
#######################################################
#                                                     #
#                        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   27 (  134),  selected   27 , name T0295TS239_2_1-D2
# Molecule2: number of CA atoms   95 (  803),  selected   27 , name T0295_D2.pdb
# PARAMETERS: T0295TS239_2_1-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:    27       249 - 275         0.52     0.52
  LCS_AVERAGE:     28.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27       249 - 275         0.52     0.52
  LCS_AVERAGE:     28.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27       249 - 275         0.52     0.52
  LCS_AVERAGE:     28.42

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     E     249     E     249     27   27   27    14   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     K     250     K     250     27   27   27    21   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     R     251     R     251     27   27   27    21   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     S     252     S     252     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     I     253     I     253     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     N     254     N     254     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     L     255     L     255     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     D     256     D     256     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     E     257     E     257     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     N     258     N     258     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     D     259     D     259     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     F     260     F     260     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     L     261     L     261     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     K     262     K     262     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     L     263     L     263     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     L     264     L     264     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     L     265     L     265     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     E     266     E     266     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     F     267     F     267     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     N     268     N     268     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     K     269     K     269     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     K     270     K     270     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     G     271     G     271     27   27   27    19   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     I     272     I     272     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     H     273     H     273     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     F     274     F     274     27   27   27    22   26   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     F     275     F     275     27   27   27     3    3   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_AVERAGE  LCS_A:  28.42  (  28.42   28.42   28.42 )

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     26     27     27     27     27     27     27     27     27     27     27     27     27     27     27     27     27     27     27 
GDT PERCENT_CA  23.16  27.37  28.42  28.42  28.42  28.42  28.42  28.42  28.42  28.42  28.42  28.42  28.42  28.42  28.42  28.42  28.42  28.42  28.42  28.42
GDT RMS_LOCAL    0.30   0.42   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52
GDT RMS_ALL_CA   0.54   0.54   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52

#      Molecule1      Molecule2       DISTANCE
LGA    E     249      E     249          1.067
LGA    K     250      K     250          0.643
LGA    R     251      R     251          0.689
LGA    S     252      S     252          0.458
LGA    I     253      I     253          0.409
LGA    N     254      N     254          0.425
LGA    L     255      L     255          0.548
LGA    D     256      D     256          0.094
LGA    E     257      E     257          0.168
LGA    N     258      N     258          0.340
LGA    D     259      D     259          0.292
LGA    F     260      F     260          0.066
LGA    L     261      L     261          0.182
LGA    K     262      K     262          0.270
LGA    L     263      L     263          0.412
LGA    L     264      L     264          0.343
LGA    L     265      L     265          0.256
LGA    E     266      E     266          0.496
LGA    F     267      F     267          0.256
LGA    N     268      N     268          0.278
LGA    K     269      K     269          0.224
LGA    K     270      K     270          0.431
LGA    G     271      G     271          0.764
LGA    I     272      I     272          0.273
LGA    H     273      H     273          0.188
LGA    F     274      F     274          0.196
LGA    F     275      F     275          1.549

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   95    4.0     27    0.52    28.158    28.338     4.345

LGA_LOCAL      RMSD =  0.521  Number of atoms =   27  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.521  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  0.521  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.534575 * X  +  -0.806862 * Y  +   0.251403 * Z  +  18.877195
  Y_new =   0.113655 * X  +  -0.226137 * Y  +  -0.967442 * Z  +  16.736811
  Z_new =   0.837444 * X  +   0.545744 * Y  +  -0.029183 * Z  +  -7.378604 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.624219   -1.517374  [ DEG:    93.0609    -86.9391 ]
  Theta =  -0.992589   -2.149003  [ DEG:   -56.8712   -123.1288 ]
  Phi   =   0.209489   -2.932103  [ DEG:    12.0029   -167.9971 ]
 
# 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_2_1-D2                             
REMARK     2: T0295_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295TS239_2_1-D2.T0295_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   95   4.0   27   0.52  28.338     0.52
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS239_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0295
PARENT 1zq9_A
ATOM   1234  N   GLU   249      23.947  13.765 -13.969  1.00  9.99
ATOM   1235  CA  GLU   249      23.173  13.135 -15.034  1.00  9.99
ATOM   1236  C   GLU   249      22.187  12.099 -14.477  1.00  9.99
ATOM   1237  O   GLU   249      21.572  11.343 -15.236  1.00  9.99
ATOM   1238  CB  GLU   249      24.126  12.475 -16.062  1.00  9.99
ATOM   1239  N   LYS   250      22.050  12.063 -13.152  1.00  9.99
ATOM   1240  CA  LYS   250      21.056  11.190 -12.514  1.00  9.99
ATOM   1241  C   LYS   250      19.747  11.892 -12.258  1.00  9.99
ATOM   1242  O   LYS   250      19.687  13.103 -12.281  1.00  9.99
ATOM   1243  CB  LYS   250      21.575  10.632 -11.205  1.00  9.99
ATOM   1244  N   ARG   251      18.710  11.099 -11.987  1.00  9.99
ATOM   1245  CA  ARG   251      17.373  11.595 -11.746  1.00  9.99
ATOM   1246  C   ARG   251      16.971  11.040 -10.377  1.00  9.99
ATOM   1247  O   ARG   251      17.266   9.868 -10.057  1.00  9.99
ATOM   1248  CB  ARG   251      16.428  11.071 -12.820  1.00  9.99
ATOM   1249  N   SER   252      16.312  11.874  -9.575  1.00  9.99
ATOM   1250  CA  SER   252      15.905  11.470  -8.229  1.00  9.99
ATOM   1251  C   SER   252      15.134  10.140  -8.204  1.00  9.99
ATOM   1252  O   SER   252      15.307   9.350  -7.307  1.00  9.99
ATOM   1253  CB  SER   252      15.090  12.563  -7.589  1.00  9.99
ATOM   1254  N   ILE   253      14.311   9.880  -9.204  1.00  9.99
ATOM   1255  CA  ILE   253      13.503   8.658  -9.242  1.00  9.99
ATOM   1256  C   ILE   253      14.323   7.357  -9.241  1.00  9.99
ATOM   1257  O   ILE   253      13.781   6.298  -8.970  1.00  9.99
ATOM   1258  CB  ILE   253      12.587   8.650 -10.475  1.00  9.99
ATOM   1259  N   ASN   254      15.598   7.446  -9.627  1.00  9.99
ATOM   1260  CA  ASN   254      16.477   6.281  -9.656  1.00  9.99
ATOM   1261  C   ASN   254      17.559   6.313  -8.560  1.00  9.99
ATOM   1262  O   ASN   254      18.467   5.485  -8.549  1.00  9.99
ATOM   1263  CB  ASN   254      17.117   6.160 -11.042  1.00  9.99
ATOM   1264  N   LEU   255      17.452   7.256  -7.628  1.00  9.99
ATOM   1265  CA  LEU   255      18.504   7.433  -6.651  1.00  9.99
ATOM   1266  C   LEU   255      17.998   6.861  -5.323  1.00  9.99
ATOM   1267  O   LEU   255      16.835   7.100  -4.939  1.00  9.99
ATOM   1268  CB  LEU   255      18.871   8.923  -6.510  1.00  9.99
ATOM   1269  N   ASP   256      18.869   6.126  -4.633  1.00  9.99
ATOM   1270  CA  ASP   256      18.552   5.509  -3.351  1.00  9.99
ATOM   1271  C   ASP   256      19.065   6.348  -2.182  1.00  9.99
ATOM   1272  O   ASP   256      19.577   7.453  -2.393  1.00  9.99
ATOM   1273  CB  ASP   256      19.085   4.064  -3.302  1.00  9.99
ATOM   1274  N   GLU   257      18.904   5.854  -0.953  1.00  9.99
ATOM   1275  CA  GLU   257      19.311   6.626   0.222  1.00  9.99
ATOM   1276  C   GLU   257      20.833   6.878   0.267  1.00  9.99
ATOM   1277  O   GLU   257      21.251   7.983   0.570  1.00  9.99
ATOM   1278  CB  GLU   257      18.830   5.971   1.544  1.00  9.99
ATOM   1279  N   ASN   258      21.633   5.857  -0.016  1.00  9.99
ATOM   1280  CA  ASN   258      23.095   6.007  -0.099  1.00  9.99
ATOM   1281  C   ASN   258      23.442   7.211  -1.002  1.00  9.99
ATOM   1282  O   ASN   258      24.247   8.070  -0.627  1.00  9.99
ATOM   1283  CB  ASN   258      23.739   4.739  -0.668  1.00  9.99
ATOM   1284  N   ASP   259      22.817   7.258  -2.184  1.00  9.99
ATOM   1285  CA  ASP   259      23.023   8.330  -3.168  1.00  9.99
ATOM   1286  C   ASP   259      22.703   9.717  -2.632  1.00  9.99
ATOM   1287  O   ASP   259      23.474  10.637  -2.828  1.00  9.99
ATOM   1288  CB  ASP   259      22.169   8.102  -4.427  1.00  9.99
ATOM   1289  N   PHE   260      21.538   9.874  -2.001  1.00  9.99
ATOM   1290  CA  PHE   260      21.169  11.178  -1.500  1.00  9.99
ATOM   1291  C   PHE   260      22.022  11.594  -0.305  1.00  9.99
ATOM   1292  O   PHE   260      22.348  12.775  -0.152  1.00  9.99
ATOM   1293  CB  PHE   260      19.677  11.225  -1.185  1.00  9.99
ATOM   1294  N   LEU   261      22.425  10.630   0.519  1.00  9.99
ATOM   1295  CA  LEU   261      23.342  10.969   1.624  1.00  9.99
ATOM   1296  C   LEU   261      24.654  11.518   1.046  1.00  9.99
ATOM   1297  O   LEU   261      25.153  12.553   1.495  1.00  9.99
ATOM   1298  CB  LEU   261      23.608   9.768   2.564  1.00  9.99
ATOM   1299  N   LYS   262      25.212  10.820   0.061  1.00  9.99
ATOM   1300  CA  LYS   262      26.437  11.296  -0.614  1.00  9.99
ATOM   1301  C   LYS   262      26.278  12.719  -1.191  1.00  9.99
ATOM   1302  O   LYS   262      27.156  13.595  -1.016  1.00  9.99
ATOM   1303  CB  LYS   262      26.867  10.329  -1.719  1.00  9.99
ATOM   1304  N   LEU   263      25.175  12.926  -1.906  1.00  9.99
ATOM   1305  CA  LEU   263      24.858  14.220  -2.487  1.00  9.99
ATOM   1306  C   LEU   263      24.734  15.304  -1.428  1.00  9.99
ATOM   1307  O   LEU   263      25.263  16.398  -1.610  1.00  9.99
ATOM   1308  CB  LEU   263      23.567  14.154  -3.306  1.00  9.99
ATOM   1309  N   LEU   264      24.014  15.010  -0.350  1.00  9.99
ATOM   1310  CA  LEU   264      23.813  15.987   0.723  1.00  9.99
ATOM   1311  C   LEU   264      25.166  16.353   1.326  1.00  9.99
ATOM   1312  O   LEU   264      25.492  17.536   1.479  1.00  9.99
ATOM   1313  CB  LEU   264      22.876  15.446   1.797  1.00  9.99
ATOM   1314  N   LEU   265      25.940  15.321   1.667  1.00  9.99
ATOM   1315  CA  LEU   265      27.312  15.501   2.195  1.00  9.99
ATOM   1316  C   LEU   265      28.129  16.413   1.293  1.00  9.99
ATOM   1317  O   LEU   265      28.811  17.337   1.766  1.00  9.99
ATOM   1318  CB  LEU   265      28.015  14.134   2.374  1.00  9.99
ATOM   1319  N   GLU   266      28.034  16.181  -0.010  1.00  9.99
ATOM   1320  CA  GLU   266      28.811  16.925  -0.983  1.00  9.99
ATOM   1321  C   GLU   266      28.394  18.380  -1.140  1.00  9.99
ATOM   1322  O   GLU   266      29.223  19.229  -1.465  1.00  9.99
ATOM   1323  CB  GLU   266      28.722  16.190  -2.331  1.00  9.99
ATOM   1324  N   PHE   267      27.098  18.668  -0.969  1.00  9.99
ATOM   1325  CA  PHE   267      26.638  20.058  -0.939  1.00  9.99
ATOM   1326  C   PHE   267      27.131  20.745   0.331  1.00  9.99
ATOM   1327  O   PHE   267      27.639  21.854   0.258  1.00  9.99
ATOM   1328  CB  PHE   267      25.103  20.148  -1.021  1.00  9.99
ATOM   1329  N   ASN   268      26.985  20.071   1.473  1.00  9.99
ATOM   1330  CA  ASN   268      27.320  20.598   2.799  1.00  9.99
ATOM   1331  C   ASN   268      28.814  20.943   2.934  1.00  9.99
ATOM   1332  O   ASN   268      29.177  21.974   3.508  1.00  9.99
ATOM   1333  CB  ASN   268      26.915  19.608   3.914  1.00  9.99
ATOM   1334  N   LYS   269      29.662  20.070   2.412  1.00  9.99
ATOM   1335  CA  LYS   269      31.104  20.269   2.392  1.00  9.99
ATOM   1336  C   LYS   269      31.503  21.552   1.648  1.00  9.99
ATOM   1337  O   LYS   269      32.593  22.073   1.870  1.00  9.99
ATOM   1338  CB  LYS   269      31.775  19.080   1.754  1.00  9.99
ATOM   1339  N   LYS   270      30.636  22.035   0.752  1.00  9.99
ATOM   1340  CA  LYS   270      30.918  23.228  -0.016  1.00  9.99
ATOM   1341  C   LYS   270      30.121  24.450   0.450  1.00  9.99
ATOM   1342  O   LYS   270      30.095  25.460  -0.246  1.00  9.99
ATOM   1343  CB  LYS   270      30.651  22.977  -1.491  1.00  9.99
ATOM   1344  N   GLY   271      29.475  24.350   1.606  1.00  9.99
ATOM   1345  CA  GLY   271      28.754  25.492   2.178  1.00  9.99
ATOM   1346  C   GLY   271      27.302  25.641   1.777  1.00  9.99
ATOM   1347  O   GLY   271      26.651  26.613   2.162  1.00  9.99
ATOM   1348  N   ILE   272      26.789  24.682   1.013  1.00  9.99
ATOM   1349  CA  ILE   272      25.351  24.690   0.645  1.00  9.99
ATOM   1350  C   ILE   272      24.547  23.841   1.610  1.00  9.99
ATOM   1351  O   ILE   272      24.730  22.610   1.701  1.00  9.99
ATOM   1352  CB  ILE   272      25.113  24.324  -0.841  1.00  9.99
ATOM   1353  N   HIS   273      23.699  24.535   2.362  1.00  9.99
ATOM   1354  CA  HIS   273      22.836  23.941   3.365  1.00  9.99
ATOM   1355  C   HIS   273      21.361  24.211   3.030  1.00  9.99
ATOM   1356  O   HIS   273      20.980  25.380   2.832  1.00  9.99
ATOM   1357  CB  HIS   273      23.203  24.491   4.750  1.00  9.99
ATOM   1358  N   PHE   274      20.554  23.142   2.987  1.00  9.99
ATOM   1359  CA  PHE   274      19.137  23.214   2.555  1.00  9.99
ATOM   1360  C   PHE   274      18.175  23.495   3.706  1.00  9.99
ATOM   1361  O   PHE   274      18.392  23.064   4.833  1.00  9.99
ATOM   1362  CB  PHE   274      18.716  21.907   1.860  1.00  9.99
ATOM   1363  N   PHE   275      17.095  24.214   3.411  1.00  9.99
ATOM   1364  CA  PHE   275      16.026  24.476   4.390  1.00  9.99
ATOM   1365  C   PHE   275      14.735  23.787   3.940  1.00  9.99
ATOM   1366  O   PHE   275      14.700  23.246   2.820  1.00  9.99
ATOM   1367  CB  PHE   275      15.780  25.973   4.489  1.00  9.99
TER
END
