
#######################################################
#                                                     #
#                        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 T0351TS102_4
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351TS102_4.T0351.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.

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

 ERROR! 0 0 5 56
 ERROR! 0 0 5 56
 ERROR! 0 0 5 56
 ERROR! 0 0 5 56
 ERROR! 0 0 5 56
 ERROR! 0 0 5 56
 ERROR! 0 0 5 56
 ERROR! 0 0 5 56
 ERROR! 0 0 5 56
 ERROR! 0 0 5 56
#      Molecule1      Molecule2       DISTANCE
LGA    H     113      M       1          0.771
LGA    H     114      I       2          0.556
LGA    H     115      L       3          0.583
LGA    -       -      Y       4           -
LGA    -       -      D       5           -
LGA    H     116      A       6          0.982
LGA    H     117      I       7          0.648
LGA    -       -      M       8           -
LGA    -       -      Y       9           -
LGA    -       -      K      10           -
LGA    -       -      Y      11           -
LGA    -       -      P      12           -
LGA    -       -      N      13           -
LGA    -       -      A      14           -
LGA    -       -      V      15           -
LGA    -       -      S      16           -
LGA    -       -      R      17           -
LGA    -       -      K      18           -
LGA    -       -      D      19           -
LGA    -       -      F      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      R      23           -
LGA    -       -      N      24           -
LGA    -       -      D      25           -
LGA    -       -      G      26           -
LGA    -       -      N      27           -
LGA    -       -      G      28           -
LGA    -       -      S      29           -
LGA    -       -      Y      30           -
LGA    -       -      I      31           -
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    -       -      W      34           -
LGA    -       -      N      35           -
LGA    -       -      L      36           -
LGA    -       -      R      37           -
LGA    -       -      A      38           -
LGA    -       -      P      39           -
LGA    -       -      L      40           -
LGA    -       -      P      41           -
LGA    -       -      T      42           -
LGA    -       -      Q      43           -
LGA    -       -      A      44           -
LGA    -       -      E      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      T      48           -
LGA    -       -      W      49           -
LGA    -       -      W      50           -
LGA    -       -      E      51           -
LGA    -       -      E      52           -
LGA    -       -      L      53           -
LGA    -       -      Q      54           -
LGA    -       -      K      55           -
LGA    -       -      N      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   56    5.0      5    0.72     0.00      8.929     0.606

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.894469 * X  +  -0.399014 * Y  +  -0.201772 * Z  + -66.365227
  Y_new =   0.107410 * X  +  -0.246300 * Y  +   0.963224 * Z  + -15.529536
  Z_new =  -0.434036 * X  +  -0.883246 * Y  +  -0.177450 * Z  +  37.357937 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.769063    1.372529  [ DEG:  -101.3599     78.6401 ]
  Theta =   0.448968    2.692624  [ DEG:    25.7240    154.2760 ]
  Phi   =   0.119510   -3.022083  [ DEG:     6.8474   -173.1526 ]
 
# 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: T0351TS102_4                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351TS102_4.T0351.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   56   5.0    5   0.72    0.00   8.929
REMARK  ---------------------------------------------------------- 
MOLECULE T0351TS102_4
PFRMAT TS
TARGET T0351
MODEL 4
PARENT 2afb_A
ATOM      1  N   HIS   113      -9.274  -5.803   6.625  1.00  1.00
ATOM      2  CA  HIS   113      -7.844  -5.691   6.164  1.00  1.00
ATOM      3  C   HIS   113      -7.358  -4.219   6.108  1.00  1.00
ATOM      4  O   HIS   113      -8.147  -3.289   6.318  1.00  1.00
ATOM      5  CB  HIS   113      -7.682  -6.386   4.799  1.00  1.00
ATOM      6  N   HIS   114      -6.064  -4.020   5.830  1.00  1.00
ATOM      7  CA  HIS   114      -5.434  -2.677   5.811  1.00  1.00
ATOM      8  C   HIS   114      -4.857  -2.313   4.426  1.00  1.00
ATOM      9  O   HIS   114      -4.322  -3.185   3.753  1.00  1.00
ATOM     10  CB  HIS   114      -4.260  -2.635   6.803  1.00  1.00
ATOM     11  N   HIS   115      -4.906  -1.035   4.029  1.00  1.00
ATOM     12  CA  HIS   115      -4.085  -0.545   2.901  1.00  1.00
ATOM     13  C   HIS   115      -2.595  -0.822   3.181  1.00  1.00
ATOM     14  O   HIS   115      -2.146  -0.679   4.308  1.00  1.00
ATOM     15  CB  HIS   115      -4.281   0.964   2.661  1.00  1.00
ATOM     16  N   HIS   116      -1.835  -1.221   2.165  1.00  1.00
ATOM     17  CA  HIS   116      -0.396  -1.374   2.303  1.00  1.00
ATOM     18  C   HIS   116       0.292  -0.447   1.338  1.00  1.00
ATOM     19  O   HIS   116       0.227  -0.673   0.153  1.00  1.00
ATOM     20  CB  HIS   116       0.038  -2.814   2.010  1.00  1.00
ATOM     21  N   HIS   117       1.003   0.558   1.831  1.00  1.00
ATOM     22  CA  HIS   117       1.693   1.502   0.954  1.00  1.00
ATOM     23  C   HIS   117       2.953   0.839   0.440  1.00  1.00
ATOM     24  O   HIS   117       4.038   1.220   0.813  1.00  1.00
ATOM     25  CB  HIS   117       1.971   2.836   1.663  1.00  1.00
TER
END
