
#######################################################
#                                                     #
#                        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   16 (  117),  selected   16 , name T0316TS211_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   16 , name T0316_D2.pdb
# PARAMETERS: T0316TS211_3-D2.T0316_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:    13       220 - 232         4.49     9.72
  LONGEST_CONTINUOUS_SEGMENT:    13       223 - 235         4.80     7.97
  LCS_AVERAGE:     21.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       225 - 231         1.98     9.13
  LCS_AVERAGE:      9.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       227 - 230         0.37    11.19
  LONGEST_CONTINUOUS_SEGMENT:     4       232 - 235         0.56    10.71
  LCS_AVERAGE:      5.83

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:   60
LCS_GDT     G     220     G     220      3    3   13     0    3    3    3    3    4    5    8   10   10   11   12   12   12   13   13   13   14   14   14 
LCS_GDT     R     221     R     221      3    3   13     0    3    3    3    5    7    8    9   10   10   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     M     222     M     222      3    5   13     0    3    3    4    5    7    8    9   10   10   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     M     223     M     223      3    5   13     3    3    3    4    4    7    7    9   10   10   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     T     224     T     224      3    6   13     3    4    4    5    7    8    8    9   10   11   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     V     225     V     225      3    7   13     3    4    4    5    7    8    8    9   10   11   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     D     226     D     226      3    7   13     3    4    4    4    7    8    8    9   10   11   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     G     227     G     227      4    7   13     4    4    4    5    6    8    8    9   10   11   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     R     228     R     228      4    7   13     4    4    4    5    7    8    8    9   10   10   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     D     229     D     229      4    7   13     4    4    4    5    7    8    8    9   10   11   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     M     230     M     230      4    7   13     4    4    4    5    7    8    8    9   10   11   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     G     231     G     231      3    7   13     3    4    4    5    7    8    8    9   10   11   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     E     232     E     232      4    5   13     3    4    4    4    5    6    8    9   10   11   11   12   12   12   13   13   13   14   14   15 
LCS_GDT     H     233     H     233      4    5   13     3    4    4    5    5    6    7    8   10   11   11   12   12   12   12   13   13   14   14   15 
LCS_GDT     A     234     A     234      4    5   13     3    4    4    5    5    6    7    8   10   11   11   12   12   12   12   13   13   13   14   15 
LCS_GDT     G     235     G     235      4    5   13     3    4    4    4    5    5    7    8    9   11   11   12   12   12   12   13   13   13   14   15 
LCS_AVERAGE  LCS_A:  12.33  (   5.83    9.48   21.67 )

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      4      4      5      7      8      8      9     10     11     11     12     12     12     13     13     13     14     14     15 
GDT PERCENT_CA   6.67   6.67   6.67   8.33  11.67  13.33  13.33  15.00  16.67  18.33  18.33  20.00  20.00  20.00  21.67  21.67  21.67  23.33  23.33  25.00
GDT RMS_LOCAL    0.37   0.37   0.37   1.23   1.85   2.07   2.07   2.50   3.08   3.76   3.55   3.84   3.84   3.84   4.49   4.49   4.49   5.62   5.62   6.20
GDT RMS_ALL_CA  11.19  11.19  11.19   8.02   9.24   9.08   9.08   8.74  12.09   8.14  10.34  10.54  10.54  10.54   9.72   9.72   9.72   8.78   8.78   7.45

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220         16.077
LGA    R     221      R     221         10.393
LGA    M     222      M     222          9.029
LGA    M     223      M     223          8.808
LGA    T     224      T     224          2.259
LGA    V     225      V     225          1.175
LGA    D     226      D     226          1.908
LGA    G     227      G     227          1.852
LGA    R     228      R     228          3.427
LGA    D     229      D     229          3.033
LGA    M     230      M     230          2.573
LGA    G     231      G     231          0.658
LGA    E     232      E     232          3.855
LGA    H     233      H     233         10.398
LGA    A     234      A     234         15.026
LGA    G     235      G     235         17.482

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16   60    4.0      9    2.50    12.917    12.735     0.346

LGA_LOCAL      RMSD =  2.504  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.738  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  7.116  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.432211 * X  +  -0.134062 * Y  +  -0.891752 * Z  +  21.449717
  Y_new =  -0.898580 * X  +   0.147165 * Y  +   0.413396 * Z  +  -1.722859
  Z_new =   0.075815 * X  +   0.979985 * Y  +  -0.184071 * Z  + -29.871809 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.756464   -1.385129  [ DEG:   100.6380    -79.3620 ]
  Theta =  -0.075887   -3.065705  [ DEG:    -4.3480   -175.6520 ]
  Phi   =  -2.019123    1.122470  [ DEG:  -115.6872     64.3128 ]
 
# 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: T0316TS211_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS211_3-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16   60   4.0    9   2.50  12.735     7.12
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS211_3-D2
PFRMAT     TS
TARGET     T0316
MODEL      3 
PARENT     1vl2_B
ATOM   1700  N   GLY   220      27.465  21.091 -20.958  1.00  0.00           N  
ATOM   1701  CA  GLY   220      28.819  21.138 -20.367  1.00  0.00           C  
ATOM   1702  C   GLY   220      29.885  20.453 -21.255  1.00  0.00           C  
ATOM   1703  O   GLY   220      29.576  19.646 -22.139  1.00  0.00           O  
ATOM   1704  N   ARG   221      31.159  20.759 -20.989  1.00  0.00           N  
ATOM   1705  CA  ARG   221      32.301  20.046 -21.645  1.00  0.00           C  
ATOM   1706  C   ARG   221      32.401  18.510 -21.345  1.00  0.00           C  
ATOM   1707  O   ARG   221      32.820  17.740 -22.210  1.00  0.00           O  
ATOM   1708  CB  ARG   221      33.642  20.724 -21.289  1.00  0.00           C  
ATOM   1709  CG  ARG   221      33.777  22.201 -21.713  1.00  0.00           C  
ATOM   1710  CD  ARG   221      35.200  22.709 -21.448  1.00  0.00           C  
ATOM   1711  NE  ARG   221      35.361  24.095 -21.942  1.00  0.00           N  
ATOM   1712  CZ  ARG   221      36.490  24.809 -21.823  1.00  0.00           C  
ATOM   1713  NH1 ARG   221      36.515  26.015 -22.345  1.00  0.00           N  
ATOM   1714  NH2 ARG   221      37.582  24.366 -21.209  1.00  0.00           N  
ATOM   1715  N   MET   222      31.958  18.087 -20.146  1.00  0.00           N  
ATOM   1716  CA  MET   222      31.671  16.666 -19.800  1.00  0.00           C  
ATOM   1717  C   MET   222      30.661  15.907 -20.730  1.00  0.00           C  
ATOM   1718  O   MET   222      30.782  14.689 -20.884  1.00  0.00           O  
ATOM   1719  CB  MET   222      31.167  16.623 -18.328  1.00  0.00           C  
ATOM   1720  CG  MET   222      32.063  17.274 -17.247  1.00  0.00           C  
ATOM   1721  SD  MET   222      33.765  16.666 -17.318  1.00  0.00           S  
ATOM   1722  CE  MET   222      33.571  14.990 -16.688  1.00  0.00           C  
ATOM   1723  N   MET   223      29.703  16.615 -21.366  1.00  0.00           N  
ATOM   1724  CA  MET   223      28.868  16.063 -22.466  1.00  0.00           C  
ATOM   1725  C   MET   223      29.603  15.714 -23.801  1.00  0.00           C  
ATOM   1726  O   MET   223      29.109  14.844 -24.524  1.00  0.00           O  
ATOM   1727  CB  MET   223      27.719  17.068 -22.752  1.00  0.00           C  
ATOM   1728  CG  MET   223      26.462  16.406 -23.334  1.00  0.00           C  
ATOM   1729  SD  MET   223      25.758  15.204 -22.174  1.00  0.00           S  
ATOM   1730  CE  MET   223      25.137  16.264 -20.849  1.00  0.00           C  
ATOM   1731  N   THR   224      30.739  16.368 -24.143  1.00  0.00           N  
ATOM   1732  CA  THR   224      31.488  16.088 -25.400  1.00  0.00           C  
ATOM   1733  C   THR   224      32.232  14.724 -25.267  1.00  0.00           C  
ATOM   1734  O   THR   224      33.175  14.566 -24.483  1.00  0.00           O  
ATOM   1735  CB  THR   224      32.442  17.253 -25.790  1.00  0.00           C  
ATOM   1736  OG1 THR   224      31.749  18.499 -25.784  1.00  0.00           O  
ATOM   1737  CG2 THR   224      33.027  17.081 -27.204  1.00  0.00           C  
ATOM   1738  N   VAL   225      31.712  13.747 -26.021  1.00  0.00           N  
ATOM   1739  CA  VAL   225      32.001  12.299 -25.858  1.00  0.00           C  
ATOM   1740  C   VAL   225      33.441  11.840 -26.284  1.00  0.00           C  
ATOM   1741  O   VAL   225      34.281  11.460 -25.472  1.00  0.00           O  
ATOM   1742  CB  VAL   225      31.320  11.584 -24.627  1.00  0.00           C  
ATOM   1743  CG1 VAL   225      31.417  12.265 -23.242  1.00  0.00           C  
ATOM   1744  CG2 VAL   225      29.828  11.276 -24.877  1.00  0.00           C  
ATOM   1745  N   ASP   226      33.680  11.846 -27.609  1.00  0.00           N  
ATOM   1746  CA  ASP   226      34.873  11.240 -28.266  1.00  0.00           C  
ATOM   1747  C   ASP   226      35.922  12.328 -28.611  1.00  0.00           C  
ATOM   1748  O   ASP   226      37.072  12.232 -28.172  1.00  0.00           O  
ATOM   1749  CB  ASP   226      34.386  10.457 -29.520  1.00  0.00           C  
ATOM   1750  CG  ASP   226      35.479   9.729 -30.314  1.00  0.00           C  
ATOM   1751  OD1 ASP   226      35.837  10.202 -31.416  1.00  0.00           O  
ATOM   1752  OD2 ASP   226      35.993   8.698 -29.830  1.00  0.00           O  
ATOM   1753  N   GLY   227      35.521  13.344 -29.403  1.00  0.00           N  
ATOM   1754  CA  GLY   227      36.388  14.482 -29.736  1.00  0.00           C  
ATOM   1755  C   GLY   227      36.759  15.342 -28.518  1.00  0.00           C  
ATOM   1756  O   GLY   227      35.967  15.556 -27.595  1.00  0.00           O  
ATOM   1757  N   ARG   228      37.973  15.887 -28.578  1.00  0.00           N  
ATOM   1758  CA  ARG   228      38.361  17.033 -27.721  1.00  0.00           C  
ATOM   1759  C   ARG   228      37.630  18.317 -28.211  1.00  0.00           C  
ATOM   1760  O   ARG   228      37.265  18.446 -29.388  1.00  0.00           O  
ATOM   1761  CB  ARG   228      39.899  17.234 -27.775  1.00  0.00           C  
ATOM   1762  CG  ARG   228      40.738  16.054 -27.242  1.00  0.00           C  
ATOM   1763  CD  ARG   228      42.243  16.332 -27.349  1.00  0.00           C  
ATOM   1764  NE  ARG   228      43.009  15.149 -26.893  1.00  0.00           N  
ATOM   1765  CZ  ARG   228      44.338  15.008 -27.014  1.00  0.00           C  
ATOM   1766  NH1 ARG   228      44.883  13.894 -26.577  1.00  0.00           N  
ATOM   1767  NH2 ARG   228      45.131  15.928 -27.551  1.00  0.00           N  
ATOM   1768  N   ASP   229      37.458  19.295 -27.310  1.00  0.00           N  
ATOM   1769  CA  ASP   229      36.969  20.642 -27.708  1.00  0.00           C  
ATOM   1770  C   ASP   229      37.990  21.364 -28.640  1.00  0.00           C  
ATOM   1771  O   ASP   229      39.195  21.093 -28.612  1.00  0.00           O  
ATOM   1772  CB  ASP   229      36.660  21.490 -26.445  1.00  0.00           C  
ATOM   1773  CG  ASP   229      35.442  21.088 -25.597  1.00  0.00           C  
ATOM   1774  OD1 ASP   229      35.222  21.752 -24.564  1.00  0.00           O  
ATOM   1775  OD2 ASP   229      34.698  20.144 -25.946  1.00  0.00           O  
ATOM   1776  N   MET   230      37.493  22.298 -29.465  1.00  0.00           N  
ATOM   1777  CA  MET   230      38.357  23.173 -30.316  1.00  0.00           C  
ATOM   1778  C   MET   230      39.419  24.035 -29.546  1.00  0.00           C  
ATOM   1779  O   MET   230      40.536  24.198 -30.044  1.00  0.00           O  
ATOM   1780  CB  MET   230      37.458  24.066 -31.209  1.00  0.00           C  
ATOM   1781  CG  MET   230      36.633  23.329 -32.285  1.00  0.00           C  
ATOM   1782  SD  MET   230      37.687  22.393 -33.422  1.00  0.00           S  
ATOM   1783  CE  MET   230      38.516  23.707 -34.342  1.00  0.00           C  
ATOM   1784  N   GLY   231      39.093  24.522 -28.329  1.00  0.00           N  
ATOM   1785  CA  GLY   231      40.097  25.063 -27.377  1.00  0.00           C  
ATOM   1786  C   GLY   231      41.177  24.094 -26.818  1.00  0.00           C  
ATOM   1787  O   GLY   231      42.319  24.512 -26.625  1.00  0.00           O  
ATOM   1788  N   GLU   232      40.814  22.825 -26.558  1.00  0.00           N  
ATOM   1789  CA  GLU   232      41.773  21.755 -26.141  1.00  0.00           C  
ATOM   1790  C   GLU   232      42.577  21.056 -27.293  1.00  0.00           C  
ATOM   1791  O   GLU   232      43.566  20.375 -27.001  1.00  0.00           O  
ATOM   1792  CB  GLU   232      41.007  20.672 -25.331  1.00  0.00           C  
ATOM   1793  CG  GLU   232      40.280  21.153 -24.049  1.00  0.00           C  
ATOM   1794  CD  GLU   232      39.489  20.088 -23.280  1.00  0.00           C  
ATOM   1795  OE1 GLU   232      39.425  18.911 -23.703  1.00  0.00           O  
ATOM   1796  OE2 GLU   232      38.911  20.448 -22.232  1.00  0.00           O  
ATOM   1797  N   HIS   233      42.183  21.207 -28.578  1.00  0.00           N  
ATOM   1798  CA  HIS   233      42.907  20.630 -29.739  1.00  0.00           C  
ATOM   1799  C   HIS   233      44.281  21.337 -29.985  1.00  0.00           C  
ATOM   1800  O   HIS   233      44.517  22.470 -29.550  1.00  0.00           O  
ATOM   1801  CB  HIS   233      41.951  20.705 -30.972  1.00  0.00           C  
ATOM   1802  CG  HIS   233      42.337  19.778 -32.131  1.00  0.00           C  
ATOM   1803  ND1 HIS   233      42.239  18.390 -32.071  1.00  0.00           N  
ATOM   1804  CD2 HIS   233      42.955  20.183 -33.331  1.00  0.00           C  
ATOM   1805  CE1 HIS   233      42.836  18.082 -33.268  1.00  0.00           C  
ATOM   1806  NE2 HIS   233      43.290  19.078 -34.089  1.00  0.00           N  
ATOM   1807  N   ALA   234      45.184  20.645 -30.703  1.00  0.00           N  
ATOM   1808  CA  ALA   234      46.514  21.189 -31.075  1.00  0.00           C  
ATOM   1809  C   ALA   234      46.447  22.450 -31.987  1.00  0.00           C  
ATOM   1810  O   ALA   234      45.618  22.531 -32.902  1.00  0.00           O  
ATOM   1811  CB  ALA   234      47.299  20.062 -31.771  1.00  0.00           C  
ATOM   1812  N   GLY   235      47.327  23.426 -31.705  1.00  0.00           N  
ATOM   1813  CA  GLY   235      47.390  24.692 -32.471  1.00  0.00           C  
ATOM   1814  C   GLY   235      48.407  24.625 -33.614  1.00  0.00           C  
ATOM   1815  O   GLY   235      49.469  25.277 -33.516  1.00  0.00           O  
ATOM   1816  OXT GLY   235      48.146  23.928 -34.621  1.00  0.00           O  
TER
END
