
#######################################################
#                                                     #
#                        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_4_2-D1
# Molecule2: number of CA atoms  180 ( 1390),  selected   19 , name T0295_D1.pdb
# PARAMETERS: T0295TS193_4_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       168 - 180         4.75    13.25
  LCS_AVERAGE:      6.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       162 - 167         1.92    25.89
  LONGEST_CONTINUOUS_SEGMENT:     6       163 - 168         1.61    27.85
  LONGEST_CONTINUOUS_SEGMENT:     6       167 - 172         1.89    18.16
  LONGEST_CONTINUOUS_SEGMENT:     6       168 - 173         1.62    17.16
  LONGEST_CONTINUOUS_SEGMENT:     6       172 - 177         0.96    16.97
  LCS_AVERAGE:      3.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       172 - 177         0.96    16.97
  LCS_AVERAGE:      2.46

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    6    9     3    3    3    3    5    6    7    7    8    8    8    8    8    8    8    8    9    9   10   10 
LCS_GDT     P     163     P     163      4    6    9     3    4    4    5    5    6    7    7    8    8    8    8    8    8    8    8    9    9   10   10 
LCS_GDT     K     164     K     164      4    6    9     3    4    5    5    5    6    7    7    8    8    8    8    8    8    8    8    9    9   10   10 
LCS_GDT     V     165     V     165      4    6    9     3    4    5    5    5    6    7    7    8    8    8    8    8    8    8    8    9    9   10   10 
LCS_GDT     D     166     D     166      4    6   10     3    4    5    5    5    6    7    7    8    8    8    8    8    8    9    9   10   13   14   15 
LCS_GDT     S     167     S     167      4    6   10     3    4    5    5    5    6    7    7    8    8    8    9   11   12   12   13   14   14   14   15 
LCS_GDT     V     168     V     168      4    6   13     4    4    5    5    6    6    7    7    8    8   10   11   11   13   13   13   14   14   14   15 
LCS_GDT     I     169     I     169      4    6   13     4    4    4    5    6    6    7    7    8    9   10   11   12   13   13   13   14   14   14   15 
LCS_GDT     V     170     V     170      4    6   13     4    4    4    5    6    6    7    7    8    9   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     K     171     K     171      4    6   13     4    4    4    5    6    6    7    9   10   10   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     L     172     L     172      6    6   13     4    5    5    6    6    7    8    9   10   10   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     I     173     I     173      6    6   13     4    5    5    6    6    7    8    9   10   10   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     P     174     P     174      6    6   13     4    5    5    6    6    7    8    9   10   10   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     K     175     K     175      6    6   13     3    4    5    6    6    7    8    9   10   10   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     E     176     E     176      6    6   13     4    5    5    6    6    7    8    9   10   10   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     S     177     S     177      6    6   13     4    5    5    6    6    7    8    8   10   10   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     S     178     S     178      3    4   13     3    3    3    3    6    7    8    9   10   10   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     F     179     F     179      3    4   13     3    3    3    3    4    4    6    9   10   10   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     L     180     L     180      3    4   13     3    3    3    3    4    7    8    9   10   10   11   11   12   13   13   13   14   14   14   15 
LCS_AVERAGE  LCS_A:   4.06  (   2.46    3.16    6.58 )

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      5      6      6      7      8      9     10     10     11     11     12     13     13     13     14     14     14     15 
GDT PERCENT_CA   2.22   2.78   2.78   3.33   3.33   3.89   4.44   5.00   5.56   5.56   6.11   6.11   6.67   7.22   7.22   7.22   7.78   7.78   7.78   8.33
GDT RMS_LOCAL    0.32   0.43   0.43   0.96   0.96   1.55   2.16   3.11   3.20   3.20   3.73   3.73   4.31   4.75   4.75   4.75   5.34   5.34   5.34   6.17
GDT RMS_ALL_CA  13.97  17.52  17.52  16.97  16.97  16.20  15.04  14.09  14.48  14.48  13.60  13.60  13.25  13.25  13.25  13.25  12.53  12.53  12.53  11.76

#      Molecule1      Molecule2       DISTANCE
LGA    P     162      P     162         24.962
LGA    P     163      P     163         25.207
LGA    K     164      K     164         28.334
LGA    V     165      V     165         22.144
LGA    D     166      D     166         16.525
LGA    S     167      S     167         13.780
LGA    V     168      V     168         10.980
LGA    I     169      I     169          8.859
LGA    V     170      V     170          6.077
LGA    K     171      K     171          3.757
LGA    L     172      L     172          3.781
LGA    I     173      I     173          2.943
LGA    P     174      P     174          3.343
LGA    K     175      K     175          3.123
LGA    E     176      E     176          2.583
LGA    S     177      S     177          4.865
LGA    S     178      S     178          1.233
LGA    F     179      F     179          3.782
LGA    L     180      L     180          3.771

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  180    4.0      9    3.11     4.583     4.276     0.280

LGA_LOCAL      RMSD =  3.111  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.316  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  9.867  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.277875 * X  +   0.951080 * Y  +  -0.135029 * Z  +   9.988797
  Y_new =   0.180824 * X  +  -0.189839 * Y  +  -0.965020 * Z  +  -4.177578
  Z_new =  -0.943445 * X  +   0.243738 * Y  +  -0.224730 * Z  +  -4.440547 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.315641   -0.825952  [ DEG:   132.6765    -47.3235 ]
  Theta =   1.232872    1.908721  [ DEG:    70.6384    109.3616 ]
  Phi   =   0.576895   -2.564697  [ DEG:    33.0537   -146.9463 ]
 
# 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_4_2-D1                             
REMARK     2: T0295_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295TS193_4_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   3.11   4.276     9.87
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS193_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT N/A
ATOM   1272  N   PRO   162       9.261  -6.013   0.766  1.00  0.00
ATOM   1273  CA  PRO   162       8.563  -6.618   1.894  1.00  0.00
ATOM   1274  C   PRO   162       8.855  -5.870   3.188  1.00  0.00
ATOM   1275  O   PRO   162       9.911  -5.253   3.335  1.00  0.00
ATOM   1276  CB  PRO   162       9.105  -8.048   1.942  1.00  0.00
ATOM   1277  CG  PRO   162      10.516  -7.928   1.471  1.00  0.00
ATOM   1278  CD  PRO   162      10.495  -6.941   0.338  1.00  0.00
ATOM   1279  N   PRO   163      10.341  -7.315   4.124  1.00  0.00
ATOM   1280  CA  PRO   163      10.207  -6.932   5.525  1.00  0.00
ATOM   1281  C   PRO   163      11.365  -6.048   5.968  1.00  0.00
ATOM   1282  O   PRO   163      11.328  -5.454   7.045  1.00  0.00
ATOM   1283  CB  PRO   163      10.204  -8.265   6.274  1.00  0.00
ATOM   1284  CG  PRO   163      10.947  -9.199   5.379  1.00  0.00
ATOM   1285  CD  PRO   163      10.592  -8.801   3.974  1.00  0.00
ATOM   1286  N   LYS   164      12.392  -5.965   5.130  1.00  0.00
ATOM   1287  CA  LYS   164      13.497  -5.041   5.363  1.00  0.00
ATOM   1288  C   LYS   164      13.139  -3.629   4.915  1.00  0.00
ATOM   1289  O   LYS   164      13.783  -2.660   5.313  1.00  0.00
ATOM   1290  CB  LYS   164      14.738  -5.484   4.585  1.00  0.00
ATOM   1291  CG  LYS   164      15.343  -6.790   5.074  1.00  0.00
ATOM   1292  CD  LYS   164      16.562  -7.176   4.251  1.00  0.00
ATOM   1293  CE  LYS   164      17.181  -8.469   4.756  1.00  0.00
ATOM   1294  NZ  LYS   164      18.390  -8.847   3.974  1.00  0.00
ATOM   1295  N   VAL   165      12.106  -3.522   4.086  1.00  0.00
ATOM   1296  CA  VAL   165      11.737  -2.246   3.484  1.00  0.00
ATOM   1297  C   VAL   165      10.383  -1.768   3.994  1.00  0.00
ATOM   1298  O   VAL   165      10.201  -0.587   4.286  1.00  0.00
ATOM   1299  CB  VAL   165      11.644  -2.351   1.950  1.00  0.00
ATOM   1300  CG1 VAL   165      11.328  -0.993   1.341  1.00  0.00
ATOM   1301  CG2 VAL   165      12.960  -2.844   1.369  1.00  0.00
ATOM   1302  N   ASP   166       9.356  -1.602   2.465  1.00  0.00
ATOM   1303  CA  ASP   166       8.608  -0.431   2.021  1.00  0.00
ATOM   1304  C   ASP   166       7.535  -0.047   3.031  1.00  0.00
ATOM   1305  O   ASP   166       7.254   1.134   3.234  1.00  0.00
ATOM   1306  CB  ASP   166       7.920  -0.710   0.682  1.00  0.00
ATOM   1307  CG  ASP   166       7.330   0.539   0.059  1.00  0.00
ATOM   1308  OD1 ASP   166       7.559   1.640   0.603  1.00  0.00
ATOM   1309  OD2 ASP   166       6.639   0.417  -0.974  1.00  0.00
ATOM   1310  N   SER   167       6.562   1.812   1.202  1.00  0.00
ATOM   1311  CA  SER   167       7.445   2.970   1.164  1.00  0.00
ATOM   1312  C   SER   167       7.007   4.032   2.164  1.00  0.00
ATOM   1313  O   SER   167       7.837   4.716   2.762  1.00  0.00
ATOM   1314  CB  SER   167       7.442   3.601  -0.230  1.00  0.00
ATOM   1315  OG  SER   167       6.165   4.130  -0.547  1.00  0.00
ATOM   1316  N   VAL   168       5.696   4.165   2.342  1.00  0.00
ATOM   1317  CA  VAL   168       5.145   5.130   3.284  1.00  0.00
ATOM   1318  C   VAL   168       5.499   4.763   4.719  1.00  0.00
ATOM   1319  O   VAL   168       5.822   5.630   5.531  1.00  0.00
ATOM   1320  CB  VAL   168       3.609   5.198   3.189  1.00  0.00
ATOM   1321  CG1 VAL   168       3.044   6.065   4.303  1.00  0.00
ATOM   1322  CG2 VAL   168       3.185   5.794   1.855  1.00  0.00
ATOM   1323  N   ILE   169       5.435   3.472   5.028  1.00  0.00
ATOM   1324  CA  ILE   169       5.769   2.985   6.361  1.00  0.00
ATOM   1325  C   ILE   169       7.237   3.233   6.687  1.00  0.00
ATOM   1326  O   ILE   169       7.575   3.635   7.800  1.00  0.00
ATOM   1327  CB  ILE   169       5.514   1.472   6.490  1.00  0.00
ATOM   1328  CG1 ILE   169       4.035   1.159   6.261  1.00  0.00
ATOM   1329  CG2 ILE   169       5.902   0.983   7.877  1.00  0.00
ATOM   1330  CD1 ILE   169       3.732  -0.320   6.163  1.00  0.00
ATOM   1331  N   VAL   170       9.369   2.408   7.214  1.00  0.00
ATOM   1332  CA  VAL   170       8.705   1.128   7.427  1.00  0.00
ATOM   1333  C   VAL   170       9.518   0.232   8.351  1.00  0.00
ATOM   1334  O   VAL   170      10.588  -0.250   7.981  1.00  0.00
ATOM   1335  CB  VAL   170       8.505   0.369   6.102  1.00  0.00
ATOM   1336  CG1 VAL   170       7.849  -0.980   6.356  1.00  0.00
ATOM   1337  CG2 VAL   170       7.616   1.166   5.160  1.00  0.00
ATOM   1338  N   LYS   171       9.004   0.011   9.557  1.00  0.00
ATOM   1339  CA  LYS   171       9.745  -0.707  10.586  1.00  0.00
ATOM   1340  C   LYS   171       8.814  -1.550  11.449  1.00  0.00
ATOM   1341  O   LYS   171       7.666  -1.175  11.687  1.00  0.00
ATOM   1342  CB  LYS   171      10.481   0.274  11.501  1.00  0.00
ATOM   1343  CG  LYS   171      11.573   1.071  10.806  1.00  0.00
ATOM   1344  CD  LYS   171      12.321   1.956  11.790  1.00  0.00
ATOM   1345  CE  LYS   171      13.360   2.812  11.083  1.00  0.00
ATOM   1346  NZ  LYS   171      14.140   3.642  12.041  1.00  0.00
ATOM   1347  N   LEU   172       7.271  -3.344  12.141  1.00  0.00
ATOM   1348  CA  LEU   172       8.356  -3.454  13.108  1.00  0.00
ATOM   1349  C   LEU   172       9.570  -4.141  12.497  1.00  0.00
ATOM   1350  O   LEU   172       9.445  -5.173  11.838  1.00  0.00
ATOM   1351  CB  LEU   172       7.910  -4.272  14.322  1.00  0.00
ATOM   1352  CG  LEU   172       8.923  -4.399  15.462  1.00  0.00
ATOM   1353  CD1 LEU   172       9.184  -3.045  16.103  1.00  0.00
ATOM   1354  CD2 LEU   172       8.405  -5.342  16.537  1.00  0.00
ATOM   1355  N   ILE   173      10.745  -3.562  12.720  1.00  0.00
ATOM   1356  CA  ILE   173      11.986  -4.119  12.194  1.00  0.00
ATOM   1357  C   ILE   173      12.972  -4.421  13.315  1.00  0.00
ATOM   1358  O   ILE   173      13.538  -3.509  13.919  1.00  0.00
ATOM   1359  CB  ILE   173      12.674  -3.145  11.219  1.00  0.00
ATOM   1360  CG1 ILE   173      11.688  -2.676  10.149  1.00  0.00
ATOM   1361  CG2 ILE   173      13.848  -3.824  10.529  1.00  0.00
ATOM   1362  CD1 ILE   173      11.155  -3.792   9.277  1.00  0.00
ATOM   1363  N   PRO   174      12.708  -1.701  14.967  1.00  0.00
ATOM   1364  CA  PRO   174      13.168  -0.761  13.951  1.00  0.00
ATOM   1365  C   PRO   174      14.688  -0.659  13.944  1.00  0.00
ATOM   1366  O   PRO   174      15.336  -0.817  14.979  1.00  0.00
ATOM   1367  CB  PRO   174      12.520   0.565  14.352  1.00  0.00
ATOM   1368  CG  PRO   174      11.330   0.171  15.160  1.00  0.00
ATOM   1369  CD  PRO   174      11.737  -1.053  15.931  1.00  0.00
ATOM   1370  N   LYS   175      15.253  -0.392  12.771  1.00  0.00
ATOM   1371  CA  LYS   175      16.698  -0.267  12.627  1.00  0.00
ATOM   1372  C   LYS   175      17.129   1.193  12.645  1.00  0.00
ATOM   1373  O   LYS   175      16.419   2.067  12.147  1.00  0.00
ATOM   1374  CB  LYS   175      17.160  -0.882  11.304  1.00  0.00
ATOM   1375  CG  LYS   175      16.936  -2.382  11.205  1.00  0.00
ATOM   1376  CD  LYS   175      17.383  -2.920   9.856  1.00  0.00
ATOM   1377  CE  LYS   175      17.173  -4.422   9.763  1.00  0.00
ATOM   1378  NZ  LYS   175      17.643  -4.969   8.460  1.00  0.00
ATOM   1379  N   GLU   176      18.320   1.470  13.191  1.00  0.00
ATOM   1380  CA  GLU   176      18.651   2.827  13.607  1.00  0.00
ATOM   1381  C   GLU   176      18.854   3.738  12.403  1.00  0.00
ATOM   1382  O   GLU   176      19.321   3.299  11.352  1.00  0.00
ATOM   1383  CB  GLU   176      19.941   2.835  14.430  1.00  0.00
ATOM   1384  CG  GLU   176      19.813   2.169  15.790  1.00  0.00
ATOM   1385  CD  GLU   176      21.108   2.199  16.577  1.00  0.00
ATOM   1386  OE1 GLU   176      22.117   2.704  16.042  1.00  0.00
ATOM   1387  OE2 GLU   176      21.115   1.715  17.729  1.00  0.00
ATOM   1388  N   SER   177      18.500   5.009  12.562  1.00  0.00
ATOM   1389  CA  SER   177      18.658   5.989  11.494  1.00  0.00
ATOM   1390  C   SER   177      20.032   6.645  11.548  1.00  0.00
ATOM   1391  O   SER   177      20.804   6.415  12.477  1.00  0.00
ATOM   1392  CB  SER   177      17.602   7.088  11.615  1.00  0.00
ATOM   1393  OG  SER   177      17.810   7.871  12.777  1.00  0.00
ATOM   1394  N   SER   178      20.329   7.465  10.545  1.00  0.00
ATOM   1395  CA  SER   178      21.605   8.167  10.483  1.00  0.00
ATOM   1396  C   SER   178      21.910   8.872  11.798  1.00  0.00
ATOM   1397  O   SER   178      21.002   9.285  12.518  1.00  0.00
ATOM   1398  CB  SER   178      21.583   9.221   9.374  1.00  0.00
ATOM   1399  OG  SER   178      20.668  10.260   9.676  1.00  0.00
ATOM   1400  N   PHE   179      23.128   9.724  11.929  1.00  0.00
ATOM   1401  CA  PHE   179      23.044  11.143  12.255  1.00  0.00
ATOM   1402  C   PHE   179      21.954  11.830  11.442  1.00  0.00
ATOM   1403  O   PHE   179      21.732  11.501  10.277  1.00  0.00
ATOM   1404  CB  PHE   179      24.371  11.841  11.954  1.00  0.00
ATOM   1405  CG  PHE   179      25.481  11.463  12.894  1.00  0.00
ATOM   1406  CD1 PHE   179      26.423  10.515  12.531  1.00  0.00
ATOM   1407  CD2 PHE   179      25.584  12.056  14.140  1.00  0.00
ATOM   1408  CE1 PHE   179      27.443  10.168  13.395  1.00  0.00
ATOM   1409  CE2 PHE   179      26.605  11.708  15.005  1.00  0.00
ATOM   1410  CZ  PHE   179      27.532  10.769  14.637  1.00  0.00
ATOM   1411  N   LEU   180      21.274  12.788  12.064  1.00  0.00
ATOM   1412  CA  LEU   180      20.199  13.517  11.403  1.00  0.00
ATOM   1413  C   LEU   180      20.678  14.144  10.100  1.00  0.00
ATOM   1414  O   LEU   180      19.900  14.321   9.162  1.00  0.00
ATOM   1415  CB  LEU   180      19.678  14.638  12.305  1.00  0.00
ATOM   1416  CG  LEU   180      18.925  14.200  13.564  1.00  0.00
ATOM   1417  CD1 LEU   180      18.613  15.398  14.447  1.00  0.00
ATOM   1418  CD2 LEU   180      17.612  13.525  13.197  1.00  0.00
TER
END
