
#######################################################
#                                                     #
#                        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_5_2-D1
# Molecule2: number of CA atoms  180 ( 1390),  selected   19 , name T0295_D1.pdb
# PARAMETERS: T0295TS193_5_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:    14       167 - 180         4.68    10.65
  LCS_AVERAGE:      6.96

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       171 - 177         1.92    15.62
  LCS_AVERAGE:      2.98

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       172 - 176         0.60    15.79
  LCS_AVERAGE:      1.99

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      3    4    8     3    3    3    4    4    4    6    7    7    7    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     P     163     P     163      3    5    8     3    3    3    4    5    5    6    7    7    7    8    8    8    8    8    8    8    9    9   10 
LCS_GDT     K     164     K     164      3    5    8     3    3    3    4    5    5    6    7    7    7    8    8    8    8    8    8    8    9    9   10 
LCS_GDT     V     165     V     165      3    5    8     0    3    3    4    5    5    6    7    7    7    8    8    8    8    9   11   12   14   16   16 
LCS_GDT     D     166     D     166      3    5   10     3    3    3    4    5    5    6    7    7    8    9   10   11   13   15   15   15   15   16   16 
LCS_GDT     S     167     S     167      3    5   14     3    3    3    4    5    5    6    7    7    8   10   13   14   14   15   15   15   15   16   16 
LCS_GDT     V     168     V     168      3    4   14     3    3    3    4    4    4    6    7    7    8   10   13   14   14   15   15   15   15   16   16 
LCS_GDT     I     169     I     169      3    4   14     3    3    3    4    4    4    5    6    7    8   10   13   14   14   15   15   15   15   16   16 
LCS_GDT     V     170     V     170      3    3   14     0    3    3    3    4    6    8    9   10   11   11   13   14   14   15   15   15   15   16   16 
LCS_GDT     K     171     K     171      4    7   14     1    4    6    7    7    7    8    9   10   11   11   13   14   14   15   15   15   15   16   16 
LCS_GDT     L     172     L     172      5    7   14     4    5    5    7    7    7    8    9   10   11   11   13   14   14   15   15   15   15   16   16 
LCS_GDT     I     173     I     173      5    7   14     4    5    6    7    7    7    8    9   10   11   11   13   14   14   15   15   15   15   16   16 
LCS_GDT     P     174     P     174      5    7   14     4    5    6    7    7    7    8    9   10   11   11   13   14   14   15   15   15   15   16   16 
LCS_GDT     K     175     K     175      5    7   14     4    5    6    7    7    7    8    9   10   11   11   12   14   14   15   15   15   15   16   16 
LCS_GDT     E     176     E     176      5    7   14     3    5    6    7    7    7    8    9   10   11   11   13   14   14   15   15   15   15   16   16 
LCS_GDT     S     177     S     177      3    7   14     3    3    3    5    6    7    8    9   10   11   11   13   14   14   15   15   15   15   16   16 
LCS_GDT     S     178     S     178      3    5   14     3    3    3    4    5    7    8    9   10   11   11   13   14   14   15   15   15   15   16   16 
LCS_GDT     F     179     F     179      3    5   14     1    3    3    4    5    6    8    9   10   11   11   13   14   14   15   15   15   15   16   16 
LCS_GDT     L     180     L     180      3    3   14     3    4    6    7    7    7    8    9   10   11   11   13   14   14   15   15   15   15   16   16 
LCS_AVERAGE  LCS_A:   3.98  (   1.99    2.98    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      4      5      6      7      7      7      8      9     10     11     11     13     14     14     15     15     15     15     16     16 
GDT PERCENT_CA   2.22   2.78   3.33   3.89   3.89   3.89   4.44   5.00   5.56   6.11   6.11   7.22   7.78   7.78   8.33   8.33   8.33   8.33   8.89   8.89
GDT RMS_LOCAL    0.19   0.60   0.95   1.20   1.20   1.20   2.15   2.55   2.86   3.25   3.25   4.52   4.68   4.68   5.03   5.03   5.03   5.03   5.70   5.70
GDT RMS_ALL_CA  15.86  15.79  14.88  15.18  15.18  15.18  14.21  14.48  13.90  12.11  12.11  10.49  10.65  10.65  10.38  10.38  10.38  10.38  10.15  10.15

#      Molecule1      Molecule2       DISTANCE
LGA    P     162      P     162         31.866
LGA    P     163      P     163         26.569
LGA    K     164      K     164         26.299
LGA    V     165      V     165         19.993
LGA    D     166      D     166         18.853
LGA    S     167      S     167         14.789
LGA    V     168      V     168         13.111
LGA    I     169      I     169         12.387
LGA    V     170      V     170          7.881
LGA    K     171      K     171          1.197
LGA    L     172      L     172          2.885
LGA    I     173      I     173          1.144
LGA    P     174      P     174          0.828
LGA    K     175      K     175          3.400
LGA    E     176      E     176          2.861
LGA    S     177      S     177          3.227
LGA    S     178      S     178          4.380
LGA    F     179      F     179          3.729
LGA    L     180      L     180          2.726

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  180    4.0      9    2.55     5.000     4.522     0.339

LGA_LOCAL      RMSD =  2.554  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.247  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  9.471  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.914092 * X  +  -0.373359 * Y  +  -0.158234 * Z  +  25.605324
  Y_new =  -0.356185 * X  +  -0.552749 * Y  +  -0.753393 * Z  +  -0.001701
  Z_new =   0.193822 * X  +   0.745031 * Y  +  -0.638249 * Z  +   4.752561 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.279152   -0.862440  [ DEG:   130.5858    -49.4142 ]
  Theta =  -0.195057   -2.946536  [ DEG:   -11.1759   -168.8241 ]
  Phi   =  -0.371561    2.770032  [ DEG:   -21.2889    158.7111 ]
 
# 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_5_2-D1                             
REMARK     2: T0295_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295TS193_5_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   2.55   4.522     9.47
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS193_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT N/A
ATOM   1272  N   PRO   162      16.985  -0.202   7.473  1.00  0.00
ATOM   1273  CA  PRO   162      16.024  -0.342   6.386  1.00  0.00
ATOM   1274  C   PRO   162      14.846  -1.214   6.800  1.00  0.00
ATOM   1275  O   PRO   162      15.015  -2.390   7.124  1.00  0.00
ATOM   1276  CB  PRO   162      16.831  -0.991   5.260  1.00  0.00
ATOM   1277  CG  PRO   162      18.245  -0.612   5.546  1.00  0.00
ATOM   1278  CD  PRO   162      18.382  -0.618   7.044  1.00  0.00
ATOM   1279  N   PRO   163      13.651  -0.633   6.786  1.00  0.00
ATOM   1280  CA  PRO   163      12.431  -1.383   7.056  1.00  0.00
ATOM   1281  C   PRO   163      12.261  -2.531   6.069  1.00  0.00
ATOM   1282  O   PRO   163      12.635  -2.420   4.901  1.00  0.00
ATOM   1283  CB  PRO   163      11.318  -0.345   6.903  1.00  0.00
ATOM   1284  CG  PRO   163      11.991   0.964   7.144  1.00  0.00
ATOM   1285  CD  PRO   163      13.370   0.837   6.559  1.00  0.00
ATOM   1286  N   LYS   164      11.695  -3.634   6.545  1.00  0.00
ATOM   1287  CA  LYS   164      11.379  -4.768   5.683  1.00  0.00
ATOM   1288  C   LYS   164      10.047  -5.397   6.065  1.00  0.00
ATOM   1289  O   LYS   164       9.493  -5.106   7.125  1.00  0.00
ATOM   1290  CB  LYS   164      12.461  -5.844   5.795  1.00  0.00
ATOM   1291  CG  LYS   164      13.813  -5.425   5.241  1.00  0.00
ATOM   1292  CD  LYS   164      14.812  -6.569   5.302  1.00  0.00
ATOM   1293  CE  LYS   164      16.164  -6.151   4.746  1.00  0.00
ATOM   1294  NZ  LYS   164      17.162  -7.253   4.825  1.00  0.00
ATOM   1295  N   VAL   165       9.300  -5.760   4.982  1.00  0.00
ATOM   1296  CA  VAL   165       8.165  -6.641   5.224  1.00  0.00
ATOM   1297  C   VAL   165       8.569  -8.105   5.110  1.00  0.00
ATOM   1298  O   VAL   165       8.966  -8.567   4.040  1.00  0.00
ATOM   1299  CB  VAL   165       7.031  -6.393   4.212  1.00  0.00
ATOM   1300  CG1 VAL   165       5.881  -7.360   4.451  1.00  0.00
ATOM   1301  CG2 VAL   165       6.500  -4.974   4.344  1.00  0.00
ATOM   1302  N   ASP   166       8.466  -8.832   6.217  1.00  0.00
ATOM   1303  CA  ASP   166       8.940 -10.209   6.277  1.00  0.00
ATOM   1304  C   ASP   166       7.778 -11.189   6.382  1.00  0.00
ATOM   1305  O   ASP   166       6.782 -10.916   7.053  1.00  0.00
ATOM   1306  CB  ASP   166       9.844 -10.412   7.496  1.00  0.00
ATOM   1307  CG  ASP   166      10.513 -11.772   7.505  1.00  0.00
ATOM   1308  OD1 ASP   166      10.466 -12.464   6.466  1.00  0.00
ATOM   1309  OD2 ASP   166      11.084 -12.146   8.551  1.00  0.00
ATOM   1310  N   SER   167       8.125  -9.819   8.487  1.00  0.00
ATOM   1311  CA  SER   167       7.045  -9.451   9.393  1.00  0.00
ATOM   1312  C   SER   167       7.235  -8.039   9.933  1.00  0.00
ATOM   1313  O   SER   167       8.356  -7.622  10.223  1.00  0.00
ATOM   1314  CB  SER   167       6.994 -10.411  10.583  1.00  0.00
ATOM   1315  OG  SER   167       6.703 -11.732  10.162  1.00  0.00
ATOM   1316  N   VAL   168       8.149  -9.062  11.939  1.00  0.00
ATOM   1317  CA  VAL   168       7.883  -8.022  12.926  1.00  0.00
ATOM   1318  C   VAL   168       9.079  -7.092  13.082  1.00  0.00
ATOM   1319  O   VAL   168       8.922  -5.875  13.178  1.00  0.00
ATOM   1320  CB  VAL   168       7.579  -8.623  14.311  1.00  0.00
ATOM   1321  CG1 VAL   168       7.502  -7.527  15.362  1.00  0.00
ATOM   1322  CG2 VAL   168       6.251  -9.364  14.291  1.00  0.00
ATOM   1323  N   ILE   169      10.275  -7.671  13.105  1.00  0.00
ATOM   1324  CA  ILE   169      11.501  -6.893  13.220  1.00  0.00
ATOM   1325  C   ILE   169      11.740  -6.052  11.972  1.00  0.00
ATOM   1326  O   ILE   169      12.260  -4.938  12.052  1.00  0.00
ATOM   1327  CB  ILE   169      12.730  -7.801  13.410  1.00  0.00
ATOM   1328  CG1 ILE   169      13.922  -6.986  13.915  1.00  0.00
ATOM   1329  CG2 ILE   169      13.117  -8.455  12.092  1.00  0.00
ATOM   1330  CD1 ILE   169      15.081  -7.833  14.396  1.00  0.00
ATOM   1331  N   VAL   170      11.357  -6.591  10.820  1.00  0.00
ATOM   1332  CA  VAL   170      11.450  -5.857   9.563  1.00  0.00
ATOM   1333  C   VAL   170      10.465  -4.696   9.529  1.00  0.00
ATOM   1334  O   VAL   170      10.792  -3.606   9.059  1.00  0.00
ATOM   1335  CB  VAL   170      11.141  -6.764   8.358  1.00  0.00
ATOM   1336  CG1 VAL   170      11.058  -5.941   7.081  1.00  0.00
ATOM   1337  CG2 VAL   170      12.231  -7.810   8.184  1.00  0.00
ATOM   1338  N   LYS   171       9.258  -4.936  10.029  1.00  0.00
ATOM   1339  CA  LYS   171       8.289  -3.867  10.238  1.00  0.00
ATOM   1340  C   LYS   171       8.844  -2.794  11.167  1.00  0.00
ATOM   1341  O   LYS   171       8.819  -1.607  10.843  1.00  0.00
ATOM   1342  CB  LYS   171       7.007  -4.420  10.864  1.00  0.00
ATOM   1343  CG  LYS   171       5.922  -3.377  11.079  1.00  0.00
ATOM   1344  CD  LYS   171       4.655  -4.006  11.637  1.00  0.00
ATOM   1345  CE  LYS   171       3.587  -2.957  11.898  1.00  0.00
ATOM   1346  NZ  LYS   171       2.348  -3.556  12.468  1.00  0.00
ATOM   1347  N   LEU   172       9.343  -3.219  12.322  1.00  0.00
ATOM   1348  CA  LEU   172       9.909  -2.296  13.298  1.00  0.00
ATOM   1349  C   LEU   172      11.150  -1.604  12.746  1.00  0.00
ATOM   1350  O   LEU   172      11.320  -0.396  12.903  1.00  0.00
ATOM   1351  CB  LEU   172      10.309  -3.042  14.573  1.00  0.00
ATOM   1352  CG  LEU   172       9.163  -3.583  15.430  1.00  0.00
ATOM   1353  CD1 LEU   172       9.699  -4.452  16.558  1.00  0.00
ATOM   1354  CD2 LEU   172       8.367  -2.442  16.045  1.00  0.00
ATOM   1355  N   ILE   173      12.014  -2.379  12.098  1.00  0.00
ATOM   1356  CA  ILE   173      13.227  -1.837  11.497  1.00  0.00
ATOM   1357  C   ILE   173      12.897  -0.821  10.411  1.00  0.00
ATOM   1358  O   ILE   173      13.543   0.221  10.305  1.00  0.00
ATOM   1359  CB  ILE   173      14.081  -2.945  10.852  1.00  0.00
ATOM   1360  CG1 ILE   173      14.524  -3.959  11.908  1.00  0.00
ATOM   1361  CG2 ILE   173      15.321  -2.351  10.203  1.00  0.00
ATOM   1362  CD1 ILE   173      15.189  -5.190  11.331  1.00  0.00
ATOM   1363  N   PRO   174      14.334   0.220  12.412  1.00  0.00
ATOM   1364  CA  PRO   174      14.684   1.635  12.400  1.00  0.00
ATOM   1365  C   PRO   174      15.796   1.919  11.397  1.00  0.00
ATOM   1366  O   PRO   174      16.750   1.152  11.280  1.00  0.00
ATOM   1367  CB  PRO   174      15.139   1.916  13.833  1.00  0.00
ATOM   1368  CG  PRO   174      14.453   0.876  14.653  1.00  0.00
ATOM   1369  CD  PRO   174      14.436  -0.372  13.817  1.00  0.00
ATOM   1370  N   LYS   175      15.665   3.027  10.675  1.00  0.00
ATOM   1371  CA  LYS   175      16.656   3.412   9.676  1.00  0.00
ATOM   1372  C   LYS   175      18.055   3.458  10.278  1.00  0.00
ATOM   1373  O   LYS   175      19.042   3.179   9.598  1.00  0.00
ATOM   1374  CB  LYS   175      16.337   4.797   9.111  1.00  0.00
ATOM   1375  CG  LYS   175      15.106   4.834   8.220  1.00  0.00
ATOM   1376  CD  LYS   175      14.851   6.237   7.690  1.00  0.00
ATOM   1377  CE  LYS   175      13.596   6.283   6.833  1.00  0.00
ATOM   1378  NZ  LYS   175      13.331   7.652   6.310  1.00  0.00
ATOM   1379  N   GLU   176      18.133   3.811  11.556  1.00  0.00
ATOM   1380  CA  GLU   176      19.414   3.940  12.239  1.00  0.00
ATOM   1381  C   GLU   176      19.877   2.601  12.799  1.00  0.00
ATOM   1382  O   GLU   176      21.009   2.469  13.266  1.00  0.00
ATOM   1383  CB  GLU   176      19.305   4.928  13.401  1.00  0.00
ATOM   1384  CG  GLU   176      18.963   6.348  12.979  1.00  0.00
ATOM   1385  CD  GLU   176      18.668   7.253  14.159  1.00  0.00
ATOM   1386  OE1 GLU   176      18.685   6.757  15.305  1.00  0.00
ATOM   1387  OE2 GLU   176      18.421   8.457  13.937  1.00  0.00
ATOM   1388  N   SER   177      22.231   2.959  15.090  1.00  0.00
ATOM   1389  CA  SER   177      21.725   4.321  15.202  1.00  0.00
ATOM   1390  C   SER   177      22.840   5.340  15.002  1.00  0.00
ATOM   1391  O   SER   177      23.801   5.382  15.770  1.00  0.00
ATOM   1392  CB  SER   177      21.112   4.553  16.584  1.00  0.00
ATOM   1393  OG  SER   177      20.610   5.873  16.704  1.00  0.00
ATOM   1394  N   SER   178      22.705   6.163  13.968  1.00  0.00
ATOM   1395  CA  SER   178      23.715   7.166  13.649  1.00  0.00
ATOM   1396  C   SER   178      23.077   8.524  13.382  1.00  0.00
ATOM   1397  O   SER   178      22.098   8.627  12.643  1.00  0.00
ATOM   1398  CB  SER   178      24.500   6.757  12.401  1.00  0.00
ATOM   1399  OG  SER   178      25.480   7.728  12.074  1.00  0.00
ATOM   1400  N   PHE   179      23.638   9.565  13.989  1.00  0.00
ATOM   1401  CA  PHE   179      23.123  10.918  13.821  1.00  0.00
ATOM   1402  C   PHE   179      22.980  11.273  12.347  1.00  0.00
ATOM   1403  O   PHE   179      23.900  11.067  11.555  1.00  0.00
ATOM   1404  CB  PHE   179      24.068  11.934  14.465  1.00  0.00
ATOM   1405  CG  PHE   179      24.153  11.822  15.960  1.00  0.00
ATOM   1406  CD1 PHE   179      25.286  11.307  16.566  1.00  0.00
ATOM   1407  CD2 PHE   179      23.101  12.230  16.760  1.00  0.00
ATOM   1408  CE1 PHE   179      25.364  11.202  17.942  1.00  0.00
ATOM   1409  CE2 PHE   179      23.179  12.126  18.136  1.00  0.00
ATOM   1410  CZ  PHE   179      24.303  11.614  18.727  1.00  0.00
ATOM   1411  N   LEU   180      21.820  11.810  11.983  1.00  0.00
ATOM   1412  CA  LEU   180      21.563  12.219  10.607  1.00  0.00
ATOM   1413  C   LEU   180      20.620  11.247   9.911  1.00  0.00
ATOM   1414  O   LEU   180      19.966  11.595   8.928  1.00  0.00
ATOM   1415  CB  LEU   180      22.868  12.267   9.810  1.00  0.00
ATOM   1416  CG  LEU   180      23.915  13.277  10.283  1.00  0.00
ATOM   1417  CD1 LEU   180      25.197  13.141   9.475  1.00  0.00
ATOM   1418  CD2 LEU   180      23.400  14.699  10.122  1.00  0.00
TER
END
