
#######################################################
#                                                     #
#                        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_3_2-D1
# Molecule2: number of CA atoms  180 ( 1390),  selected   19 , name T0295_D1.pdb
# PARAMETERS: T0295TS193_3_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:    12       169 - 180         4.46    15.75
  LCS_AVERAGE:      6.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       162 - 168         1.41    25.45
  LCS_AVERAGE:      3.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       162 - 165         0.86    26.14
  LONGEST_CONTINUOUS_SEGMENT:     4       164 - 167         0.86    25.53
  LONGEST_CONTINUOUS_SEGMENT:     4       165 - 168         0.27    22.65
  LCS_AVERAGE:      1.87

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    7   10     3    4    6    6    7    7    8    8    8    8    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     P     163     P     163      4    7   10     3    3    4    6    7    7    8    8    8    8    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     K     164     K     164      4    7   10     3    4    6    6    7    7    8    8    8    8    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     V     165     V     165      4    7   10     4    4    6    6    7    7    8    8    8    8    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     D     166     D     166      4    7   10     4    4    6    6    7    7    8    8    8    8    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     S     167     S     167      4    7   10     4    4    6    6    7    7    8    8    8    8    9    9    9   10   10   11   11   12   14   14 
LCS_GDT     V     168     V     168      4    7   11     4    4    6    6    7    7    8    8    8    8    9   10   10   10   11   13   13   13   14   14 
LCS_GDT     I     169     I     169      3    6   12     3    3    4    4    6    6    8    8    8    8    9   10   12   12   12   13   13   13   14   14 
LCS_GDT     V     170     V     170      3    5   12     3    3    4    4    4    5    6    7    9   10   11   11   12   12   12   13   13   13   14   14 
LCS_GDT     K     171     K     171      3    5   12     3    3    4    4    4    5    6    7    9   10   11   11   12   12   12   13   13   13   14   14 
LCS_GDT     L     172     L     172      3    5   12     3    3    4    4    4    5    6    7    9   10   11   11   12   12   12   13   13   13   14   14 
LCS_GDT     I     173     I     173      3    5   12     3    3    4    4    4    5    6    7    8    9   11   11   12   12   12   13   13   13   14   14 
LCS_GDT     P     174     P     174      3    5   12     2    3    4    4    5    5    6    7    9   10   11   11   12   12   12   13   13   13   14   14 
LCS_GDT     K     175     K     175      3    5   12     2    3    3    4    5    5    6    7    9   10   11   11   12   12   12   13   13   13   14   14 
LCS_GDT     E     176     E     176      3    5   12     3    3    3    4    5    5    6    7    9   10   11   11   12   12   12   13   13   13   14   14 
LCS_GDT     S     177     S     177      3    5   12     3    3    3    4    5    5    6    7    9   10   11   11   12   12   12   13   13   13   14   14 
LCS_GDT     S     178     S     178      3    5   12     3    3    4    4    5    5    5    7    9   10   11   11   12   12   12   13   13   13   14   14 
LCS_GDT     F     179     F     179      3    4   12     2    3    4    4    5    5    6    7    9   10   11   11   12   12   12   13   13   13   14   14 
LCS_GDT     L     180     L     180      3    4   12     2    3    4    4    5    5    6    7    9   10   11   11   12   12   12   13   13   13   14   14 
LCS_AVERAGE  LCS_A:   3.77  (   1.87    3.16    6.29 )

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      4      4      6      6      7      7      8      8      9     10     11     11     12     12     12     13     13     13     14     14 
GDT PERCENT_CA   2.22   2.22   3.33   3.33   3.89   3.89   4.44   4.44   5.00   5.56   6.11   6.11   6.67   6.67   6.67   7.22   7.22   7.22   7.78   7.78
GDT RMS_LOCAL    0.27   0.27   1.18   1.18   1.41   1.41   2.13   2.13   3.31   3.65   3.91   3.91   4.46   4.46   4.46   5.37   5.37   5.37   6.15   6.15
GDT RMS_ALL_CA  22.65  22.65  25.26  25.26  25.45  25.45  24.30  24.30  18.72  16.93  16.83  16.83  15.75  15.75  15.75  13.58  13.58  13.58  12.62  12.62

#      Molecule1      Molecule2       DISTANCE
LGA    P     162      P     162          1.654
LGA    P     163      P     163          2.319
LGA    K     164      K     164          1.950
LGA    V     165      V     165          0.422
LGA    D     166      D     166          2.034
LGA    S     167      S     167          1.946
LGA    V     168      V     168          2.027
LGA    I     169      I     169          3.497
LGA    V     170      V     170         10.003
LGA    K     171      K     171         14.074
LGA    L     172      L     172         19.899
LGA    I     173      I     173         26.142
LGA    P     174      P     174         27.313
LGA    K     175      K     175         27.450
LGA    E     176      E     176         33.972
LGA    S     177      S     177         38.964
LGA    S     178      S     178         38.442
LGA    F     179      F     179         42.075
LGA    L     180      L     180         48.827

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  180    4.0      8    2.13     4.306     4.215     0.358

LGA_LOCAL      RMSD =  2.132  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 24.298  Number of atoms =   19 
Std_ALL_ATOMS  RMSD = 10.455  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.644384 * X  +   0.078727 * Y  +  -0.760639 * Z  +  -5.420593
  Y_new =  -0.570381 * X  +  -0.613052 * Y  +  -0.546656 * Z  +  -2.101168
  Z_new =  -0.509348 * X  +   0.786110 * Y  +  -0.350136 * Z  +   2.959963 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.989821   -1.151772  [ DEG:   114.0084    -65.9916 ]
  Theta =   0.534427    2.607166  [ DEG:    30.6204    149.3796 ]
  Phi   =  -0.724554    2.417039  [ DEG:   -41.5139    138.4861 ]
 
# 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_3_2-D1                             
REMARK     2: T0295_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295TS193_3_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    8   2.13   4.215    10.45
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS193_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT N/A
ATOM   1272  N   PRO   162     -14.980  -1.411   7.490  1.00  0.00
ATOM   1273  CA  PRO   162     -14.257  -2.256   6.548  1.00  0.00
ATOM   1274  C   PRO   162     -13.820  -1.467   5.321  1.00  0.00
ATOM   1275  O   PRO   162     -14.590  -0.680   4.770  1.00  0.00
ATOM   1276  CB  PRO   162     -15.265  -3.347   6.179  1.00  0.00
ATOM   1277  CG  PRO   162     -16.195  -3.404   7.344  1.00  0.00
ATOM   1278  CD  PRO   162     -16.356  -1.987   7.820  1.00  0.00
ATOM   1279  N   PRO   163     -12.578  -1.678   4.899  1.00  0.00
ATOM   1280  CA  PRO   163     -12.040  -0.996   3.728  1.00  0.00
ATOM   1281  C   PRO   163     -12.604  -1.583   2.440  1.00  0.00
ATOM   1282  O   PRO   163     -12.792  -2.795   2.329  1.00  0.00
ATOM   1283  CB  PRO   163     -10.530  -1.221   3.829  1.00  0.00
ATOM   1284  CG  PRO   163     -10.293  -1.518   5.271  1.00  0.00
ATOM   1285  CD  PRO   163     -11.493  -2.289   5.742  1.00  0.00
ATOM   1286  N   LYS   164     -12.873  -0.717   1.470  1.00  0.00
ATOM   1287  CA  LYS   164     -13.405  -1.148   0.183  1.00  0.00
ATOM   1288  C   LYS   164     -12.674  -0.474  -0.970  1.00  0.00
ATOM   1289  O   LYS   164     -12.359   0.714  -0.908  1.00  0.00
ATOM   1290  CB  LYS   164     -14.891  -0.798   0.072  1.00  0.00
ATOM   1291  CG  LYS   164     -15.775  -1.516   1.077  1.00  0.00
ATOM   1292  CD  LYS   164     -17.239  -1.161   0.877  1.00  0.00
ATOM   1293  CE  LYS   164     -18.118  -1.836   1.918  1.00  0.00
ATOM   1294  NZ  LYS   164     -19.558  -1.513   1.723  1.00  0.00
ATOM   1295  N   VAL   165     -10.332   1.399  -0.214  1.00  0.00
ATOM   1296  CA  VAL   165      -9.834   0.051   0.030  1.00  0.00
ATOM   1297  C   VAL   165      -9.236  -0.071   1.426  1.00  0.00
ATOM   1298  O   VAL   165      -8.869   0.928   2.043  1.00  0.00
ATOM   1299  CB  VAL   165      -8.738  -0.337  -0.980  1.00  0.00
ATOM   1300  CG1 VAL   165      -9.289  -0.318  -2.397  1.00  0.00
ATOM   1301  CG2 VAL   165      -7.574   0.638  -0.904  1.00  0.00
ATOM   1302  N   ASP   166      -9.142  -1.302   1.917  1.00  0.00
ATOM   1303  CA  ASP   166      -8.512  -1.566   3.206  1.00  0.00
ATOM   1304  C   ASP   166      -7.026  -1.236   3.172  1.00  0.00
ATOM   1305  O   ASP   166      -6.366  -1.407   2.147  1.00  0.00
ATOM   1306  CB  ASP   166      -8.662  -3.041   3.583  1.00  0.00
ATOM   1307  CG  ASP   166      -8.114  -3.348   4.963  1.00  0.00
ATOM   1308  OD1 ASP   166      -8.705  -2.874   5.957  1.00  0.00
ATOM   1309  OD2 ASP   166      -7.092  -4.062   5.051  1.00  0.00
ATOM   1310  N   SER   167      -6.504  -0.763   4.298  1.00  0.00
ATOM   1311  CA  SER   167      -5.084  -0.451   4.413  1.00  0.00
ATOM   1312  C   SER   167      -4.422  -1.295   5.494  1.00  0.00
ATOM   1313  O   SER   167      -5.098  -1.944   6.292  1.00  0.00
ATOM   1314  CB  SER   167      -4.887   1.023   4.775  1.00  0.00
ATOM   1315  OG  SER   167      -5.393   1.870   3.757  1.00  0.00
ATOM   1316  N   VAL   168      -3.113  -2.506   7.191  1.00  0.00
ATOM   1317  CA  VAL   168      -2.378  -2.359   5.939  1.00  0.00
ATOM   1318  C   VAL   168      -1.950  -3.715   5.390  1.00  0.00
ATOM   1319  O   VAL   168      -1.730  -3.867   4.189  1.00  0.00
ATOM   1320  CB  VAL   168      -1.106  -1.512   6.128  1.00  0.00
ATOM   1321  CG1 VAL   168      -1.465  -0.113   6.604  1.00  0.00
ATOM   1322  CG2 VAL   168      -0.189  -2.151   7.160  1.00  0.00
ATOM   1323  N   ILE   169      -1.834  -4.698   6.277  1.00  0.00
ATOM   1324  CA  ILE   169      -1.408  -6.036   5.887  1.00  0.00
ATOM   1325  C   ILE   169      -2.585  -7.002   5.859  1.00  0.00
ATOM   1326  O   ILE   169      -3.001  -7.459   4.794  1.00  0.00
ATOM   1327  CB  ILE   169      -0.364  -6.604   6.866  1.00  0.00
ATOM   1328  CG1 ILE   169       0.889  -5.725   6.879  1.00  0.00
ATOM   1329  CG2 ILE   169       0.039  -8.012   6.458  1.00  0.00
ATOM   1330  CD1 ILE   169       1.895  -6.111   7.941  1.00  0.00
ATOM   1331  N   VAL   170      -3.118  -7.312   7.036  1.00  0.00
ATOM   1332  CA  VAL   170      -4.200  -8.282   7.157  1.00  0.00
ATOM   1333  C   VAL   170      -5.311  -7.993   6.155  1.00  0.00
ATOM   1334  O   VAL   170      -5.664  -8.847   5.342  1.00  0.00
ATOM   1335  CB  VAL   170      -4.826  -8.257   8.564  1.00  0.00
ATOM   1336  CG1 VAL   170      -6.015  -9.202   8.634  1.00  0.00
ATOM   1337  CG2 VAL   170      -3.806  -8.687   9.607  1.00  0.00
ATOM   1338  N   LYS   171      -3.852 -10.164   5.124  1.00  0.00
ATOM   1339  CA  LYS   171      -3.591  -9.767   3.746  1.00  0.00
ATOM   1340  C   LYS   171      -4.740 -10.170   2.829  1.00  0.00
ATOM   1341  O   LYS   171      -5.146  -9.406   1.954  1.00  0.00
ATOM   1342  CB  LYS   171      -2.315 -10.434   3.229  1.00  0.00
ATOM   1343  CG  LYS   171      -1.045  -9.956   3.912  1.00  0.00
ATOM   1344  CD  LYS   171       0.184 -10.637   3.331  1.00  0.00
ATOM   1345  CE  LYS   171       1.454 -10.173   4.028  1.00  0.00
ATOM   1346  NZ  LYS   171       2.665 -10.843   3.478  1.00  0.00
ATOM   1347  N   LEU   172      -4.499 -11.334   0.989  1.00  0.00
ATOM   1348  CA  LEU   172      -3.634 -10.684   0.011  1.00  0.00
ATOM   1349  C   LEU   172      -4.448 -10.068  -1.120  1.00  0.00
ATOM   1350  O   LEU   172      -3.978  -9.170  -1.819  1.00  0.00
ATOM   1351  CB  LEU   172      -2.663 -11.696  -0.601  1.00  0.00
ATOM   1352  CG  LEU   172      -1.602 -12.271   0.340  1.00  0.00
ATOM   1353  CD1 LEU   172      -0.797 -13.356  -0.358  1.00  0.00
ATOM   1354  CD2 LEU   172      -0.641 -11.184   0.796  1.00  0.00
ATOM   1355  N   ILE   173      -5.671 -10.556  -1.296  1.00  0.00
ATOM   1356  CA  ILE   173      -6.524 -10.108  -2.390  1.00  0.00
ATOM   1357  C   ILE   173      -6.682  -8.594  -2.383  1.00  0.00
ATOM   1358  O   ILE   173      -6.844  -7.972  -3.432  1.00  0.00
ATOM   1359  CB  ILE   173      -7.934 -10.720  -2.294  1.00  0.00
ATOM   1360  CG1 ILE   173      -8.709 -10.482  -3.591  1.00  0.00
ATOM   1361  CG2 ILE   173      -8.710 -10.093  -1.146  1.00  0.00
ATOM   1362  CD1 ILE   173      -8.117 -11.183  -4.794  1.00  0.00
ATOM   1363  N   PRO   174      -6.633  -8.005  -1.192  1.00  0.00
ATOM   1364  CA  PRO   174      -6.787  -6.563  -1.044  1.00  0.00
ATOM   1365  C   PRO   174      -5.604  -5.818  -1.650  1.00  0.00
ATOM   1366  O   PRO   174      -5.706  -4.635  -1.978  1.00  0.00
ATOM   1367  CB  PRO   174      -6.862  -6.352   0.470  1.00  0.00
ATOM   1368  CG  PRO   174      -7.273  -7.680   1.011  1.00  0.00
ATOM   1369  CD  PRO   174      -6.669  -8.708   0.097  1.00  0.00
ATOM   1370  N   LYS   175      -4.484  -6.516  -1.798  1.00  0.00
ATOM   1371  CA  LYS   175      -3.269  -5.913  -2.332  1.00  0.00
ATOM   1372  C   LYS   175      -3.148  -6.152  -3.831  1.00  0.00
ATOM   1373  O   LYS   175      -2.116  -5.856  -4.434  1.00  0.00
ATOM   1374  CB  LYS   175      -2.033  -6.509  -1.655  1.00  0.00
ATOM   1375  CG  LYS   175      -1.943  -6.223  -0.165  1.00  0.00
ATOM   1376  CD  LYS   175      -0.647  -6.758   0.422  1.00  0.00
ATOM   1377  CE  LYS   175      -0.533  -6.427   1.901  1.00  0.00
ATOM   1378  NZ  LYS   175       0.707  -6.990   2.503  1.00  0.00
ATOM   1379  N   GLU   176      -4.262  -5.183  -4.523  1.00  0.00
ATOM   1380  CA  GLU   176      -4.541  -5.856  -5.786  1.00  0.00
ATOM   1381  C   GLU   176      -5.973  -5.603  -6.241  1.00  0.00
ATOM   1382  O   GLU   176      -6.800  -5.111  -5.473  1.00  0.00
ATOM   1383  CB  GLU   176      -4.350  -7.367  -5.642  1.00  0.00
ATOM   1384  CG  GLU   176      -2.902  -7.795  -5.463  1.00  0.00
ATOM   1385  CD  GLU   176      -2.024  -7.376  -6.626  1.00  0.00
ATOM   1386  OE1 GLU   176      -2.316  -7.785  -7.770  1.00  0.00
ATOM   1387  OE2 GLU   176      -1.044  -6.637  -6.395  1.00  0.00
ATOM   1388  N   SER   177      -6.260  -5.945  -7.492  1.00  0.00
ATOM   1389  CA  SER   177      -7.626  -5.917  -7.999  1.00  0.00
ATOM   1390  C   SER   177      -8.524  -6.863  -7.213  1.00  0.00
ATOM   1391  O   SER   177      -8.090  -7.932  -6.781  1.00  0.00
ATOM   1392  CB  SER   177      -7.661  -6.341  -9.468  1.00  0.00
ATOM   1393  OG  SER   177      -8.991  -6.390  -9.954  1.00  0.00
ATOM   1394  N   SER   178      -9.779  -6.465  -7.030  1.00  0.00
ATOM   1395  CA  SER   178     -10.707  -7.217  -6.194  1.00  0.00
ATOM   1396  C   SER   178     -10.943  -8.616  -6.751  1.00  0.00
ATOM   1397  O   SER   178     -10.884  -8.829  -7.962  1.00  0.00
ATOM   1398  CB  SER   178     -12.059  -6.503  -6.118  1.00  0.00
ATOM   1399  OG  SER   178     -12.708  -6.504  -7.378  1.00  0.00
ATOM   1400  N   PHE   179     -11.209  -9.565  -5.861  1.00  0.00
ATOM   1401  CA  PHE   179     -11.535 -10.926  -6.266  1.00  0.00
ATOM   1402  C   PHE   179     -12.819 -10.964  -7.085  1.00  0.00
ATOM   1403  O   PHE   179     -13.777 -10.249  -6.790  1.00  0.00
ATOM   1404  CB  PHE   179     -11.728 -11.819  -5.039  1.00  0.00
ATOM   1405  CG  PHE   179     -10.455 -12.115  -4.298  1.00  0.00
ATOM   1406  CD1 PHE   179      -9.230 -11.741  -4.823  1.00  0.00
ATOM   1407  CD2 PHE   179     -10.483 -12.765  -3.077  1.00  0.00
ATOM   1408  CE1 PHE   179      -8.059 -12.013  -4.140  1.00  0.00
ATOM   1409  CE2 PHE   179      -9.312 -13.037  -2.395  1.00  0.00
ATOM   1410  CZ  PHE   179      -8.103 -12.663  -2.922  1.00  0.00
ATOM   1411  N   LEU   180     -12.834 -11.804  -8.115  1.00  0.00
ATOM   1412  CA  LEU   180     -13.971 -11.881  -9.025  1.00  0.00
ATOM   1413  C   LEU   180     -14.551 -13.288  -9.065  1.00  0.00
ATOM   1414  O   LEU   180     -15.502 -13.558  -9.798  1.00  0.00
ATOM   1415  CB  LEU   180     -13.546 -11.503 -10.446  1.00  0.00
ATOM   1416  CG  LEU   180     -13.019 -10.079 -10.640  1.00  0.00
ATOM   1417  CD1 LEU   180     -12.476  -9.894 -12.048  1.00  0.00
ATOM   1418  CD2 LEU   180     -14.129  -9.062 -10.420  1.00  0.00
TER
END
