
#######################################################
#                                                     #
#                        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 (   25),  selected    5 , name T0348TS102_1
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS102_1.T0348.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    -       -      D       2           -
LGA    -       -      A       3           -
LGA    -       -      K       4           -
LGA    -       -      F       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      I       8           -
LGA    -       -      L       9           -
LGA    -       -      V      10           -
LGA    -       -      C      11           -
LGA    -       -      P      12           -
LGA    -       -      L      13           -
LGA    -       -      C      14           -
LGA    -       -      K      15           -
LGA    -       -      G      16           -
LGA    -       -      P      17           -
LGA    -       -      L      18           -
LGA    -       -      V      19           -
LGA    -       -      F      20           -
LGA    -       -      D      21           -
LGA    H      64      K      22          0.428
LGA    H      65      S      23          0.616
LGA    H      66      K      24          0.457
LGA    H      67      D      25          0.403
LGA    H      68      E      26          0.767
LGA    -       -      L      27           -
LGA    -       -      I      28           -
LGA    -       -      C      29           -
LGA    -       -      K      30           -
LGA    -       -      G      31           -
LGA    -       -      D      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      A      35           -
LGA    -       -      F      36           -
LGA    -       -      P      37           -
LGA    -       -      I      38           -
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    -       -      M      44           -
LGA    -       -      M      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    -       -      E      49           -
LGA    -       -      A      50           -
LGA    -       -      R      51           -
LGA    -       -      E      52           -
LGA    -       -      L      53           -
LGA    -       -      A      54           -
LGA    -       -      P      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      E      58           -
LGA    -       -      V      59           -
LGA    -       -      K      60           -
LGA    -       -      L      61           -
LGA    -       -      E      62           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   61    5.0      5    0.55     0.00      8.197     0.767

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.998344 * X  +  -0.024102 * Y  +   0.052226 * Z  + -184.294754
  Y_new =  -0.055440 * X  +  -0.161297 * Y  +   0.985348 * Z  +  10.619310
  Z_new =  -0.015325 * X  +  -0.986612 * Y  +  -0.162366 * Z  + 232.197113 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.733904    1.407689  [ DEG:   -99.3454     80.6546 ]
  Theta =   0.015326    3.126267  [ DEG:     0.8781    179.1219 ]
  Phi   =  -0.055475    3.086118  [ DEG:    -3.1785    176.8215 ]
 
# 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: T0348TS102_1                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS102_1.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   61   5.0    5   0.55    0.00   8.197
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS102_1
PFRMAT TS
TARGET T0348
MODEL 1
PARENT 1vlv_A
ATOM      1  N   HIS    64      16.982  27.280  46.159  1.00  1.00
ATOM      2  CA  HIS    64      17.893  26.700  47.187  1.00  1.00
ATOM      3  C   HIS    64      18.305  25.288  46.796  1.00  1.00
ATOM      4  O   HIS    64      18.577  24.483  47.703  1.00  1.00
ATOM      5  CB  HIS    64      17.211  26.570  48.584  1.00  1.00
ATOM      6  N   HIS    65      18.385  24.987  45.486  1.00  1.00
ATOM      7  CA  HIS    65      18.310  23.588  44.917  1.00  1.00
ATOM      8  C   HIS    65      16.876  23.014  44.960  1.00  1.00
ATOM      9  O   HIS    65      16.381  22.566  43.925  1.00  1.00
ATOM     10  CB  HIS    65      19.264  22.580  45.557  1.00  1.00
ATOM     11  N   HIS    66      16.267  22.954  46.152  1.00  1.00
ATOM     12  CA  HIS    66      14.791  22.902  46.279  1.00  1.00
ATOM     13  C   HIS    66      14.402  24.161  46.998  1.00  1.00
ATOM     14  O   HIS    66      14.686  24.327  48.181  1.00  1.00
ATOM     15  CB  HIS    66      14.256  21.664  47.017  1.00  1.00
ATOM     16  N   HIS    67      13.782  25.065  46.253  1.00  1.00
ATOM     17  CA  HIS    67      13.277  26.310  46.800  1.00  1.00
ATOM     18  C   HIS    67      12.109  26.091  47.814  1.00  1.00
ATOM     19  O   HIS    67      11.121  25.415  47.500  1.00  1.00
ATOM     20  CB  HIS    67      12.846  27.196  45.622  1.00  1.00
ATOM     21  N   HIS    68      12.230  26.674  49.013  1.00  1.00
ATOM     22  CA  HIS    68      11.194  26.595  50.034  1.00  1.00
ATOM     23  C   HIS    68      10.046  27.561  49.700  1.00  1.00
ATOM     24  O   HIS    68      10.305  28.760  49.493  1.00  1.00
ATOM     25  CB  HIS    68      11.748  26.943  51.429  1.00  1.00
TER
END
