
#######################################################
#                                                     #
#                        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   13 (   13),  selected   13 , name T0320TS464_5_1-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS464_5_1-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    Y     292      H     246          3.605
LGA    L     293      F     247          0.551
LGA    V     294      E     248          3.045
LGA    D     295      W     249          2.899
LGA    D     296      E     250          1.184
LGA    T     297      I     251          1.735
LGA    L     298      I     252          2.217
LGA    E     299      H     253          1.057
LGA    R     300      A     254          0.942
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    A     301      K     257          2.314
LGA    G     302      D     258          2.701
LGA    R     303      R     263          3.715
LGA    I     304      S     264          3.737
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)   13   73    5.0     13    2.52     7.69     15.053     0.496

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.260695 * X  +  -0.881771 * Y  +   0.393087 * Z  +  42.108212
  Y_new =  -0.856769 * X  +   0.398969 * Y  +   0.326758 * Z  +  -6.767453
  Z_new =  -0.444955 * X  +  -0.251601 * Y  +  -0.859483 * Z  +  27.957870 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.856814    0.284778  [ DEG:  -163.6834     16.3166 ]
  Theta =   0.461125    2.680468  [ DEG:    26.4205    153.5795 ]
  Phi   =  -1.866172    1.275421  [ DEG:  -106.9238     73.0762 ]
 
# 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: T0320TS464_5_1-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_5_1-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   13   73   5.0   13   2.52    7.69  15.053
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_5_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM     59  CA  TYR   292      -1.764  14.246   9.874  1.00  0.00
ATOM     60  CA  LEU   293       0.861  16.555  11.415  1.00  0.00
ATOM     61  CA  VAL   294       0.628  19.155   8.644  1.00  0.00
ATOM     62  CA  ASP   295      -3.205  19.153   8.973  1.00  0.00
ATOM     63  CA  ASP   296      -2.752  20.159  12.624  1.00  0.00
ATOM     64  CA  THR   297      -0.371  22.989  11.767  1.00  0.00
ATOM     65  CA  LEU   298      -2.743  24.357   9.122  1.00  0.00
ATOM     66  CA  GLU   299      -5.576  24.318  11.692  1.00  0.00
ATOM     67  CA  ARG   300      -3.361  25.963  14.317  1.00  0.00
ATOM     68  CA  ALA   301      -2.798  28.908  11.967  1.00  0.00
ATOM     69  CA  GLY   302      -6.347  29.259  10.683  1.00  0.00
ATOM     70  CA  ARG   303      -5.559  27.961   7.186  1.00  0.00
ATOM     71  CA  ILE   304      -7.359  24.563   7.178  1.00  0.00
TER
END
