
#######################################################
#                                                     #
#                        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   24 (  119),  selected   24 , name T0295TS239_3_2-D2
# Molecule2: number of CA atoms   95 (  803),  selected   24 , name T0295_D2.pdb
# PARAMETERS: T0295TS239_3_2-D2.T0295_D2.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:    24       252 - 275         0.45     0.45
  LCS_AVERAGE:     25.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       252 - 275         0.45     0.45
  LCS_AVERAGE:     25.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       252 - 275         0.45     0.45
  LCS_AVERAGE:     25.26

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:   95
LCS_GDT     S     252     S     252     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     I     253     I     253     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     N     254     N     254     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     L     255     L     255     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     D     256     D     256     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     E     257     E     257     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     N     258     N     258     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     D     259     D     259     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     F     260     F     260     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     L     261     L     261     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     K     262     K     262     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     L     263     L     263     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     L     264     L     264     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     L     265     L     265     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     E     266     E     266     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     F     267     F     267     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     N     268     N     268     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     K     269     K     269     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     K     270     K     270     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     G     271     G     271     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     I     272     I     272     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     H     273     H     273     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     F     274     F     274     24   24   24    22   23   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_GDT     F     275     F     275     24   24   24     3    3   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24   24 
LCS_AVERAGE  LCS_A:  25.26  (  25.26   25.26   25.26 )

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     22     23     24     24     24     24     24     24     24     24     24     24     24     24     24     24     24     24     24     24 
GDT PERCENT_CA  23.16  24.21  25.26  25.26  25.26  25.26  25.26  25.26  25.26  25.26  25.26  25.26  25.26  25.26  25.26  25.26  25.26  25.26  25.26  25.26
GDT RMS_LOCAL    0.30   0.32   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45
GDT RMS_ALL_CA   0.47   0.47   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45   0.45

#      Molecule1      Molecule2       DISTANCE
LGA    S     252      S     252          0.527
LGA    I     253      I     253          0.564
LGA    N     254      N     254          0.527
LGA    L     255      L     255          0.614
LGA    D     256      D     256          0.161
LGA    E     257      E     257          0.124
LGA    N     258      N     258          0.359
LGA    D     259      D     259          0.313
LGA    F     260      F     260          0.083
LGA    L     261      L     261          0.237
LGA    K     262      K     262          0.277
LGA    L     263      L     263          0.345
LGA    L     264      L     264          0.261
LGA    L     265      L     265          0.158
LGA    E     266      E     266          0.355
LGA    F     267      F     267          0.113
LGA    N     268      N     268          0.160
LGA    K     269      K     269          0.134
LGA    K     270      K     270          0.333
LGA    G     271      G     271          0.624
LGA    I     272      I     272          0.139
LGA    H     273      H     273          0.265
LGA    F     274      F     274          0.236
LGA    F     275      F     275          1.493

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24   95    4.0     24    0.45    25.000    25.180     4.339

LGA_LOCAL      RMSD =  0.453  Number of atoms =   24  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.453  Number of atoms =   24 
Std_ALL_ATOMS  RMSD =  0.453  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.524258 * X  +  -0.814524 * Y  +   0.248406 * Z  +  19.010677
  Y_new =   0.109750 * X  +  -0.224646 * Y  +  -0.968240 * Z  +  16.817356
  Z_new =   0.844458 * X  +   0.534870 * Y  +  -0.028379 * Z  +  -7.360678 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.623804   -1.517789  [ DEG:    93.0371    -86.9629 ]
  Theta =  -1.005552   -2.136040  [ DEG:   -57.6139   -122.3861 ]
  Phi   =   0.206363   -2.935230  [ DEG:    11.8237   -168.1763 ]
 
# 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: T0295TS239_3_2-D2                             
REMARK     2: T0295_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295TS239_3_2-D2.T0295_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24   95   4.0   24   0.45  25.180     0.45
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS239_3_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT 1zq9_A
ATOM   1249  N   SER   252      16.457  11.969  -9.601  1.00  9.99
ATOM   1250  CA  SER   252      16.032  11.563  -8.261  1.00  9.99
ATOM   1251  C   SER   252      15.255  10.236  -8.250  1.00  9.99
ATOM   1252  O   SER   252      15.415   9.443  -7.353  1.00  9.99
ATOM   1253  CB  SER   252      15.212  12.657  -7.629  1.00  9.99
ATOM   1254  N   ILE   253      14.444   9.981  -9.261  1.00  9.99
ATOM   1255  CA  ILE   253      13.633   8.762  -9.312  1.00  9.99
ATOM   1256  C   ILE   253      14.449   7.458  -9.304  1.00  9.99
ATOM   1257  O   ILE   253      13.899   6.400  -9.043  1.00  9.99
ATOM   1258  CB  ILE   253      12.733   8.760 -10.557  1.00  9.99
ATOM   1259  N   ASN   254      15.728   7.544  -9.674  1.00  9.99
ATOM   1260  CA  ASN   254      16.603   6.376  -9.695  1.00  9.99
ATOM   1261  C   ASN   254      17.672   6.401  -8.585  1.00  9.99
ATOM   1262  O   ASN   254      18.576   5.570  -8.564  1.00  9.99
ATOM   1263  CB  ASN   254      17.261   6.255 -11.072  1.00  9.99
ATOM   1264  N   LEU   255      17.556   7.342  -7.651  1.00  9.99
ATOM   1265  CA  LEU   255      18.597   7.513  -6.661  1.00  9.99
ATOM   1266  C   LEU   255      18.071   6.940  -5.341  1.00  9.99
ATOM   1267  O   LEU   255      16.905   7.181  -4.971  1.00  9.99
ATOM   1268  CB  LEU   255      18.966   9.002  -6.512  1.00  9.99
ATOM   1269  N   ASP   256      18.931   6.200  -4.642  1.00  9.99
ATOM   1270  CA  ASP   256      18.596   5.581  -3.366  1.00  9.99
ATOM   1271  C   ASP   256      19.096   6.415  -2.188  1.00  9.99
ATOM   1272  O   ASP   256      19.614   7.519  -2.389  1.00  9.99
ATOM   1273  CB  ASP   256      19.123   4.134  -3.313  1.00  9.99
ATOM   1274  N   GLU   257      18.918   5.919  -0.962  1.00  9.99
ATOM   1275  CA  GLU   257      19.313   6.687   0.220  1.00  9.99
ATOM   1276  C   GLU   257      20.835   6.934   0.285  1.00  9.99
ATOM   1277  O   GLU   257      21.253   8.036   0.596  1.00  9.99
ATOM   1278  CB  GLU   257      18.812   6.030   1.534  1.00  9.99
ATOM   1279  N   ASN   258      21.634   5.911   0.009  1.00  9.99
ATOM   1280  CA  ASN   258      23.098   6.056  -0.054  1.00  9.99
ATOM   1281  C   ASN   258      23.461   7.260  -0.950  1.00  9.99
ATOM   1282  O   ASN   258      24.264   8.115  -0.563  1.00  9.99
ATOM   1283  CB  ASN   258      23.745   4.786  -0.618  1.00  9.99
ATOM   1284  N   ASP   259      22.852   7.312  -2.140  1.00  9.99
ATOM   1285  CA  ASP   259      23.073   8.386  -3.118  1.00  9.99
ATOM   1286  C   ASP   259      22.751   9.772  -2.583  1.00  9.99
ATOM   1287  O   ASP   259      23.528  10.691  -2.767  1.00  9.99
ATOM   1288  CB  ASP   259      22.235   8.164  -4.389  1.00  9.99
ATOM   1289  N   PHE   260      21.579   9.933  -1.966  1.00  9.99
ATOM   1290  CA  PHE   260      21.208  11.237  -1.468  1.00  9.99
ATOM   1291  C   PHE   260      22.047  11.647  -0.261  1.00  9.99
ATOM   1292  O   PHE   260      22.376  12.825  -0.101  1.00  9.99
ATOM   1293  CB  PHE   260      19.713  11.287  -1.171  1.00  9.99
ATOM   1294  N   LEU   261      22.437  10.679   0.566  1.00  9.99
ATOM   1295  CA  LEU   261      23.340  11.012   1.683  1.00  9.99
ATOM   1296  C   LEU   261      24.661  11.558   1.124  1.00  9.99
ATOM   1297  O   LEU   261      25.158  12.590   1.581  1.00  9.99
ATOM   1298  CB  LEU   261      23.590   9.808   2.624  1.00  9.99
ATOM   1299  N   LYS   262      25.230  10.860   0.144  1.00  9.99
ATOM   1300  CA  LYS   262      26.465  11.334  -0.514  1.00  9.99
ATOM   1301  C   LYS   262      26.318  12.759  -1.090  1.00  9.99
ATOM   1302  O   LYS   262      27.197  13.631  -0.901  1.00  9.99
ATOM   1303  CB  LYS   262      26.905  10.368  -1.616  1.00  9.99
ATOM   1304  N   LEU   263      25.225  12.972  -1.818  1.00  9.99
ATOM   1305  CA  LEU   263      24.920  14.268  -2.399  1.00  9.99
ATOM   1306  C   LEU   263      24.786  15.349  -1.340  1.00  9.99
ATOM   1307  O   LEU   263      25.322  16.442  -1.512  1.00  9.99
ATOM   1308  CB  LEU   263      23.640  14.208  -3.236  1.00  9.99
ATOM   1309  N   LEU   264      24.051  15.055  -0.271  1.00  9.99
ATOM   1310  CA  LEU   264      23.841  16.031   0.801  1.00  9.99
ATOM   1311  C   LEU   264      25.187  16.391   1.422  1.00  9.99
ATOM   1312  O   LEU   264      25.515  17.572   1.583  1.00  9.99
ATOM   1313  CB  LEU   264      22.888  15.491   1.862  1.00  9.99
ATOM   1314  N   LEU   265      25.953  15.355   1.771  1.00  9.99
ATOM   1315  CA  LEU   265      27.318  15.528   2.317  1.00  9.99
ATOM   1316  C   LEU   265      28.150  16.440   1.427  1.00  9.99
ATOM   1317  O   LEU   265      28.829  17.360   1.912  1.00  9.99
ATOM   1318  CB  LEU   265      28.014  14.159   2.501  1.00  9.99
ATOM   1319  N   GLU   266      28.070  16.211   0.122  1.00  9.99
ATOM   1320  CA  GLU   266      28.863  16.955  -0.838  1.00  9.99
ATOM   1321  C   GLU   266      28.453  18.412  -0.997  1.00  9.99
ATOM   1322  O   GLU   266      29.289  19.259  -1.310  1.00  9.99
ATOM   1323  CB  GLU   266      28.789  16.224  -2.189  1.00  9.99
ATOM   1324  N   PHE   267      27.156  18.705  -0.842  1.00  9.99
ATOM   1325  CA  PHE   267      26.701  20.096  -0.815  1.00  9.99
ATOM   1326  C   PHE   267      27.180  20.778   0.463  1.00  9.99
ATOM   1327  O   PHE   267      27.692  21.886   0.400  1.00  9.99
ATOM   1328  CB  PHE   267      25.167  20.191  -0.916  1.00  9.99
ATOM   1329  N   ASN   268      27.016  20.102   1.602  1.00  9.99
ATOM   1330  CA  ASN   268      27.336  20.624   2.933  1.00  9.99
ATOM   1331  C   ASN   268      28.830  20.964   3.088  1.00  9.99
ATOM   1332  O   ASN   268      29.189  21.992   3.669  1.00  9.99
ATOM   1333  CB  ASN   268      26.914  19.633   4.040  1.00  9.99
ATOM   1334  N   LYS   269      29.681  20.089   2.575  1.00  9.99
ATOM   1335  CA  LYS   269      31.124  20.283   2.573  1.00  9.99
ATOM   1336  C   LYS   269      31.537  21.567   1.838  1.00  9.99
ATOM   1337  O   LYS   269      32.626  22.083   2.075  1.00  9.99
ATOM   1338  CB  LYS   269      31.799  19.093   1.941  1.00  9.99
ATOM   1339  N   LYS   270      30.683  22.055   0.932  1.00  9.99
ATOM   1340  CA  LYS   270      30.979  23.249   0.170  1.00  9.99
ATOM   1341  C   LYS   270      30.180  24.472   0.629  1.00  9.99
ATOM   1342  O   LYS   270      30.166  25.484  -0.064  1.00  9.99
ATOM   1343  CB  LYS   270      30.730  23.002  -1.308  1.00  9.99
ATOM   1344  N   GLY   271      29.519  24.371   1.777  1.00  9.99
ATOM   1345  CA  GLY   271      28.795  25.515   2.342  1.00  9.99
ATOM   1346  C   GLY   271      27.349  25.669   1.923  1.00  9.99
ATOM   1347  O   GLY   271      26.696  26.643   2.303  1.00  9.99
ATOM   1348  N   ILE   272      26.843  24.714   1.150  1.00  9.99
ATOM   1349  CA  ILE   272      25.409  24.728   0.764  1.00  9.99
ATOM   1350  C   ILE   272      24.590  23.880   1.717  1.00  9.99
ATOM   1351  O   ILE   272      24.767  22.648   1.807  1.00  9.99
ATOM   1352  CB  ILE   272      25.189  24.367  -0.725  1.00  9.99
ATOM   1353  N   HIS   273      23.735  24.575   2.460  1.00  9.99
ATOM   1354  CA  HIS   273      22.857  23.982   3.450  1.00  9.99
ATOM   1355  C   HIS   273      21.388  24.257   3.097  1.00  9.99
ATOM   1356  O   HIS   273      21.013  25.428   2.897  1.00  9.99
ATOM   1357  CB  HIS   273      23.209  24.527   4.841  1.00  9.99
ATOM   1358  N   PHE   274      20.577  23.192   3.042  1.00  9.99
ATOM   1359  CA  PHE   274      19.166  23.269   2.592  1.00  9.99
ATOM   1360  C   PHE   274      18.190  23.551   3.731  1.00  9.99
ATOM   1361  O   PHE   274      18.392  23.117   4.859  1.00  9.99
ATOM   1362  CB  PHE   274      18.749  21.966   1.888  1.00  9.99
ATOM   1363  N   PHE   275      17.117  24.275   3.424  1.00  9.99
ATOM   1364  CA  PHE   275      16.037  24.537   4.390  1.00  9.99
ATOM   1365  C   PHE   275      14.749  23.854   3.922  1.00  9.99
ATOM   1366  O   PHE   275      14.727  23.316   2.800  1.00  9.99
ATOM   1367  CB  PHE   275      15.794  26.035   4.489  1.00  9.99
TER
END
