
#######################################################
#                                                     #
#                        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_1_2-D1
# Molecule2: number of CA atoms  180 ( 1390),  selected   19 , name T0295_D1.pdb
# PARAMETERS: T0295TS193_1_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         4.63    14.75
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       174 - 179         1.87    21.45
  LCS_AVERAGE:      2.63

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       162 - 165         0.71    25.79
  LONGEST_CONTINUOUS_SEGMENT:     4       175 - 178         0.92    24.77
  LCS_AVERAGE:      1.90

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    5   10     3    4    4    4    4    5    5    6    6    8    8    9    9   10   10   11   12   12   13   13 
LCS_GDT     P     163     P     163      4    5   10     3    4    4    4    4    5    5    6    6    8    8    9    9   10   10   11   12   12   13   14 
LCS_GDT     K     164     K     164      4    5   10     3    4    4    4    4    5    5    5    6    7    8    9    9    9    9   10   12   12   13   14 
LCS_GDT     V     165     V     165      4    5   10     0    4    4    4    4    5    5    6    6    8    8    9    9    9   10   11   12   14   14   15 
LCS_GDT     D     166     D     166      3    5   10     0    3    3    3    4    5    5    6    6    8    8    9    9   10   12   13   14   14   15   15 
LCS_GDT     S     167     S     167      3    3   10     0    3    3    3    3    3    5    6    7    8    8    9   10   11   12   13   14   14   15   15 
LCS_GDT     V     168     V     168      3    3   10     0    3    3    3    3    3    5    6    7    8    8    9   10   11   12   13   14   14   15   15 
LCS_GDT     I     169     I     169      3    3   12     1    3    3    3    3    4    5    6    7    8   10   11   11   12   12   13   14   14   15   15 
LCS_GDT     V     170     V     170      3    4   12     0    3    4    4    4    5    5    6    7    9   10   11   11   12   12   13   14   14   15   15 
LCS_GDT     K     171     K     171      3    4   12     3    3    4    4    4    5    5    6    7    9   10   11   11   12   12   13   14   14   15   15 
LCS_GDT     L     172     L     172      3    4   12     3    3    4    4    5    6    7    7    7    9   10   11   11   12   12   13   14   14   15   15 
LCS_GDT     I     173     I     173      3    4   12     3    3    4    4    4    5    5    7    8    9   10   11   11   12   12   13   14   14   15   15 
LCS_GDT     P     174     P     174      3    6   12     3    3    3    4    6    7    7    7    8    9   10   11   11   12   12   13   14   14   15   15 
LCS_GDT     K     175     K     175      4    6   12     3    3    4    5    6    7    7    7    8    9   10   11   11   12   12   13   14   14   15   15 
LCS_GDT     E     176     E     176      4    6   12     3    3    4    5    6    7    7    7    8    9    9   11   11   12   12   13   14   14   15   15 
LCS_GDT     S     177     S     177      4    6   12     3    3    4    5    6    7    7    7    8    9    9   10   11   12   12   12   12   13   15   15 
LCS_GDT     S     178     S     178      4    6   12     3    3    4    5    6    7    7    7    8    9   10   11   11   12   12   13   14   14   15   15 
LCS_GDT     F     179     F     179      3    6   12     3    3    3    5    6    7    7    7    8    9   10   11   11   12   12   13   14   14   15   15 
LCS_GDT     L     180     L     180      3    4   12     3    3    3    4    5    7    7    7    8    9   10   11   11   12   12   13   14   14   15   15 
LCS_AVERAGE  LCS_A:   3.60  (   1.90    2.63    6.26 )

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      3      4      4      5      6      7      7      7      8      9     10     11     11     12     12     13     14     14     15     15 
GDT PERCENT_CA   1.67   2.22   2.22   2.78   3.33   3.89   3.89   3.89   4.44   5.00   5.56   6.11   6.11   6.67   6.67   7.22   7.78   7.78   8.33   8.33
GDT RMS_LOCAL    0.03   0.71   0.71   1.21   1.87   2.14   2.14   2.14   2.83   3.15   4.07   4.29   4.25   4.63   4.63   5.32   5.63   5.63   6.09   6.07
GDT RMS_ALL_CA  12.46  25.79  25.79  24.72  21.45  20.78  20.78  20.78  21.22  19.12  10.63  13.46  16.06  14.75  14.75   9.09   9.39   9.39   9.77   9.33

#      Molecule1      Molecule2       DISTANCE
LGA    P     162      P     162         42.152
LGA    P     163      P     163         39.701
LGA    K     164      K     164         37.751
LGA    V     165      V     165         33.353
LGA    D     166      D     166         27.006
LGA    S     167      S     167         23.922
LGA    V     168      V     168         21.007
LGA    I     169      I     169         14.783
LGA    V     170      V     170         10.517
LGA    K     171      K     171         10.117
LGA    L     172      L     172          7.426
LGA    I     173      I     173          7.050
LGA    P     174      P     174          1.441
LGA    K     175      K     175          2.152
LGA    E     176      E     176          1.328
LGA    S     177      S     177          2.812
LGA    S     178      S     178          1.548
LGA    F     179      F     179          2.718
LGA    L     180      L     180          2.423

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  180    4.0      7    2.14     4.028     3.789     0.313

LGA_LOCAL      RMSD =  2.139  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 20.777  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  8.365  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.723996 * X  +   0.675833 * Y  +   0.138125 * Z  +  25.834387
  Y_new =  -0.680175 * X  +   0.666093 * Y  +   0.306076 * Z  + -12.694720
  Z_new =   0.114852 * X  +  -0.315547 * Y  +   0.941934 * Z  +  19.007753 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.323249    2.818344  [ DEG:   -18.5208    161.4792 ]
  Theta =  -0.115106   -3.026486  [ DEG:    -6.5951   -173.4049 ]
  Phi   =  -0.754200    2.387392  [ DEG:   -43.2125    136.7875 ]
 
# 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_1_2-D1                             
REMARK     2: T0295_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295TS193_1_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    7   2.14   3.789     8.36
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS193_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT N/A
ATOM   1272  N   PRO   162      23.416 -14.018  15.195  1.00  0.00
ATOM   1273  CA  PRO   162      23.609 -13.592  16.577  1.00  0.00
ATOM   1274  C   PRO   162      22.453 -12.720  17.051  1.00  0.00
ATOM   1275  O   PRO   162      21.836 -12.007  16.259  1.00  0.00
ATOM   1276  CB  PRO   162      24.923 -12.808  16.542  1.00  0.00
ATOM   1277  CG  PRO   162      24.941 -12.171  15.193  1.00  0.00
ATOM   1278  CD  PRO   162      24.407 -13.201  14.238  1.00  0.00
ATOM   1279  N   PRO   163      23.694 -11.341  15.179  1.00  0.00
ATOM   1280  CA  PRO   163      22.999 -10.357  14.358  1.00  0.00
ATOM   1281  C   PRO   163      22.236 -11.027  13.223  1.00  0.00
ATOM   1282  O   PRO   163      22.726 -11.975  12.607  1.00  0.00
ATOM   1283  CB  PRO   163      24.119  -9.461  13.825  1.00  0.00
ATOM   1284  CG  PRO   163      25.217  -9.601  14.826  1.00  0.00
ATOM   1285  CD  PRO   163      25.187 -11.033  15.280  1.00  0.00
ATOM   1286  N   LYS   164      21.035 -10.530  12.948  1.00  0.00
ATOM   1287  CA  LYS   164      20.221 -11.050  11.857  1.00  0.00
ATOM   1288  C   LYS   164      20.637 -10.446  10.522  1.00  0.00
ATOM   1289  O   LYS   164      21.276  -9.395  10.477  1.00  0.00
ATOM   1290  CB  LYS   164      18.745 -10.721  12.086  1.00  0.00
ATOM   1291  CG  LYS   164      18.176 -11.284  13.379  1.00  0.00
ATOM   1292  CD  LYS   164      18.130 -12.804  13.347  1.00  0.00
ATOM   1293  CE  LYS   164      17.393 -13.359  14.554  1.00  0.00
ATOM   1294  NZ  LYS   164      17.283 -14.843  14.504  1.00  0.00
ATOM   1295  N   VAL   165      20.270 -11.116   9.434  1.00  0.00
ATOM   1296  CA  VAL   165      20.594 -10.639   8.095  1.00  0.00
ATOM   1297  C   VAL   165      19.890  -9.321   7.795  1.00  0.00
ATOM   1298  O   VAL   165      18.664  -9.234   7.849  1.00  0.00
ATOM   1299  CB  VAL   165      20.164 -11.651   7.016  1.00  0.00
ATOM   1300  CG1 VAL   165      20.437 -11.096   5.627  1.00  0.00
ATOM   1301  CG2 VAL   165      20.930 -12.955   7.172  1.00  0.00
ATOM   1302  N   ASP   166      18.390 -11.371   8.494  1.00  0.00
ATOM   1303  CA  ASP   166      16.935 -11.291   8.534  1.00  0.00
ATOM   1304  C   ASP   166      16.469 -10.247   9.541  1.00  0.00
ATOM   1305  O   ASP   166      15.555  -9.469   9.265  1.00  0.00
ATOM   1306  CB  ASP   166      16.334 -12.640   8.937  1.00  0.00
ATOM   1307  CG  ASP   166      16.434 -13.675   7.833  1.00  0.00
ATOM   1308  OD1 ASP   166      16.745 -13.291   6.686  1.00  0.00
ATOM   1309  OD2 ASP   166      16.198 -14.868   8.115  1.00  0.00
ATOM   1310  N   SER   167      17.101 -10.233  10.709  1.00  0.00
ATOM   1311  CA  SER   167      16.762  -9.274  11.754  1.00  0.00
ATOM   1312  C   SER   167      17.212  -7.869  11.379  1.00  0.00
ATOM   1313  O   SER   167      16.616  -6.880  11.805  1.00  0.00
ATOM   1314  CB  SER   167      17.442  -9.654  13.071  1.00  0.00
ATOM   1315  OG  SER   167      18.850  -9.543  12.969  1.00  0.00
ATOM   1316  N   VAL   168      18.269  -7.786  10.577  1.00  0.00
ATOM   1317  CA  VAL   168      18.760  -6.504  10.085  1.00  0.00
ATOM   1318  C   VAL   168      17.693  -5.782   9.270  1.00  0.00
ATOM   1319  O   VAL   168      17.561  -4.561   9.346  1.00  0.00
ATOM   1320  CB  VAL   168      19.994  -6.680   9.181  1.00  0.00
ATOM   1321  CG1 VAL   168      21.136  -7.316   9.958  1.00  0.00
ATOM   1322  CG2 VAL   168      19.663  -7.574   7.995  1.00  0.00
ATOM   1323  N   ILE   169      16.513  -6.522   9.003  1.00  0.00
ATOM   1324  CA  ILE   169      15.325  -5.916   8.415  1.00  0.00
ATOM   1325  C   ILE   169      14.620  -5.005   9.412  1.00  0.00
ATOM   1326  O   ILE   169      14.169  -3.915   9.060  1.00  0.00
ATOM   1327  CB  ILE   169      14.311  -6.985   7.965  1.00  0.00
ATOM   1328  CG1 ILE   169      14.870  -7.790   6.791  1.00  0.00
ATOM   1329  CG2 ILE   169      13.010  -6.331   7.525  1.00  0.00
ATOM   1330  CD1 ILE   169      14.060  -9.024   6.457  1.00  0.00
ATOM   1331  N   VAL   170      14.528  -5.458  10.658  1.00  0.00
ATOM   1332  CA  VAL   170      13.909  -4.669  11.716  1.00  0.00
ATOM   1333  C   VAL   170      14.775  -3.473  12.090  1.00  0.00
ATOM   1334  O   VAL   170      14.263  -2.404  12.423  1.00  0.00
ATOM   1335  CB  VAL   170      13.696  -5.505  12.992  1.00  0.00
ATOM   1336  CG1 VAL   170      13.221  -4.621  14.135  1.00  0.00
ATOM   1337  CG2 VAL   170      12.653  -6.585  12.754  1.00  0.00
ATOM   1338  N   LYS   171      16.089  -3.660  12.032  1.00  0.00
ATOM   1339  CA  LYS   171      17.029  -2.594  12.363  1.00  0.00
ATOM   1340  C   LYS   171      16.994  -1.486  11.318  1.00  0.00
ATOM   1341  O   LYS   171      17.181  -0.312  11.638  1.00  0.00
ATOM   1342  CB  LYS   171      18.458  -3.141  12.426  1.00  0.00
ATOM   1343  CG  LYS   171      18.721  -4.050  13.615  1.00  0.00
ATOM   1344  CD  LYS   171      20.153  -4.560  13.614  1.00  0.00
ATOM   1345  CE  LYS   171      20.417  -5.469  14.803  1.00  0.00
ATOM   1346  NZ  LYS   171      21.809  -5.998  14.800  1.00  0.00
ATOM   1347  N   LEU   172      16.753  -1.866  10.067  1.00  0.00
ATOM   1348  CA  LEU   172      16.912  -0.949   8.945  1.00  0.00
ATOM   1349  C   LEU   172      15.582  -0.313   8.561  1.00  0.00
ATOM   1350  O   LEU   172      15.513   0.491   7.631  1.00  0.00
ATOM   1351  CB  LEU   172      17.455  -1.689   7.720  1.00  0.00
ATOM   1352  CG  LEU   172      18.805  -2.387   7.894  1.00  0.00
ATOM   1353  CD1 LEU   172      19.192  -3.133   6.627  1.00  0.00
ATOM   1354  CD2 LEU   172      19.898  -1.376   8.203  1.00  0.00
ATOM   1355  N   ILE   173      16.138   2.595   7.136  1.00  0.00
ATOM   1356  CA  ILE   173      16.910   2.773   8.360  1.00  0.00
ATOM   1357  C   ILE   173      16.000   2.851   9.579  1.00  0.00
ATOM   1358  O   ILE   173      14.898   3.397   9.509  1.00  0.00
ATOM   1359  CB  ILE   173      17.742   4.068   8.319  1.00  0.00
ATOM   1360  CG1 ILE   173      18.780   3.999   7.196  1.00  0.00
ATOM   1361  CG2 ILE   173      18.472   4.274   9.637  1.00  0.00
ATOM   1362  CD1 ILE   173      19.844   2.946   7.412  1.00  0.00
ATOM   1363  N   PRO   174      16.466   2.304  10.696  1.00  0.00
ATOM   1364  CA  PRO   174      15.693   2.309  11.932  1.00  0.00
ATOM   1365  C   PRO   174      16.568   2.668  13.127  1.00  0.00
ATOM   1366  O   PRO   174      16.162   3.436  13.999  1.00  0.00
ATOM   1367  CB  PRO   174      15.159   0.879  12.040  1.00  0.00
ATOM   1368  CG  PRO   174      15.128   0.384  10.633  1.00  0.00
ATOM   1369  CD  PRO   174      16.333   0.978   9.957  1.00  0.00
ATOM   1370  N   LYS   175      17.772   2.106  13.163  1.00  0.00
ATOM   1371  CA  LYS   175      18.694   2.340  14.267  1.00  0.00
ATOM   1372  C   LYS   175      19.851   3.233  13.838  1.00  0.00
ATOM   1373  O   LYS   175      20.119   3.389  12.647  1.00  0.00
ATOM   1374  CB  LYS   175      19.277   1.017  14.769  1.00  0.00
ATOM   1375  CG  LYS   175      18.230  -0.008  15.173  1.00  0.00
ATOM   1376  CD  LYS   175      17.462   0.443  16.405  1.00  0.00
ATOM   1377  CE  LYS   175      16.475  -0.619  16.860  1.00  0.00
ATOM   1378  NZ  LYS   175      15.314  -0.732  15.934  1.00  0.00
ATOM   1379  N   GLU   176      20.535   3.817  14.815  1.00  0.00
ATOM   1380  CA  GLU   176      21.668   4.693  14.541  1.00  0.00
ATOM   1381  C   GLU   176      22.807   3.929  13.878  1.00  0.00
ATOM   1382  O   GLU   176      23.604   4.503  13.136  1.00  0.00
ATOM   1383  CB  GLU   176      22.200   5.305  15.839  1.00  0.00
ATOM   1384  CG  GLU   176      21.206   6.205  16.553  1.00  0.00
ATOM   1385  CD  GLU   176      21.732   6.719  17.879  1.00  0.00
ATOM   1386  OE1 GLU   176      22.867   6.353  18.248  1.00  0.00
ATOM   1387  OE2 GLU   176      21.009   7.486  18.549  1.00  0.00
ATOM   1388  N   SER   177      22.246   3.002  12.156  1.00  0.00
ATOM   1389  CA  SER   177      22.234   3.684  10.868  1.00  0.00
ATOM   1390  C   SER   177      21.173   4.776  10.834  1.00  0.00
ATOM   1391  O   SER   177      20.222   4.706  10.054  1.00  0.00
ATOM   1392  CB  SER   177      21.934   2.695   9.740  1.00  0.00
ATOM   1393  OG  SER   177      20.652   2.113   9.899  1.00  0.00
ATOM   1394  N   SER   178      21.341   5.785  11.682  1.00  0.00
ATOM   1395  CA  SER   178      20.404   6.901  11.740  1.00  0.00
ATOM   1396  C   SER   178      21.126   8.234  11.598  1.00  0.00
ATOM   1397  O   SER   178      22.312   8.345  11.908  1.00  0.00
ATOM   1398  CB  SER   178      19.658   6.906  13.076  1.00  0.00
ATOM   1399  OG  SER   178      18.784   8.017  13.168  1.00  0.00
ATOM   1400  N   PHE   179      20.404   9.244  11.125  1.00  0.00
ATOM   1401  CA  PHE   179      20.974  10.575  10.946  1.00  0.00
ATOM   1402  C   PHE   179      21.605  11.083  12.235  1.00  0.00
ATOM   1403  O   PHE   179      22.614  11.788  12.208  1.00  0.00
ATOM   1404  CB  PHE   179      19.891  11.569  10.525  1.00  0.00
ATOM   1405  CG  PHE   179      20.408  12.957  10.270  1.00  0.00
ATOM   1406  CD1 PHE   179      21.065  13.261   9.090  1.00  0.00
ATOM   1407  CD2 PHE   179      20.235  13.958  11.209  1.00  0.00
ATOM   1408  CE1 PHE   179      21.540  14.537   8.856  1.00  0.00
ATOM   1409  CE2 PHE   179      20.710  15.234  10.976  1.00  0.00
ATOM   1410  CZ  PHE   179      21.361  15.526   9.806  1.00  0.00
ATOM   1411  N   LEU   180      21.005  10.721  13.364  1.00  0.00
ATOM   1412  CA  LEU   180      21.519  11.125  14.668  1.00  0.00
ATOM   1413  C   LEU   180      22.707  10.269  15.082  1.00  0.00
ATOM   1414  O   LEU   180      23.333  10.515  16.113  1.00  0.00
ATOM   1415  CB  LEU   180      20.435  10.982  15.739  1.00  0.00
ATOM   1416  CG  LEU   180      19.194  11.861  15.569  1.00  0.00
ATOM   1417  CD1 LEU   180      18.159  11.541  16.635  1.00  0.00
ATOM   1418  CD2 LEU   180      19.558  13.333  15.687  1.00  0.00
TER
END
