     173     I     173      4    8   13     3    3    5    6    7    8    8    9    9   11   11   12   12   12   13   14   14   14   14   15 
LCS_GDT     P     174     P     174      4    5   13     3    3    5    6    7    8    8    9    9   11   11   12   12   12   13   14   14   14   14   15 
LCS_GDT     K     175     K     175      6    6   13     4    5    6    6    6    6    8    9    9    9    9   10   11   11   13   14   14   14   14   15 
LCS_GDT     E     176     E     176      6    6   12     4    5    6    6    6    6    8    9    9    9    9    9   11   11   11   13   14   14   14   15 
LCS_GDT     S     177     S     177      6    6   11     4    5    6    6    6    6    8    9    9    9    9    9    9   11   11   12   12   14   14   15 
LCS_GDT     S     178     S     178      6    6   11     4    5    6    6    6    6    8    9    9    9    9    9    9   11   11   11   11   14   14   15 
LCS_GDT     F     179     F     179      6    6   11     3    5    6    6    6    6    8    9    9    9    9    9    9   11   11   11   11   14   14   15 
LCS_GDT     L     180     L     180      6    6   11     3    3    6    6    6    6    7    9    9    9    9    9    9   11   11   11   11   11   11   15 
LCS_AVERAGE  LCS_A:   4.42  (   2.66    3.65    6.96 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
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_CA      5      5      6      6      7      8      8      9     10     11     11     12     12     12     13     14     14     14     14     15 
GDT PERCENT_CA   2.78   2.78   3.33   3.33   3.89   4.44   4.44   5.00   5.56   6.11   6.11   6.67   6.67   6.67   7.22   7.78   7.78   7.78   7.78   8.33
GDT RMS_LOCAL    0.36   0.36   0.75   0.75   1.46   1.84   1.84   2.31   3.20   3.34   3.34   3.85   3.85   3.85   4.45   5.10   5.10   5.10   5.10   6.90
GDT RMS_ALL_CA  14.58  14.58  19.87  19.87  13.93  13.16  13.16  10.22  14.38  11.22  11.22  11.94  11.94  11.94  12.68  11.84  11.84  11.84  11.84   9.42

#      Molecule1      Molecule2       DISTANCE
LGA    P     162      P     162         17.975
LGA    P     163      P     163         13.548
LGA    K     164      K     164         11.505
LGA    V     165      V     165          7.679
LGA    D     166      D     166          2.643
LGA    S     167      S     167          0.970
LGA    V     168      V     168          2.161
LGA    I     169      I     169          3.236
LGA    V     170      V     170          0.849
LGA    K     171      K     171          0.872
LGA    L     172      L     172          3.737
LGA    I     173      I     173          2.007
LGA    P     174      P     174          2.336
LGA    K     175      K     175          9.714
LGA    E     176      E     176         11.910
LGA    S     177      S     177         13.960
LGA    S     178      S     178         14.939
LGA    F     179      F     179         16.486
LGA    L     180      L     180         17.661

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  180    4.0      9    2.31     4.722     4.552     0.374

LGA_LOCAL      RMSD =  2.309  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.219  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  8.204  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.011773 * X  +  -0.990438 * Y  +   0.137454 * Z  +   5.347585
  Y_new =  -0.321958 * X  +  -0.133898 * Y  +  -0.937238 * Z  + -14.363324
  Z_new =   0.946681 * X  +  -0.033220 * Y  +  -0.320456 * Z  +   3.606658 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.038297    0.103296  [ DEG:  -174.0816      5.9184 ]
  Theta =  -1.242772   -1.898820  [ DEG:   -71.2056   -108.7944 ]
  Phi   =  -1.534245    1.607348  [ DEG:   -87.9058     92.0942 ]
 
# 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: T0295TS193_2_2-D1                             
REMARK     2: T0295_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295TS193_2_2-D1.T0295_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19  180   4.0    9   2.31   4.552     8.20
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS193_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT N/A
ATOM   1272  N   PRO   162      -1.405 -10.293  -4.179  1.00  0.00
ATOM   1273  CA  PRO   162      -1.807  -9.779  -2.875  1.00  0.00
ATOM   1274  C   PRO   162      -2.873  -8.699  -3.014  1.00  0.00
ATOM   1275  O   PRO   162      -3.004  -8.074  -4.065  1.00  0.00
ATOM   1276  CB  PRO   162      -0.513  -9.214  -2.285  1.00  0.00
ATOM   1277  CG  PRO   162       0.574  -9.926  -3.018  1.00  0.00
ATOM   1278  CD  PRO   162       0.060 -10.147  -4.413  1.00  0.00
ATOM   1279  N   PRO   163      -3.634  -8.486  -1.945  1.00  0.00
ATOM   1280  CA  PRO   163      -4.556  -7.358  -1.875  1.00  0.00
ATOM   1281  C   PRO   163      -3.848  -6.047  -2.191  1.00  0.00
ATOM   1282  O   PRO   163      -2.700  -5.840  -1.799  1.00  0.00
ATOM   1283  CB  PRO   163      -5.063  -7.385  -0.431  1.00  0.00
ATOM   1284  CG  PRO   163      -4.941  -8.814  -0.019  1.00  0.00
ATOM   1285  CD  PRO   163      -3.675  -9.323  -0.648  1.00  0.00
ATOM   1286  N   LYS   164      -4.540  -5.163  -2.902  1.00  0.00
ATOM   1287  CA  LYS   164      -3.988  -3.859  -3.250  1.00  0.00
ATOM   1288  C   LYS   164      -3.632  -3.061  -2.003  1.00  0.00
ATOM   1289  O   LYS   164      -2.606  -2.382  -1.960  1.00  0.00
ATOM   1290  CB  LYS   164      -5.002  -3.047  -4.059  1.00  0.00
ATOM   1291  CG  LYS   164      -5.293  -3.616  -5.439  1.00  0.00
ATOM   1292  CD  LYS   164      -6.282  -2.746  -6.197  1.00  0.00
ATOM   1293  CE  LYS   164      -6.587  -3.325  -7.569  1.00  0.00
ATOM   1294  NZ  LYS   164      -7.567  -2.491  -8.318  1.00  0.00
ATOM   1295  N   VAL   165      -2.587  -2.358   0.289  1.00  0.00
ATOM   1296  CA  VAL   165      -3.280  -3.634   0.421  1.00  0.00
ATOM   1297  C   VAL   165      -4.386  -3.556   1.465  1.00  0.00
ATOM   1298  O   VAL   165      -4.547  -2.537   2.137  1.00  0.00
ATOM   1299  CB  VAL   165      -2.317  -4.757   0.850  1.00  0.00
ATOM   1300  CG1 VAL   165      -1.224  -4.948  -0.191  1.00  0.00
ATOM   1301  CG2 VAL   165      -1.662  -4.419   2.180  1.00  0.00
ATOM   1302  N   ASP   166      -5.147  -4.637   1.595  1.00  0.00
ATOM   1303  CA  ASP   166      -6.222  -4.703   2.578  1.00  0.00
ATOM   1304  C   ASP   166      -5.801  -4.069   3.899  1.00  0.00
ATOM   1305  O   ASP   166      -4.670  -4.247   4.350  1.00  0.00
ATOM   1306  CB  ASP   166      -6.609  -6.157   2.852  1.00  0.00
ATOM   1307  CG  ASP   166      -7.844  -6.278   3.723  1.00  0.00
ATOM   1308  OD1 ASP   166      -8.392  -5.229   4.126  1.00  0.00
ATOM   1309  OD2 ASP   166      -8.264  -7.420   4.005  1.00  0.00
ATOM   1310  N   SER   167      -4.316  -2.570   2.892  1.00  0.00
ATOM   1311  CA  SER   167      -4.652  -1.520   3.847  1.00  0.00
ATOM   1312  C   SER   167      -3.914  -1.717   5.165  1.00  0.00
ATOM   1313  O   SER   167      -4.516  -1.662   6.238  1.00  0.00
ATOM   1314  CB  SER   167      -6.154  -1.521   4.140  1.00  0.00
ATOM   1315  OG  SER   167      -6.901  -1.228   2.972  1.00  0.00
ATOM   1316  N   VAL   168      -2.609  -1.947   5.078  1.00  0.00
ATOM   1317  CA  VAL   168      -1.788  -2.160   6.264  1.00  0.00
ATOM   1318  C   VAL   168      -0.321  -1.865   5.979  1.00  0.00
ATOM   1319  O   VAL   168       0.131  -1.957   4.838  1.00  0.00
ATOM   1320  CB  VAL   168      -1.881  -3.614   6.762  1.00  0.00
ATOM   1321  CG1 VAL   168      -1.311  -4.569   5.724  1.00  0.00
ATOM   1322  CG2 VAL   168      -1.098  -3.786   8.054  1.00  0.00
ATOM   1323  N   ILE   169       0.420  -1.510   7.023  1.00  0.00
ATOM   1324  CA  ILE   169       1.849  -1.253   6.897  1.00  0.00
ATOM   1325  C   ILE   169       2.661  -2.220   7.749  1.00  0.00
ATOM   1326  O   ILE   169       2.438  -2.339   8.953  1.00  0.00
ATOM   1327  CB  ILE   169       2.208   0.175   7.349  1.00  0.00
ATOM   1328  CG1 ILE   169       1.483   1.207   6.481  1.00  0.00
ATOM   1329  CG2 ILE   169       3.706   0.412   7.229  1.00  0.00
ATOM   1330  CD1 ILE   169       1.599   2.625   6.995  1.00  0.00
ATOM   1331  N   VAL   170       3.604  -2.911   7.117  1.00  0.00
ATOM   1332  CA  VAL   170       4.420  -3.902   7.807  1.00  0.00
ATOM   1333  C   VAL   170       5.839  -3.390   8.026  1.00  0.00
ATOM   1334  O   VAL   170       6.462  -2.848   7.114  1.00  0.00
ATOM   1335  CB  VAL   170       4.519  -5.212   7.002  1.00  0.00
ATOM   1336  CG1 VAL   170       5.415  -6.211   7.718  1.00  0.00
ATOM   1337  CG2 VAL   170       3.143  -5.836   6.831  1.00  0.00
ATOM   1338  N   LYS   171       6.344  -3.568   9.242  1.00  0.00
ATOM   1339  CA  LYS   171       7.699  -3.144   9.577  1.00  0.00
ATOM   1340  C   LYS   171       8.509  -4.298  10.157  1.00  0.00
ATOM   1341  O   LYS   171       8.019  -5.050  11.001  1.00  0.00
ATOM   1342  CB  LYS   171       7.667  -2.019  10.613  1.00  0.00
ATOM   1343  CG  LYS   171       6.997  -0.745  10.125  1.00  0.00
ATOM   1344  CD  LYS   171       7.059   0.350  11.178  1.00  0.00
ATOM   1345  CE  LYS   171       6.171   0.024  12.367  1.00  0.00
ATOM   1346  NZ  LYS   171       6.271   1.056  13.435  1.00  0.00
ATOM   1347  N   LEU   172      10.055  -5.366  11.905  1.00  0.00
ATOM   1348  CA  LEU   172      10.094  -4.059  12.551  1.00  0.00
ATOM   1349  C   LEU   172      11.214  -3.198  11.983  1.00  0.00
ATOM   1350  O   LEU   172      12.370  -3.619  11.932  1.00  0.00
ATOM   1351  CB  LEU   172      10.329  -4.212  14.055  1.00  0.00
ATOM   1352  CG  LEU   172      10.309  -2.923  14.879  1.00  0.00
ATOM   1353  CD1 LEU   172       8.922  -2.297  14.863  1.00  0.00
ATOM   1354  CD2 LEU   172      10.688  -3.203  16.325  1.00  0.00
ATOM   1355  N   ILE   173      10.866  -1.988  11.556  1.00  0.00
ATOM   1356  CA  ILE   173      11.846  -1.055  11.014  1.00  0.00
ATOM   1357  C   ILE   173      12.510  -0.249  12.123  1.00  0.00
ATOM   1358  O   ILE   173      12.098  -0.312  13.281  1.00  0.00
ATOM   1359  CB  ILE   173      11.194  -0.055  10.041  1.00  0.00
ATOM   1360  CG1 ILE   173      10.573  -0.794   8.854  1.00  0.00
ATOM   1361  CG2 ILE   173      12.229   0.924   9.510  1.00  0.00
ATOM   1362  CD1 ILE   173       9.671   0.071   8.000  1.00  0.00
ATOM   1363  N   PRO   174      13.356   1.073  12.031  1.00  0.00
ATOM   1364  CA  PRO   174      12.733   2.286  12.547  1.00  0.00
ATOM   1365  C   PRO   174      11.314   2.443  12.018  1.00  0.00
ATOM   1366  O   PRO   174      11.107   2.692  10.830  1.00  0.00
ATOM   1367  CB  PRO   174      13.643   3.410  12.047  1.00  0.00
ATOM   1368  CG  PRO   174      14.972   2.759  11.858  1.00  0.00
ATOM   1369  CD  PRO   174      14.689   1.383  11.324  1.00  0.00
ATOM   1370  N   LYS   175      10.337   2.296  12.906  1.00  0.00
ATOM   1371  CA  LYS   175       8.932   2.370  12.521  1.00  0.00
ATOM   1372  C   LYS   175       8.625   3.684  11.814  1.00  0.00
ATOM   1373  O   LYS   175       7.602   3.812  11.140  1.00  0.00
ATOM   1374  CB  LYS   175       8.033   2.273  13.755  1.00  0.00
ATOM   1375  CG  LYS   175       8.111   3.478  14.677  1.00  0.00
ATOM   1376  CD  LYS   175       7.231   3.295  15.902  1.00  0.00
ATOM   1377  CE  LYS   175       7.282   4.515  16.807  1.00  0.00
ATOM   1378  NZ  LYS   175       6.424   4.349  18.013  1.00  0.00
ATOM   1379  N   GLU   176       9.514   4.658  11.972  1.00  0.00
ATOM   1380  CA  GLU   176       9.340   5.963  11.346  1.00  0.00
ATOM   1381  C   GLU   176       9.606   5.896   9.847  1.00  0.00
ATOM   1382  O   GLU   176       9.491   6.896   9.141  1.00  0.00
ATOM   1383  CB  GLU   176      10.307   6.982  11.954  1.00  0.00
ATOM   1384  CG  GLU   176      10.002   7.341  13.399  1.00  0.00
ATOM   1385  CD  GLU   176      11.075   8.211  14.022  1.00  0.00
ATOM   1386  OE1 GLU   176      12.094   8.472  13.348  1.00  0.00
ATOM   1387  OE2 GLU   176      10.898   8.633  15.184  1.00  0.00
ATOM   1388  N   SER   177       9.965   4.709   9.368  1.00  0.00
ATOM   1389  CA  SER   177      10.257   4.510   7.953  1.00  0.00
ATOM   1390  C   SER   177       9.036   3.989   7.206  1.00  0.00
ATOM   1391  O   SER   177       8.923   4.154   5.992  1.00  0.00
ATOM   1392  CB  SER   177      11.389   3.497   7.777  1.00  0.00
ATOM   1393  OG  SER   177      12.591   3.968   8.359  1.00  0.00
ATOM   1394  N   SER   178       8.123   3.360   7.939  1.00  0.00
ATOM   1395  CA  SER   178       6.925   2.785   7.342  1.00  0.00
ATOM   1396  C   SER   178       6.307   3.733   6.322  1.00  0.00
ATOM   1397  O   SER   178       6.142   3.383   5.154  1.00  0.00
ATOM   1398  CB  SER   178       5.875   2.497   8.418  1.00  0.00
ATOM   1399  OG  SER   178       5.512   3.680   9.106  1.00  0.00
ATOM   1400  N   PHE   179       5.968   4.937   6.771  1.00  0.00
ATOM   1401  CA  PHE   179       5.367   5.939   5.899  1.00  0.00
ATOM   1402  C   PHE   179       6.260   6.231   4.700  1.00  0.00
ATOM   1403  O   PHE   179       5.773   6.480   3.597  1.00  0.00
ATOM   1404  CB  PHE   179       5.148   7.249   6.659  1.00  0.00
ATOM   1405  CG  PHE   179       4.520   8.333   5.830  1.00  0.00
ATOM   1406  CD1 PHE   179       3.174   8.286   5.511  1.00  0.00
ATOM   1407  CD2 PHE   179       5.274   9.398   5.371  1.00  0.00
ATOM   1408  CE1 PHE   179       2.595   9.284   4.748  1.00  0.00
ATOM   1409  CE2 PHE   179       4.695  10.395   4.608  1.00  0.00
ATOM   1410  CZ  PHE   179       3.362  10.341   4.297  1.00  0.00
ATOM   1411  N   LEU   180       7.510   6.877   4.969  1.00  0.00
ATOM   1412  CA  LEU   180       8.503   6.329   4.054  1.00  0.00
ATOM   1413  C   LEU   180       8.779   4.861   4.356  1.00  0.00
ATOM   1414  O   LEU   180       9.298   4.523   5.419  1.00  0.00
ATOM   1415  CB  LEU   180       9.822   7.093   4.174  1.00  0.00
ATOM   1416  CG  LEU   180      10.935   6.681   3.209  1.00  0.00
ATOM   1417  CD1 LEU   180      10.533   6.968   1.770  1.00  0.00
ATOM   1418  CD2 LEU   180      12.216   7.447   3.505  1.00  0.00
TER
END
