
#######################################################
#                                                     #
#                        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   20 (  156),  selected   20 , name T0316TS609_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS609_3-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      G     220           -
LGA    -       -      R     221           -
LGA    -       -      M     222           -
LGA    -       -      M     223           -
LGA    G     220      T     224          1.970
LGA    R     221      V     225           #
LGA    M     222      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    M     223      D     229          3.158
LGA    T     224      M     230          1.480
LGA    V     225      G     231          4.416
LGA    D     226      E     232          1.868
LGA    G     227      H     233          2.418
LGA    R     228      A     234          2.802
LGA    -       -      G     235           -
LGA    D     229      L     236          4.392
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    M     230      Y     239          2.026
LGA    G     231      T     240          3.083
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    E     232      Q     243          3.181
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    H     233      G     246          2.811
LGA    A     234      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    -       -      P     259           -
LGA    -       -      W     260           -
LGA    G     235      F     261          1.785
LGA    L     236      V     262           #
LGA    M     237      V     263           -
LGA    Y     238      G     264           -
LGA    Y     239      K     265           -
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      Q     276           -
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    -       -      H     280           -
LGA    -       -      D     281           -
LGA    -       -      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   20   60    5.0     13    2.87     0.00     14.566     0.438

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.410943 * X  +  -0.542747 * Y  +   0.732497 * Z  +  72.732391
  Y_new =  -0.294542 * X  +  -0.681343 * Y  +  -0.670087 * Z  + 144.941330
  Z_new =   0.862769 * X  +  -0.491119 * Y  +   0.120131 * Z  + -120.760719 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.330899    1.810693  [ DEG:   -76.2549    103.7451 ]
  Theta =  -1.040721   -2.100872  [ DEG:   -59.6289   -120.3711 ]
  Phi   =  -2.519715    0.621877  [ DEG:  -144.3691     35.6309 ]
 
# 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: T0316TS609_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS609_3-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20   60   5.0   13   2.87    0.00  14.566
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS609_3-D2
PFRMAT TS
TARGET T0316
MODEL 3
PARENT 1gpm_A                                           
ATOM   1736  N   GLY   220      36.391  14.811 -26.273  1.00 44.30       1SG    
ATOM   1737  CA  GLY   220      35.158  15.524 -26.135  1.00 44.30       1SG    
ATOM   1738  C   GLY   220      35.427  16.988 -25.965  1.00 44.30       1SG    
ATOM   1739  O   GLY   220      36.252  17.584 -26.655  1.00 44.30       1SG    
ATOM   1740  N   ARG   221      34.707  17.582 -24.997  1.00164.64       1SG    
ATOM   1741  CA  ARG   221      34.694  18.968 -24.627  1.00164.64       1SG    
ATOM   1742  CB  ARG   221      33.644  19.256 -23.539  1.00164.64       1SG    
ATOM   1743  CG  ARG   221      33.561  20.716 -23.090  1.00164.64       1SG    
ATOM   1744  CD  ARG   221      32.487  20.953 -22.023  1.00164.64       1SG    
ATOM   1745  NE  ARG   221      31.165  20.674 -22.656  1.00164.64       1SG    
ATOM   1746  CZ  ARG   221      30.132  20.171 -21.918  1.00164.64       1SG    
ATOM   1747  NH1 ARG   221      30.297  19.908 -20.589  1.00164.64       1SG    
ATOM   1748  NH2 ARG   221      28.928  19.924 -22.511  1.00164.64       1SG    
ATOM   1749  C   ARG   221      36.038  19.335 -24.089  1.00164.64       1SG    
ATOM   1750  O   ARG   221      36.388  20.510 -23.995  1.00164.64       1SG    
ATOM   1751  N   MET   222      36.829  18.333 -23.682  1.00157.18       1SG    
ATOM   1752  CA  MET   222      38.094  18.629 -23.076  1.00157.18       1SG    
ATOM   1753  CB  MET   222      38.898  17.354 -22.763  1.00157.18       1SG    
ATOM   1754  CG  MET   222      40.249  17.596 -22.082  1.00157.18       1SG    
ATOM   1755  SD  MET   222      40.156  18.093 -20.335  1.00157.18       1SG    
ATOM   1756  CE  MET   222      39.876  19.854 -20.671  1.00157.18       1SG    
ATOM   1757  C   MET   222      38.920  19.455 -24.017  1.00157.18       1SG    
ATOM   1758  O   MET   222      39.662  20.335 -23.584  1.00157.18       1SG    
ATOM   1759  N   MET   223      38.888  19.126 -25.321  1.00154.91       1SG    
ATOM   1760  CA  MET   223      39.577  19.872 -26.341  1.00154.91       1SG    
ATOM   1761  CB  MET   223      39.761  19.061 -27.640  1.00154.91       1SG    
ATOM   1762  CG  MET   223      38.493  18.869 -28.476  1.00154.91       1SG    
ATOM   1763  SD  MET   223      38.019  20.306 -29.484  1.00154.91       1SG    
ATOM   1764  CE  MET   223      39.393  20.112 -30.656  1.00154.91       1SG    
ATOM   1765  C   MET   223      38.868  21.157 -26.658  1.00154.91       1SG    
ATOM   1766  O   MET   223      39.499  22.121 -27.088  1.00154.91       1SG    
ATOM   1767  N   THR   224      37.522  21.184 -26.531  1.00115.19       1SG    
ATOM   1768  CA  THR   224      36.742  22.334 -26.907  1.00115.19       1SG    
ATOM   1769  CB  THR   224      35.258  22.087 -26.952  1.00115.19       1SG    
ATOM   1770  OG1 THR   224      34.618  23.140 -27.658  1.00115.19       1SG    
ATOM   1771  CG2 THR   224      34.701  22.025 -25.523  1.00115.19       1SG    
ATOM   1772  C   THR   224      36.983  23.496 -25.992  1.00115.19       1SG    
ATOM   1773  O   THR   224      36.990  24.642 -26.441  1.00115.19       1SG    
ATOM   1774  N   VAL   225      37.163  23.252 -24.681  1.00 47.54       1SG    
ATOM   1775  CA  VAL   225      37.346  24.355 -23.781  1.00 47.54       1SG    
ATOM   1776  CB  VAL   225      36.866  24.058 -22.389  1.00 47.54       1SG    
ATOM   1777  CG1 VAL   225      37.185  25.262 -21.487  1.00 47.54       1SG    
ATOM   1778  CG2 VAL   225      35.371  23.707 -22.456  1.00 47.54       1SG    
ATOM   1779  C   VAL   225      38.807  24.664 -23.703  1.00 47.54       1SG    
ATOM   1780  O   VAL   225      39.619  23.819 -23.327  1.00 47.54       1SG    
ATOM   1781  N   ASP   226      39.179  25.912 -24.055  1.00 33.72       1SG    
ATOM   1782  CA  ASP   226      40.562  26.284 -24.045  1.00 33.72       1SG    
ATOM   1783  CB  ASP   226      40.853  27.624 -24.745  1.00 33.72       1SG    
ATOM   1784  CG  ASP   226      40.626  27.456 -26.239  1.00 33.72       1SG    
ATOM   1785  OD1 ASP   226      40.270  26.323 -26.662  1.00 33.72       1SG    
ATOM   1786  OD2 ASP   226      40.811  28.458 -26.979  1.00 33.72       1SG    
ATOM   1787  C   ASP   226      40.998  26.439 -22.627  1.00 33.72       1SG    
ATOM   1788  O   ASP   226      40.227  26.862 -21.767  1.00 33.72       1SG    
ATOM   1789  N   GLY   227      42.265  26.084 -22.349  1.00 38.27       1SG    
ATOM   1790  CA  GLY   227      42.803  26.269 -21.038  1.00 38.27       1SG    
ATOM   1791  C   GLY   227      42.206  25.266 -20.111  1.00 38.27       1SG    
ATOM   1792  O   GLY   227      41.739  24.206 -20.528  1.00 38.27       1SG    
ATOM   1793  N   ARG   228      42.197  25.610 -18.808  1.00 93.01       1SG    
ATOM   1794  CA  ARG   228      41.732  24.708 -17.799  1.00 93.01       1SG    
ATOM   1795  CB  ARG   228      41.857  25.249 -16.365  1.00 93.01       1SG    
ATOM   1796  CG  ARG   228      41.348  24.259 -15.315  1.00 93.01       1SG    
ATOM   1797  CD  ARG   228      41.317  24.823 -13.893  1.00 93.01       1SG    
ATOM   1798  NE  ARG   228      42.724  24.954 -13.426  1.00 93.01       1SG    
ATOM   1799  CZ  ARG   228      43.327  23.904 -12.795  1.00 93.01       1SG    
ATOM   1800  NH1 ARG   228      42.645  22.737 -12.612  1.00 93.01       1SG    
ATOM   1801  NH2 ARG   228      44.612  24.021 -12.351  1.00 93.01       1SG    
ATOM   1802  C   ARG   228      40.296  24.415 -18.039  1.00 93.01       1SG    
ATOM   1803  O   ARG   228      39.521  25.282 -18.441  1.00 93.01       1SG    
ATOM   1804  N   ASP   229      39.916  23.145 -17.804  1.00 92.66       1SG    
ATOM   1805  CA  ASP   229      38.559  22.752 -17.994  1.00 92.66       1SG    
ATOM   1806  CB  ASP   229      38.406  21.332 -18.567  1.00 92.66       1SG    
ATOM   1807  CG  ASP   229      36.971  21.174 -19.046  1.00 92.66       1SG    
ATOM   1808  OD1 ASP   229      36.209  22.175 -18.966  1.00 92.66       1SG    
ATOM   1809  OD2 ASP   229      36.615  20.050 -19.491  1.00 92.66       1SG    
ATOM   1810  C   ASP   229      37.919  22.780 -16.650  1.00 92.66       1SG    
ATOM   1811  O   ASP   229      38.377  22.123 -15.714  1.00 92.66       1SG    
ATOM   1812  N   MET   230      36.849  23.584 -16.516  1.00 71.72       1SG    
ATOM   1813  CA  MET   230      36.134  23.662 -15.279  1.00 71.72       1SG    
ATOM   1814  CB  MET   230      36.031  25.074 -14.675  1.00 71.72       1SG    
ATOM   1815  CG  MET   230      37.303  25.587 -14.003  1.00 71.72       1SG    
ATOM   1816  SD  MET   230      37.127  27.258 -13.306  1.00 71.72       1SG    
ATOM   1817  CE  MET   230      35.818  26.809 -12.126  1.00 71.72       1SG    
ATOM   1818  C   MET   230      34.736  23.246 -15.575  1.00 71.72       1SG    
ATOM   1819  O   MET   230      34.275  23.329 -16.712  1.00 71.72       1SG    
ATOM   1820  N   GLY   231      34.025  22.775 -14.539  1.00 19.64       1SG    
ATOM   1821  CA  GLY   231      32.681  22.321 -14.718  1.00 19.64       1SG    
ATOM   1822  C   GLY   231      31.859  23.473 -15.197  1.00 19.64       1SG    
ATOM   1823  O   GLY   231      30.972  23.306 -16.034  1.00 19.64       1SG    
ATOM   1824  N   GLU   232      32.134  24.682 -14.673  1.00 65.67       1SG    
ATOM   1825  CA  GLU   232      31.350  25.830 -15.026  1.00 65.67       1SG    
ATOM   1826  CB  GLU   232      31.816  27.108 -14.301  1.00 65.67       1SG    
ATOM   1827  CG  GLU   232      30.905  28.321 -14.517  1.00 65.67       1SG    
ATOM   1828  CD  GLU   232      31.256  28.968 -15.848  1.00 65.67       1SG    
ATOM   1829  OE1 GLU   232      32.464  29.254 -16.066  1.00 65.67       1SG    
ATOM   1830  OE2 GLU   232      30.322  29.187 -16.664  1.00 65.67       1SG    
ATOM   1831  C   GLU   232      31.468  26.066 -16.498  1.00 65.67       1SG    
ATOM   1832  O   GLU   232      30.474  26.335 -17.171  1.00 65.67       1SG    
ATOM   1833  N   HIS   233      32.694  25.956 -17.040  1.00 64.24       1SG    
ATOM   1834  CA  HIS   233      32.927  26.193 -18.436  1.00 64.24       1SG    
ATOM   1835  ND1 HIS   233      35.597  27.323 -16.879  1.00 64.24       1SG    
ATOM   1836  CG  HIS   233      35.206  27.276 -18.199  1.00 64.24       1SG    
ATOM   1837  CB  HIS   233      34.419  26.151 -18.805  1.00 64.24       1SG    
ATOM   1838  NE2 HIS   233      36.356  29.183 -17.832  1.00 64.24       1SG    
ATOM   1839  CD2 HIS   233      35.678  28.420 -18.767  1.00 64.24       1SG    
ATOM   1840  CE1 HIS   233      36.281  28.484 -16.714  1.00 64.24       1SG    
ATOM   1841  C   HIS   233      32.230  25.141 -19.240  1.00 64.24       1SG    
ATOM   1842  O   HIS   233      31.656  25.427 -20.290  1.00 64.24       1SG    
ATOM   1843  N   ALA   234      32.257  23.886 -18.757  1.00 31.65       1SG    
ATOM   1844  CA  ALA   234      31.691  22.791 -19.489  1.00 31.65       1SG    
ATOM   1845  CB  ALA   234      31.835  21.459 -18.736  1.00 31.65       1SG    
ATOM   1846  C   ALA   234      30.230  23.043 -19.690  1.00 31.65       1SG    
ATOM   1847  O   ALA   234      29.706  22.844 -20.785  1.00 31.65       1SG    
ATOM   1848  N   GLY   235      29.535  23.489 -18.629  1.00 23.63       1SG    
ATOM   1849  CA  GLY   235      28.129  23.772 -18.706  1.00 23.63       1SG    
ATOM   1850  C   GLY   235      27.931  24.937 -19.623  1.00 23.63       1SG    
ATOM   1851  O   GLY   235      26.956  25.008 -20.369  1.00 23.63       1SG    
ATOM   1852  N   LEU   236      28.875  25.887 -19.574  1.00100.36       1SG    
ATOM   1853  CA  LEU   236      28.835  27.116 -20.311  1.00100.36       1SG    
ATOM   1854  CB  LEU   236      30.069  27.985 -19.973  1.00100.36       1SG    
ATOM   1855  CG  LEU   236      30.134  29.415 -20.558  1.00100.36       1SG    
ATOM   1856  CD1 LEU   236      31.418  30.119 -20.091  1.00100.36       1SG    
ATOM   1857  CD2 LEU   236      30.013  29.452 -22.089  1.00100.36       1SG    
ATOM   1858  C   LEU   236      28.839  26.771 -21.766  1.00100.36       1SG    
ATOM   1859  O   LEU   236      28.212  27.450 -22.579  1.00100.36       1SG    
ATOM   1860  N   MET   237      29.499  25.658 -22.125  1.00 75.03       1SG    
ATOM   1861  CA  MET   237      29.705  25.326 -23.503  1.00 75.03       1SG    
ATOM   1862  CB  MET   237      30.386  23.964 -23.707  1.00 75.03       1SG    
ATOM   1863  CG  MET   237      30.789  23.721 -25.163  1.00 75.03       1SG    
ATOM   1864  SD  MET   237      31.517  22.090 -25.496  1.00 75.03       1SG    
ATOM   1865  CE  MET   237      29.924  21.217 -25.501  1.00 75.03       1SG    
ATOM   1866  C   MET   237      28.401  25.257 -24.227  1.00 75.03       1SG    
ATOM   1867  O   MET   237      28.321  25.713 -25.366  1.00 75.03       1SG    
ATOM   1868  N   TYR   238      27.337  24.689 -23.629  1.00294.52       1SG    
ATOM   1869  CA  TYR   238      26.139  24.631 -24.415  1.00294.52       1SG    
ATOM   1870  CB  TYR   238      25.016  23.718 -23.866  1.00294.52       1SG    
ATOM   1871  CG  TYR   238      24.521  24.192 -22.540  1.00294.52       1SG    
ATOM   1872  CD1 TYR   238      23.666  25.267 -22.444  1.00294.52       1SG    
ATOM   1873  CD2 TYR   238      24.885  23.533 -21.388  1.00294.52       1SG    
ATOM   1874  CE1 TYR   238      23.207  25.693 -21.219  1.00294.52       1SG    
ATOM   1875  CE2 TYR   238      24.430  23.952 -20.160  1.00294.52       1SG    
ATOM   1876  CZ  TYR   238      23.591  25.037 -20.074  1.00294.52       1SG    
ATOM   1877  OH  TYR   238      23.123  25.471 -18.817  1.00294.52       1SG    
ATOM   1878  C   TYR   238      25.607  26.017 -24.594  1.00294.52       1SG    
ATOM   1879  O   TYR   238      25.572  26.817 -23.659  1.00294.52       1SG    
ATOM   1880  N   TYR   239      25.220  26.343 -25.843  1.00271.36       1SG    
ATOM   1881  CA  TYR   239      24.660  27.627 -26.148  1.00271.36       1SG    
ATOM   1882  CB  TYR   239      25.389  28.402 -27.263  1.00271.36       1SG    
ATOM   1883  CG  TYR   239      26.776  28.727 -26.830  1.00271.36       1SG    
ATOM   1884  CD1 TYR   239      27.797  27.828 -27.034  1.00271.36       1SG    
ATOM   1885  CD2 TYR   239      27.060  29.933 -26.230  1.00271.36       1SG    
ATOM   1886  CE1 TYR   239      29.080  28.122 -26.640  1.00271.36       1SG    
ATOM   1887  CE2 TYR   239      28.342  30.233 -25.834  1.00271.36       1SG    
ATOM   1888  CZ  TYR   239      29.354  29.327 -26.039  1.00271.36       1SG    
ATOM   1889  OH  TYR   239      30.671  29.632 -25.635  1.00271.36       1SG    
ATOM   1890  C   TYR   239      23.301  27.361 -26.701  1.00271.36       1SG    
ATOM   1891  O   TYR   239      23.106  26.408 -27.452  1.00271.36       1SG    
TER
END
