
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms   89 (  757),  selected   15 , name T0299_D2.pdb
# PARAMETERS: T0299TS277_4-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          4.54     4.54
  LCS_AVERAGE:     16.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        79 - 88          1.82     8.86
  LCS_AVERAGE:      9.74

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        81 - 87          0.93     8.62
  LCS_AVERAGE:      6.44

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      6   10   15     4    4    6    8    9   10   10   11   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     E      80     E      80      6   10   15     4    4    6    8    9   10   10   11   11   12   12   12   12   14   15   15   15   15   15   15 
LCS_GDT     D      81     D      81      7   10   15     4    4    7    8    9   10   10   11   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     F      82     F      82      7   10   15     4    5    7    8    9   10   10   11   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     E      83     E      83      7   10   15     4    5    7    8    9   10   10   11   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     A      84     A      84      7   10   15     4    5    7    8    9   10   10   11   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     E      85     E      85      7   10   15     4    5    7    8    9   10   10   11   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     L      86     L      86      7   10   15     4    5    7    8    9   10   10   11   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     E      87     E      87      7   10   15     4    5    7    7    9   10   10   11   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     N      88     N      88      5   10   15     4    4    6    7    8   10   10   11   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     L      89     L      89      5    8   15     4    4    5    7    8    9    9   11   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     P      90     P      90      5    7   15     4    4    5    5    5    9    9   10   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     A      91     A      91      5    6   15     4    4    5    5    5    6    7    8   11   12   12   12   13   14   15   15   15   15   15   15 
LCS_GDT     W      92     W      92      5    6   15     0    3    5    5    5    6    9   10   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_GDT     W      93     W      93      0    3   15     0    0    3    3    3    3    4    4   11   12   12   13   13   14   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:  11.01  (   6.44    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     10     11     11     12     12     13     13     14     15     15     15     15     15     15 
GDT PERCENT_CA   4.49   5.62   7.87   8.99  10.11  11.24  11.24  12.36  12.36  13.48  13.48  14.61  14.61  15.73  16.85  16.85  16.85  16.85  16.85  16.85
GDT RMS_LOCAL    0.16   0.47   0.93   1.37   1.57   1.82   1.82   2.44   2.44   2.92   2.92   3.98   3.81   4.23   4.54   4.54   4.54   4.54   4.54   4.54
GDT RMS_ALL_CA  14.19   7.61   8.62   9.92   9.43   8.86   8.86   7.34   7.34   6.39   6.39   4.60   4.95   4.62   4.54   4.54   4.54   4.54   4.54   4.54

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      L      79          2.933
LGA    E      80      E      80          3.789
LGA    D      81      D      81          2.812
LGA    F      82      F      82          2.358
LGA    E      83      E      83          2.062
LGA    A      84      A      84          1.624
LGA    E      85      E      85          2.351
LGA    L      86      L      86          2.418
LGA    E      87      E      87          2.004
LGA    N      88      N      88          1.283
LGA    L      89      L      89          3.616
LGA    P      90      P      90          5.351
LGA    A      91      A      91         12.376
LGA    W      92      W      92         13.354
LGA    W      93      W      93         13.412

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   89    4.0     11    2.44    10.955    10.945     0.434

LGA_LOCAL      RMSD =  2.435  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.395  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  4.538  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.299275 * X  +  -0.747561 * Y  +  -0.592948 * Z  +  59.724823
  Y_new =  -0.554645 * X  +  -0.369360 * Y  +   0.745615 * Z  +  17.614061
  Z_new =  -0.776404 * X  +   0.552019 * Y  +  -0.304091 * Z  +  -6.345700 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.074307   -1.067286  [ DEG:   118.8490    -61.1510 ]
  Theta =   0.888940    2.252653  [ DEG:    50.9325    129.0675 ]
  Phi   =  -2.065603    1.075989  [ DEG:  -118.3504     61.6496 ]
 
# 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_4-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0299TS277_4-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   2.44  10.945     4.54
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS277_4-D2
PFRMAT TS 
TARGET T0299
MODEL 4
PARENT 1DD3_A
ATOM   1439  H   LEU    79      -7.446  53.469  -3.488  1.00  0.00                              
ATOM   1441  N   LEU    79      -7.409  54.291  -3.953  1.00  0.00                              
ATOM   1443  CA  LEU    79      -8.397  55.345  -3.654  1.00  0.00                              
ATOM   1445  CB  LEU    79      -9.656  54.722  -3.076  1.00  0.00                              
ATOM   1447  C   LEU    79      -7.794  56.442  -2.679  1.00  0.00                              
ATOM   1449  O   LEU    79      -6.583  56.468  -2.452  1.00  0.00                              
ATOM   1451  CG  LEU    79     -10.360  53.707  -3.991  1.00  0.00                              
ATOM   1453  CD1 LEU    79     -10.968  52.572  -3.172  1.00  0.00                              
ATOM   1455  CD2 LEU    79     -11.425  54.399  -4.833  1.00  0.00                              
ATOM   1457  H   GLU    80      -9.604  57.195  -2.235  1.00  0.00                              
ATOM   1459  N   GLU    80      -8.676  57.309  -2.085  1.00  0.00                              
ATOM   1461  CA  GLU    80      -8.212  58.455  -1.202  1.00  0.00                              
ATOM   1463  CB  GLU    80      -7.437  57.957   0.044  1.00  0.00                              
ATOM   1465  C   GLU    80      -7.361  59.488  -1.985  1.00  0.00                              
ATOM   1467  O   GLU    80      -7.580  60.697  -1.862  1.00  0.00                              
ATOM   1469  CG  GLU    80      -8.285  57.147   1.012  1.00  0.00                              
ATOM   1471  CD  GLU    80      -7.475  56.529   2.139  1.00  0.00                              
ATOM   1473  OE1 GLU    80      -6.255  56.799   2.219  1.00  0.00                              
ATOM   1475  OE2 GLU    80      -8.053  55.761   2.940  1.00  0.00                              
ATOM   1477  H   ASP    81      -6.186  58.086  -2.756  1.00  0.00                              
ATOM   1479  N   ASP    81      -6.363  59.011  -2.756  1.00  0.00                              
ATOM   1481  CA  ASP    81      -5.537  59.901  -3.607  1.00  0.00                              
ATOM   1483  CB  ASP    81      -4.055  59.468  -3.586  1.00  0.00                              
ATOM   1485  C   ASP    81      -6.064  59.909  -5.040  1.00  0.00                              
ATOM   1487  O   ASP    81      -5.575  60.641  -5.884  1.00  0.00                              
ATOM   1489  CG  ASP    81      -3.441  59.542  -2.205  1.00  0.00                              
ATOM   1491  OD1 ASP    81      -3.618  60.576  -1.525  1.00  0.00                              
ATOM   1493  OD2 ASP    81      -2.793  58.561  -1.783  1.00  0.00                              
ATOM   1495  H   PHE    82      -7.462  58.611  -4.579  1.00  0.00                              
ATOM   1497  N   PHE    82      -7.098  59.123  -5.285  1.00  0.00                              
ATOM   1499  CA  PHE    82      -7.685  58.992  -6.623  1.00  0.00                              
ATOM   1501  CB  PHE    82      -8.852  57.972  -6.561  1.00  0.00                              
ATOM   1503  C   PHE    82      -8.176  60.349  -7.160  1.00  0.00                              
ATOM   1505  O   PHE    82      -8.086  60.615  -8.366  1.00  0.00                              
ATOM   1507  CG  PHE    82      -9.414  57.588  -7.890  1.00  0.00                              
ATOM   1509  CD1 PHE    82      -8.764  56.667  -8.688  1.00  0.00                              
ATOM   1511  CE1 PHE    82      -9.269  56.340  -9.966  1.00  0.00                              
ATOM   1513  CZ  PHE    82     -10.413  56.966 -10.436  1.00  0.00                              
ATOM   1515  CD2 PHE    82     -10.624  58.126  -8.333  1.00  0.00                              
ATOM   1517  CE2 PHE    82     -11.136  57.796  -9.599  1.00  0.00                              
ATOM   1519  H   GLU    83      -8.656  60.988  -5.346  1.00  0.00                              
ATOM   1521  N   GLU    83      -8.653  61.220  -6.262  1.00  0.00                              
ATOM   1523  CA  GLU    83      -9.190  62.514  -6.674  1.00  0.00                              
ATOM   1525  CB  GLU    83     -10.554  62.775  -5.995  1.00  0.00                              
ATOM   1527  C   GLU    83      -8.198  63.669  -6.388  1.00  0.00                              
ATOM   1529  O   GLU    83      -8.547  64.848  -6.530  1.00  0.00                              
ATOM   1531  CG  GLU    83     -11.699  61.916  -6.565  1.00  0.00                              
ATOM   1533  CD  GLU    83     -12.941  61.850  -5.662  1.00  0.00                              
ATOM   1535  OE1 GLU    83     -13.387  62.913  -5.170  1.00  0.00                              
ATOM   1537  OE2 GLU    83     -13.480  60.736  -5.468  1.00  0.00                              
ATOM   1539  H   ALA    84      -6.750  62.427  -5.878  1.00  0.00                              
ATOM   1541  N   ALA    84      -6.960  63.328  -6.007  1.00  0.00                              
ATOM   1543  CA  ALA    84      -5.933  64.351  -5.750  1.00  0.00                              
ATOM   1545  CB  ALA    84      -5.668  64.467  -4.248  1.00  0.00                              
ATOM   1547  C   ALA    84      -4.620  64.040  -6.500  1.00  0.00                              
ATOM   1549  O   ALA    84      -3.943  64.953  -6.976  1.00  0.00                              
ATOM   1551  H   GLU    85      -4.864  62.081  -6.302  1.00  0.00                              
ATOM   1553  N   GLU    85      -4.275  62.751  -6.623  1.00  0.00                              
ATOM   1555  CA  GLU    85      -3.010  62.352  -7.269  1.00  0.00                              
ATOM   1557  CB  GLU    85      -2.825  60.828  -7.221  1.00  0.00                              
ATOM   1559  C   GLU    85      -2.941  62.848  -8.714  1.00  0.00                              
ATOM   1561  O   GLU    85      -1.847  62.967  -9.284  1.00  0.00                              
ATOM   1563  CG  GLU    85      -1.384  60.373  -7.389  1.00  0.00                              
ATOM   1565  CD  GLU    85      -0.967  60.209  -8.840  1.00  0.00                              
ATOM   1567  OE1 GLU    85      -1.838  59.897  -9.683  1.00  0.00                              
ATOM   1569  OE2 GLU    85       0.236  60.370  -9.134  1.00  0.00                              
ATOM   1571  H   LEU    86      -4.906  62.982  -8.823  1.00  0.00                              
ATOM   1573  N   LEU    86      -4.087  63.149  -9.290  1.00  0.00                              
ATOM   1575  CA  LEU    86      -4.146  63.688 -10.637  1.00  0.00                              
ATOM   1577  CB  LEU    86      -5.606  63.959 -11.032  1.00  0.00                              
ATOM   1579  C   LEU    86      -3.338  64.988 -10.752  1.00  0.00                              
ATOM   1581  O   LEU    86      -2.723  65.251 -11.796  1.00  0.00                              
ATOM   1583  CG  LEU    86      -5.837  64.417 -12.467  1.00  0.00                              
ATOM   1585  CD1 LEU    86      -5.297  63.372 -13.418  1.00  0.00                              
ATOM   1587  CD2 LEU    86      -7.319  64.658 -12.712  1.00  0.00                              
ATOM   1589  H   GLU    87      -3.829  65.566  -8.918  1.00  0.00                              
ATOM   1591  N   GLU    87      -3.363  65.818  -9.702  1.00  0.00                              
ATOM   1593  CA  GLU    87      -2.693  67.120  -9.753  1.00  0.00                              
ATOM   1595  CB  GLU    87      -3.738  68.259  -9.791  1.00  0.00                              
ATOM   1597  C   GLU    87      -1.709  67.338  -8.576  1.00  0.00                              
ATOM   1599  O   GLU    87      -0.776  68.141  -8.694  1.00  0.00                              
ATOM   1601  CG  GLU    87      -4.638  68.227 -11.035  1.00  0.00                              
ATOM   1603  CD  GLU    87      -5.703  69.324 -11.055  1.00  0.00                              
ATOM   1605  OE1 GLU    87      -6.421  69.493 -10.037  1.00  0.00                              
ATOM   1607  OE2 GLU    87      -5.837  70.005 -12.094  1.00  0.00                              
ATOM   1609  H   ASN    88      -2.665  66.032  -7.389  1.00  0.00                              
ATOM   1611  N   ASN    88      -1.947  66.641  -7.414  1.00  0.00                              
ATOM   1613  CA  ASN    88      -1.100  66.829  -6.163  1.00  0.00                              
ATOM   1615  CB  ASN    88      -1.826  66.239  -4.909  1.00  0.00                              
ATOM   1617  C   ASN    88       0.318  66.221  -6.304  1.00  0.00                              
ATOM   1619  O   ASN    88       1.079  66.604  -7.193  1.00  0.00                              
ATOM   1621  CG  ASN    88      -1.125  66.573  -3.555  1.00  0.00                              
ATOM   1623  ND2 ASN    88      -1.432  65.797  -2.520  1.00  0.00                              
ATOM   1625 HD21 ASN    88      -2.050  65.097  -2.649  1.00  0.00                              
ATOM   1627 HD22 ASN    88      -1.025  65.954  -1.685  1.00  0.00                              
ATOM   1629  OD1 ASN    88      -0.349  67.537  -3.448  1.00  0.00                              
ATOM   1631  H   LEU    89       0.039  65.004  -4.759  1.00  0.00                              
ATOM   1633  N   LEU    89       0.672  65.295  -5.396  1.00  0.00                              
ATOM   1635  CA  LEU    89       2.025  64.709  -5.384  1.00  0.00                              
ATOM   1637  CB  LEU    89       2.648  64.861  -3.994  1.00  0.00                              
ATOM   1639  C   LEU    89       2.015  63.222  -5.786  1.00  0.00                              
ATOM   1641  O   LEU    89       1.100  62.472  -5.416  1.00  0.00                              
ATOM   1643  CG  LEU    89       2.794  66.289  -3.466  1.00  0.00                              
ATOM   1645  CD1 LEU    89       3.271  66.267  -2.020  1.00  0.00                              
ATOM   1647  CD2 LEU    89       3.764  67.074  -4.337  1.00  0.00                              
ATOM   1649  N   PRO    90       3.036  62.776  -6.515  1.00  0.00                              
ATOM   1651  CA  PRO    90       3.107  61.381  -6.938  1.00  0.00                              
ATOM   1653  CB  PRO    90       4.219  61.383  -7.980  1.00  0.00                              
ATOM   1655  C   PRO    90       3.429  60.436  -5.783  1.00  0.00                              
ATOM   1657  O   PRO    90       4.510  60.512  -5.196  1.00  0.00                              
ATOM   1659  CG  PRO    90       5.127  62.481  -7.523  1.00  0.00                              
ATOM   1661  CD  PRO    90       4.188  63.556  -7.015  1.00  0.00                              
ATOM   1663  H   ALA    91       1.636  59.643  -5.829  1.00  0.00                              
ATOM   1665  N   ALA    91       2.467  59.578  -5.427  1.00  0.00                              
ATOM   1667  CA  ALA    91       2.674  58.558  -4.360  1.00  0.00                              
ATOM   1669  CB  ALA    91       1.332  58.155  -3.768  1.00  0.00                              
ATOM   1671  C   ALA    91       3.428  57.305  -4.908  1.00  0.00                              
ATOM   1673  O   ALA    91       3.598  57.166  -6.125  1.00  0.00                              
ATOM   1675  H   TRP    92       3.789  56.553  -3.052  1.00  0.00                              
ATOM   1677  N   TRP    92       3.937  56.407  -3.978  1.00  0.00                              
ATOM   1679  CA  TRP    92       4.732  55.191  -4.407  1.00  0.00                              
ATOM   1681  CB  TRP    92       5.900  55.642  -5.278  1.00  0.00                              
ATOM   1683  C   TRP    92       5.322  54.401  -3.193  1.00  0.00                              
ATOM   1685  O   TRP    92       5.126  54.780  -2.029  1.00  0.00                              
ATOM   1687  CG  TRP    92       6.773  56.637  -4.605  1.00  0.00                              
ATOM   1689  CD1 TRP    92       6.521  57.285  -3.426  1.00  0.00                              
ATOM   1691  NE1 TRP    92       7.576  58.085  -3.100  1.00  0.00                              
ATOM   1693  HE1 TRP    92       7.620  58.647  -2.332  1.00  0.00                              
ATOM   1695  CD2 TRP    92       8.015  57.138  -5.080  1.00  0.00                              
ATOM   1697  CE2 TRP    92       8.526  57.986  -4.078  1.00  0.00                              
ATOM   1699  CE3 TRP    92       8.785  56.897  -6.219  1.00  0.00                              
ATOM   1701  CZ3 TRP    92      10.041  57.466  -6.302  1.00  0.00                              
ATOM   1703  CH2 TRP    92      10.548  58.247  -5.258  1.00  0.00                              
ATOM   1705  CZ2 TRP    92       9.815  58.489  -4.124  1.00  0.00                              
ATOM   1707  H   TRP    93       6.027  52.949  -4.406  1.00  0.00                              
ATOM   1709  N   TRP    93       6.022  53.244  -3.505  1.00  0.00                              
ATOM   1711  CA  TRP    93       6.750  52.433  -2.478  1.00  0.00                              
ATOM   1713  CB  TRP    93       8.126  53.131  -2.103  1.00  0.00                              
ATOM   1715  C   TRP    93       5.906  52.239  -1.220  1.00  0.00                              
ATOM   1717  O   TRP    93       5.481  51.121  -0.918  1.00  0.00                              
ATOM   1719  CG  TRP    93       9.087  53.365  -3.286  1.00  0.00                              
ATOM   1721  CD1 TRP    93       8.973  52.842  -4.545  1.00  0.00                              
ATOM   1723  NE1 TRP    93      10.045  53.239  -5.321  1.00  0.00                              
ATOM   1725  HE1 TRP    93      10.179  53.001  -6.234  1.00  0.00                              
ATOM   1727  CD2 TRP    93      10.308  54.136  -3.276  1.00  0.00                              
ATOM   1729  CE2 TRP    93      10.859  54.056  -4.574  1.00  0.00                              
ATOM   1731  CE3 TRP    93      10.994  54.872  -2.285  1.00  0.00                              
ATOM   1733  CZ3 TRP    93      12.220  55.449  -2.612  1.00  0.00                              
ATOM   1735  CH2 TRP    93      12.749  55.337  -3.910  1.00  0.00                              
ATOM   1737  CZ2 TRP    93      12.065  54.687  -4.916  1.00  0.00                              
TER 
END
