
#######################################################
#                                                     #
#                        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    5 (   35),  selected    5 , name T0320TS186_3-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS186_3-D2.T0320_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    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    G     256      E     248          0.977
LGA    K     257      W     249          1.111
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    D     258      I     252          1.189
LGA    A     259      H     253          1.752
LGA    E     260      A     254          2.141
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   73    5.0      5    1.50     0.00      6.639     0.312

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.607194 * X  +  -0.781637 * Y  +  -0.142686 * Z  +   7.333992
  Y_new =  -0.195356 * X  +  -0.320930 * Y  +   0.926736 * Z  + -33.194065
  Z_new =  -0.770163 * X  +  -0.534834 * Y  +  -0.347564 * Z  +  93.147125 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.147069    0.994523  [ DEG:  -123.0180     56.9820 ]
  Theta =   0.879097    2.262495  [ DEG:    50.3686    129.6314 ]
  Phi   =  -0.311277    2.830316  [ DEG:   -17.8348    162.1652 ]
 
# 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: T0320TS186_3-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS186_3-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   73   5.0    5   1.50    0.00   6.639
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS186_3-D2
PFRMAT TS
TARGET T0320
MODEL  3
PARENT 1cz1_A
ATOM   1700  N   GLY   256      -1.202  17.348   8.784  1.00  0.00
ATOM   1701  CA  GLY   256      -2.383  16.726   8.206  1.00  0.00
ATOM   1702  C   GLY   256      -3.646  17.392   8.744  1.00  0.00
ATOM   1703  O   GLY   256      -4.705  17.271   8.137  1.00  0.00
ATOM   1704  N   LYS   257      -3.547  18.071   9.885  1.00  0.00
ATOM   1705  CA  LYS   257      -4.770  18.648  10.449  1.00  0.00
ATOM   1706  C   LYS   257      -4.923  20.146  10.200  1.00  0.00
ATOM   1707  O   LYS   257      -6.052  20.636  10.282  1.00  0.00
ATOM   1708  CB  LYS   257      -4.804  18.452  11.966  1.00  0.00
ATOM   1709  CG  LYS   257      -5.170  17.043  12.401  1.00  0.00
ATOM   1710  CD  LYS   257      -4.004  16.086  12.214  1.00  0.00
ATOM   1711  CE  LYS   257      -4.374  14.674  12.637  1.00  0.00
ATOM   1712  NZ  LYS   257      -5.425  14.089  11.758  1.00  0.00
ATOM   1713  N   ASP   258      -3.825  20.848  10.014  1.00  0.00
ATOM   1714  CA  ASP   258      -3.902  22.296   9.745  1.00  0.00
ATOM   1715  C   ASP   258      -4.320  23.095  10.963  1.00  0.00
ATOM   1716  O   ASP   258      -5.118  24.033  10.858  1.00  0.00
ATOM   1717  CB  ASP   258      -4.922  22.583   8.640  1.00  0.00
ATOM   1718  CG  ASP   258      -4.527  21.972   7.310  1.00  0.00
ATOM   1719  OD1 ASP   258      -3.389  22.219   6.858  1.00  0.00
ATOM   1720  OD2 ASP   258      -5.356  21.249   6.719  1.00  0.00
ATOM   1721  N   ALA   259      -3.793  22.793  12.139  1.00  0.00
ATOM   1722  CA  ALA   259      -4.182  23.514  13.347  1.00  0.00
ATOM   1723  C   ALA   259      -3.654  24.955  13.301  1.00  0.00
ATOM   1724  O   ALA   259      -2.580  25.183  12.745  1.00  0.00
ATOM   1725  CB  ALA   259      -3.613  22.828  14.580  1.00  0.00
ATOM   1726  N   GLU   260      -4.404  25.881  13.864  1.00  0.00
ATOM   1727  CA  GLU   260      -4.014  27.283  13.899  1.00  0.00
ATOM   1728  C   GLU   260      -3.741  27.693  15.367  1.00  0.00
ATOM   1729  O   GLU   260      -2.829  28.522  15.539  1.00  0.00
ATOM   1730  CB  GLU   260      -5.128  28.163  13.329  1.00  0.00
ATOM   1731  CG  GLU   260      -5.338  28.007  11.831  1.00  0.00
ATOM   1732  CD  GLU   260      -6.595  28.700  11.344  1.00  0.00
ATOM   1733  OE1 GLU   260      -7.325  29.267  12.184  1.00  0.00
ATOM   1734  OE2 GLU   260      -6.850  28.676  10.121  1.00  0.00
TER
END
