
#######################################################
#                                                     #
#                        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   15 (  150),  selected   15 , name T0299TS277_3-D2
# Molecule2: number of CA atoms   89 (  757),  selected   15 , name T0299_D2.pdb
# PARAMETERS: T0299TS277_3-D2.T0299_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:    15        79 - 93          3.96     3.96
  LCS_AVERAGE:     16.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        81 - 90          1.86     4.68
  LCS_AVERAGE:      9.74

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        85 - 90          0.99     6.26
  LCS_AVERAGE:      5.17

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:   89
LCS_GDT     L      79     L      79      3    4   15     3    3    4    4    4    4    6    7    8   11   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     E      80     E      80      3    4   15     3    3    4    4    4    4    6    7    9   10   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     D      81     D      81      5   10   15     3    3    5    7    9   10   11   11   12   12   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     F      82     F      82      5   10   15     4    4    7    8    9   10   11   11   12   12   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     E      83     E      83      5   10   15     4    4    6    8    9   10   11   11   12   12   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     A      84     A      84      5   10   15     4    4    7    8    9   10   11   11   12   12   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     E      85     E      85      6   10   15     4    5    6    8    8   10   11   11   12   12   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     L      86     L      86      6   10   15     3    5    6    8    9   10   11   11   12   12   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     E      87     E      87      6   10   15     3    5    7    8    9   10   11   11   12   12   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     N      88     N      88      6   10   15     3    5    7    8    9   10   11   11   12   12   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     L      89     L      89      6   10   15     3    5    7    8    9   10   11   11   12   12   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     P      90     P      90      6   10   15     3    4    7    8    9   10   11   11   12   12   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     A      91     A      91      4    9   15     3    3    4    5    6    9   11   11   12   12   13   13   15   15   15   15   15   15   15   15 
LCS_GDT     W      92     W      92      3    9   15     3    4    7    8    9   10   11   11   12   12   14   14   15   15   15   15   15   15   15   15 
LCS_GDT     W      93     W      93      0    4   15     0    0    3    3    3    4    4    4    8   12   14   14   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:  10.59  (   5.17    9.74   16.85 )

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      7      8      9     10     11     11     12     12     14     14     15     15     15     15     15     15     15     15 
GDT PERCENT_CA   4.49   5.62   7.87   8.99  10.11  11.24  12.36  12.36  13.48  13.48  15.73  15.73  16.85  16.85  16.85  16.85  16.85  16.85  16.85  16.85
GDT RMS_LOCAL    0.23   0.63   1.07   1.18   1.41   1.65   1.91   1.91   2.28   2.28   3.75   3.75   3.96   3.96   3.96   3.96   3.96   3.96   3.96   3.96
GDT RMS_ALL_CA   9.50   6.97   4.72   4.74   4.82   4.54   4.63   4.63   4.75   4.75   4.02   4.02   3.96   3.96   3.96   3.96   3.96   3.96   3.96   3.96

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      L      79         11.240
LGA    E      80      E      80         10.958
LGA    D      81      D      81          3.561
LGA    F      82      F      82          1.593
LGA    E      83      E      83          2.267
LGA    A      84      A      84          1.051
LGA    E      85      E      85          2.988
LGA    L      86      L      86          1.916
LGA    E      87      E      87          0.854
LGA    N      88      N      88          0.458
LGA    L      89      L      89          1.930
LGA    P      90      P      90          0.883
LGA    A      91      A      91          5.530
LGA    W      92      W      92          1.893
LGA    W      93      W      93          6.508

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   89    4.0     11    1.91    10.955    11.290     0.548

LGA_LOCAL      RMSD =  1.906  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.916  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  3.960  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.230586 * X  +   0.755875 * Y  +  -0.612766 * Z  +  -4.555504
  Y_new =  -0.331372 * X  +  -0.531096 * Y  +  -0.779827 * Z  +  53.641357
  Z_new =  -0.914890 * X  +   0.382871 * Y  +   0.128013 * Z  +   3.890490 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.248130   -1.893462  [ DEG:    71.5126   -108.4874 ]
  Theta =   1.155234    1.986359  [ DEG:    66.1900    113.8100 ]
  Phi   =  -0.962860    2.178732  [ DEG:   -55.1678    124.8322 ]
 
# 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: T0299TS277_3-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0299TS277_3-D2.T0299_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   89   4.0   11   1.91  11.290     3.96
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS277_3-D2
PFRMAT TS 
TARGET T0299
MODEL 3
PARENT 1CTF
ATOM   1439  H   LEU    79       1.238  55.461  -2.946  1.00  0.00                              
ATOM   1441  N   LEU    79       0.632  54.738  -3.020  1.00  0.00                              
ATOM   1443  CA  LEU    79      -0.161  54.316  -1.909  1.00  0.00                              
ATOM   1445  CB  LEU    79       0.285  52.955  -1.472  1.00  0.00                              
ATOM   1447  C   LEU    79      -0.175  55.253  -0.754  1.00  0.00                              
ATOM   1449  O   LEU    79       0.869  55.605  -0.195  1.00  0.00                              
ATOM   1451  CG  LEU    79      -0.528  52.316  -0.423  1.00  0.00                              
ATOM   1453  CD1 LEU    79      -0.139  52.843   0.917  1.00  0.00                              
ATOM   1455  CD2 LEU    79      -2.005  52.519  -0.707  1.00  0.00                              
ATOM   1457  H   GLU    80      -2.123  55.393  -0.824  1.00  0.00                              
ATOM   1459  N   GLU    80      -1.344  55.638  -0.345  1.00  0.00                              
ATOM   1461  CA  GLU    80      -1.448  56.443   0.809  1.00  0.00                              
ATOM   1463  CB  GLU    80      -0.085  56.997   1.166  1.00  0.00                              
ATOM   1465  C   GLU    80      -2.407  57.543   0.624  1.00  0.00                              
ATOM   1467  O   GLU    80      -2.127  58.682   1.003  1.00  0.00                              
ATOM   1469  CG  GLU    80      -0.033  57.674   2.509  1.00  0.00                              
ATOM   1471  CD  GLU    80       1.386  57.991   2.961  1.00  0.00                              
ATOM   1473  OE1 GLU    80       2.300  57.985   2.108  1.00  0.00                              
ATOM   1475  OE2 GLU    80       1.592  58.228   4.176  1.00  0.00                              
ATOM   1477  H   ASP    81      -3.722  56.369  -0.229  1.00  0.00                              
ATOM   1479  N   ASP    81      -3.556  57.252   0.063  1.00  0.00                              
ATOM   1481  CA  ASP    81      -4.567  58.258  -0.115  1.00  0.00                              
ATOM   1483  CB  ASP    81      -3.911  59.602  -0.437  1.00  0.00                              
ATOM   1485  C   ASP    81      -5.572  57.851  -1.232  1.00  0.00                              
ATOM   1487  O   ASP    81      -6.463  57.014  -0.999  1.00  0.00                              
ATOM   1489  CG  ASP    81      -4.886  60.755  -0.391  1.00  0.00                              
ATOM   1491  OD1 ASP    81      -6.036  60.551   0.070  1.00  0.00                              
ATOM   1493  OD2 ASP    81      -4.508  61.879  -0.789  1.00  0.00                              
ATOM   1495  H   PHE    82      -4.839  59.173  -2.529  1.00  0.00                              
ATOM   1497  N   PHE    82      -5.463  58.474  -2.421  1.00  0.00                              
ATOM   1499  CA  PHE    82      -6.309  58.083  -3.562  1.00  0.00                              
ATOM   1501  CB  PHE    82      -7.540  57.314  -3.111  1.00  0.00                              
ATOM   1503  C   PHE    82      -6.747  59.270  -4.443  1.00  0.00                              
ATOM   1505  O   PHE    82      -6.100  59.583  -5.453  1.00  0.00                              
ATOM   1507  CG  PHE    82      -8.423  56.974  -4.257  1.00  0.00                              
ATOM   1509  CD1 PHE    82      -7.923  56.278  -5.350  1.00  0.00                              
ATOM   1511  CE1 PHE    82      -8.730  55.984  -6.433  1.00  0.00                              
ATOM   1513  CZ  PHE    82     -10.063  56.387  -6.435  1.00  0.00                              
ATOM   1515  CD2 PHE    82      -9.757  57.387  -4.275  1.00  0.00                              
ATOM   1517  CE2 PHE    82     -10.571  57.104  -5.357  1.00  0.00                              
ATOM   1519  H   GLU    83      -8.304  59.635  -3.287  1.00  0.00                              
ATOM   1521  N   GLU    83      -7.870  59.890  -4.088  1.00  0.00                              
ATOM   1523  CA  GLU    83      -8.433  60.950  -4.885  1.00  0.00                              
ATOM   1525  CB  GLU    83      -9.439  61.752  -4.057  1.00  0.00                              
ATOM   1527  C   GLU    83      -7.351  61.871  -5.427  1.00  0.00                              
ATOM   1529  O   GLU    83      -7.266  62.088  -6.635  1.00  0.00                              
ATOM   1531  CG  GLU    83     -10.465  62.505  -4.885  1.00  0.00                              
ATOM   1533  CD  GLU    83     -11.318  63.456  -4.055  1.00  0.00                              
ATOM   1535  OE1 GLU    83     -11.132  63.500  -2.818  1.00  0.00                              
ATOM   1537  OE2 GLU    83     -12.165  64.171  -4.642  1.00  0.00                              
ATOM   1539  H   ALA    84      -6.565  62.173  -3.637  1.00  0.00                              
ATOM   1541  N   ALA    84      -6.489  62.397  -4.541  1.00  0.00                              
ATOM   1543  CA  ALA    84      -5.404  63.298  -4.971  1.00  0.00                              
ATOM   1545  CB  ALA    84      -4.830  64.049  -3.775  1.00  0.00                              
ATOM   1547  C   ALA    84      -4.284  62.523  -5.699  1.00  0.00                              
ATOM   1549  O   ALA    84      -3.103  62.607  -5.301  1.00  0.00                              
ATOM   1551  H   GLU    85      -5.581  61.617  -6.914  1.00  0.00                              
ATOM   1553  N   GLU    85      -4.669  61.715  -6.738  1.00  0.00                              
ATOM   1555  CA  GLU    85      -3.692  60.932  -7.548  1.00  0.00                              
ATOM   1557  CB  GLU    85      -4.414  59.755  -8.276  1.00  0.00                              
ATOM   1559  C   GLU    85      -2.929  61.806  -8.578  1.00  0.00                              
ATOM   1561  O   GLU    85      -1.707  61.804  -8.605  1.00  0.00                              
ATOM   1563  CG  GLU    85      -3.493  58.874  -9.140  1.00  0.00                              
ATOM   1565  CD  GLU    85      -4.148  57.569  -9.599  1.00  0.00                              
ATOM   1567  OE1 GLU    85      -5.159  57.148  -8.980  1.00  0.00                              
ATOM   1569  OE2 GLU    85      -3.637  56.950 -10.554  1.00  0.00                              
ATOM   1571  H   LEU    86      -4.590  62.530  -9.385  1.00  0.00                              
ATOM   1573  N   LEU    86      -3.644  62.530  -9.435  1.00  0.00                              
ATOM   1575  CA  LEU    86      -2.968  63.331 -10.476  1.00  0.00                              
ATOM   1577  CB  LEU    86      -3.350  62.862 -11.878  1.00  0.00                              
ATOM   1579  C   LEU    86      -3.245  64.818 -10.303  1.00  0.00                              
ATOM   1581  O   LEU    86      -3.612  65.509 -11.258  1.00  0.00                              
ATOM   1583  CG  LEU    86      -3.918  61.447 -11.999  1.00  0.00                              
ATOM   1585  CD1 LEU    86      -5.083  61.440 -12.981  1.00  0.00                              
ATOM   1587  CD2 LEU    86      -2.825  60.479 -12.459  1.00  0.00                              
ATOM   1589  H   GLU    87      -2.788  64.733  -8.393  1.00  0.00                              
ATOM   1591  N   GLU    87      -3.047  65.314  -9.091  1.00  0.00                              
ATOM   1593  CA  GLU    87      -3.232  66.726  -8.805  1.00  0.00                              
ATOM   1595  CB  GLU    87      -4.591  66.949  -8.149  1.00  0.00                              
ATOM   1597  C   GLU    87      -2.123  67.234  -7.883  1.00  0.00                              
ATOM   1599  O   GLU    87      -1.997  68.441  -7.657  1.00  0.00                              
ATOM   1601  CG  GLU    87      -5.754  66.462  -8.986  1.00  0.00                              
ATOM   1603  CD  GLU    87      -6.078  67.398 -10.151  1.00  0.00                              
ATOM   1605  OE1 GLU    87      -5.468  68.487 -10.231  1.00  0.00                              
ATOM   1607  OE2 GLU    87      -6.957  67.050 -10.976  1.00  0.00                              
ATOM   1609  H   ASN    88      -1.418  65.404  -7.615  1.00  0.00                              
ATOM   1611  N   ASN    88      -1.315  66.303  -7.354  1.00  0.00                              
ATOM   1613  CA  ASN    88      -0.248  66.648  -6.411  1.00  0.00                              
ATOM   1615  CB  ASN    88      -0.811  66.739  -4.985  1.00  0.00                              
ATOM   1617  C   ASN    88       0.895  65.615  -6.460  1.00  0.00                              
ATOM   1619  O   ASN    88       0.848  64.602  -5.760  1.00  0.00                              
ATOM   1621  CG  ASN    88       0.231  67.164  -3.967  1.00  0.00                              
ATOM   1623  ND2 ASN    88      -0.208  67.435  -2.746  1.00  0.00                              
ATOM   1625 HD21 ASN    88      -1.131  67.359  -2.571  1.00  0.00                              
ATOM   1627 HD22 ASN    88       0.406  67.691  -2.077  1.00  0.00                              
ATOM   1629  OD1 ASN    88       1.420  67.239  -4.275  1.00  0.00                              
ATOM   1631  H   LEU    89       1.886  66.639  -7.847  1.00  0.00                              
ATOM   1633  N   LEU    89       1.910  65.863  -7.308  1.00  0.00                              
ATOM   1635  CA  LEU    89       3.067  64.945  -7.408  1.00  0.00                              
ATOM   1637  CB  LEU    89       2.553  63.478  -7.524  1.00  0.00                              
ATOM   1639  C   LEU    89       3.980  65.297  -8.632  1.00  0.00                              
ATOM   1641  O   LEU    89       3.581  65.093  -9.785  1.00  0.00                              
ATOM   1643  CG  LEU    89       3.610  62.358  -7.546  1.00  0.00                              
ATOM   1645  CD1 LEU    89       4.526  62.473  -6.324  1.00  0.00                              
ATOM   1647  CD2 LEU    89       2.913  60.957  -7.625  1.00  0.00                              
ATOM   1649  N   PRO    90       5.233  65.799  -8.387  1.00  0.00                              
ATOM   1651  CA  PRO    90       6.149  66.151  -9.491  1.00  0.00                              
ATOM   1653  CB  PRO    90       7.035  67.193  -8.852  1.00  0.00                              
ATOM   1655  C   PRO    90       6.983  64.949  -9.930  1.00  0.00                              
ATOM   1657  O   PRO    90       7.508  64.915 -11.042  1.00  0.00                              
ATOM   1659  CG  PRO    90       7.233  66.658  -7.460  1.00  0.00                              
ATOM   1661  CD  PRO    90       5.853  66.093  -7.070  1.00  0.00                              
ATOM   1663  H   ALA    91       6.763  64.107  -8.154  1.00  0.00                              
ATOM   1665  N   ALA    91       7.131  63.978  -9.004  1.00  0.00                              
ATOM   1667  CA  ALA    91       7.865  62.718  -9.268  1.00  0.00                              
ATOM   1669  CB  ALA    91       7.009  61.547  -8.828  1.00  0.00                              
ATOM   1671  C   ALA    91       8.227  62.545 -10.741  1.00  0.00                              
ATOM   1673  O   ALA    91       7.364  62.166 -11.553  1.00  0.00                              
ATOM   1675  H   TRP    92      10.152  63.040 -10.461  1.00  0.00                              
ATOM   1677  N   TRP    92       9.515  62.752 -11.101  1.00  0.00                              
ATOM   1679  CA  TRP    92       9.929  62.557 -12.489  1.00  0.00                              
ATOM   1681  CB  TRP    92       9.438  63.710 -13.371  1.00  0.00                              
ATOM   1683  C   TRP    92      11.438  62.341 -12.675  1.00  0.00                              
ATOM   1685  O   TRP    92      12.244  62.737 -11.843  1.00  0.00                              
ATOM   1687  CG  TRP    92      10.167  64.998 -13.225  1.00  0.00                              
ATOM   1689  CD1 TRP    92      11.084  65.368 -12.264  1.00  0.00                              
ATOM   1691  NE1 TRP    92      11.462  66.651 -12.460  1.00  0.00                              
ATOM   1693  HE1 TRP    92      12.068  67.135 -11.906  1.00  0.00                              
ATOM   1695  CD2 TRP    92       9.998  66.093 -14.046  1.00  0.00                              
ATOM   1697  CE2 TRP    92      10.797  67.143 -13.517  1.00  0.00                              
ATOM   1699  CE3 TRP    92       9.208  66.346 -15.154  1.00  0.00                              
ATOM   1701  CZ3 TRP    92       9.196  67.614 -15.677  1.00  0.00                              
ATOM   1703  CH2 TRP    92       9.942  68.642 -15.093  1.00  0.00                              
ATOM   1705  CZ2 TRP    92      10.737  68.420 -14.002  1.00  0.00                              
ATOM   1707  H   TRP    93      11.125  61.343 -14.357  1.00  0.00                              
ATOM   1709  N   TRP    93      11.800  61.697 -13.794  1.00  0.00                              
ATOM   1711  CA  TRP    93      13.199  61.504 -14.145  1.00  0.00                              
ATOM   1713  CB  TRP    93      13.464  60.091 -14.656  1.00  0.00                              
ATOM   1715  C   TRP    93      13.622  62.521 -15.205  1.00  0.00                              
ATOM   1717  O   TRP    93      13.645  62.209 -16.401  1.00  0.00                              
ATOM   1719  CG  TRP    93      14.830  59.605 -14.382  1.00  0.00                              
ATOM   1721  CD1 TRP    93      15.333  59.165 -13.211  1.00  0.00                              
ATOM   1723  NE1 TRP    93      16.654  58.891 -13.352  1.00  0.00                              
ATOM   1725  HE1 TRP    93      17.217  58.554 -12.667  1.00  0.00                              
ATOM   1727  CD2 TRP    93      15.855  59.480 -15.328  1.00  0.00                              
ATOM   1729  CE2 TRP    93      17.014  59.124 -14.627  1.00  0.00                              
ATOM   1731  CE3 TRP    93      15.967  59.834 -16.671  1.00  0.00                              
ATOM   1733  CZ3 TRP    93      17.199  59.886 -17.230  1.00  0.00                              
ATOM   1735  CH2 TRP    93      18.339  59.577 -16.488  1.00  0.00                              
ATOM   1737  CZ2 TRP    93      18.259  59.178 -15.196  1.00  0.00                              
TER 
END
