
#######################################################
#                                                     #
#                        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_2
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351TS102_2.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.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      L       3           -
LGA    -       -      Y       4           -
LGA    -       -      D       5           -
LGA    -       -      A       6           -
LGA    -       -      I       7           -
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    H     113      T      48          1.578
LGA    H     114      W      49          0.932
LGA    H     115      W      50          1.269
LGA    -       -      E      51           -
LGA    -       -      E      52           -
LGA    H     116      L      53          0.995
LGA    H     117      Q      54          0.722
LGA    -       -      K      55           -
LGA    -       -      N      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   56    5.0      5    1.14     0.00      8.788     0.404

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.029481 * X  +   0.933749 * Y  +   0.356711 * Z  + -17.387102
  Y_new =   0.402528 * X  +  -0.315560 * Y  +   0.859298 * Z  + -35.143097
  Z_new =   0.914933 * X  +   0.168919 * Y  +  -0.366557 * Z  + -47.112934 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.709772   -0.431820  [ DEG:   155.2585    -24.7415 ]
  Theta =  -1.155342   -1.986251  [ DEG:   -66.1962   -113.8038 ]
  Phi   =   1.643906   -1.497687  [ DEG:    94.1889    -85.8111 ]
 
# 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_2                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351TS102_2.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   1.14    0.00   8.788
REMARK  ---------------------------------------------------------- 
MOLECULE T0351TS102_2
PFRMAT TS
TARGET T0351
MODEL 2
PARENT 2aml_A
ATOM      1  N   HIS   113      -0.379  -9.014  -4.825  1.00  1.00
ATOM      2  CA  HIS   113      -0.841  -8.064  -3.759  1.00  1.00
ATOM      3  C   HIS   113       0.123  -8.234  -2.577  1.00  1.00
ATOM      4  O   HIS   113       0.262  -9.333  -2.029  1.00  1.00
ATOM      5  CB  HIS   113      -2.282  -8.372  -3.278  1.00  1.00
ATOM      6  N   HIS   114       0.820  -7.158  -2.198  1.00  1.00
ATOM      7  CA  HIS   114       1.729  -7.168  -1.053  1.00  1.00
ATOM      8  C   HIS   114       0.889  -7.215   0.213  1.00  1.00
ATOM      9  O   HIS   114       0.084  -6.292   0.494  1.00  1.00
ATOM     10  CB  HIS   114       2.598  -5.906  -1.085  1.00  1.00
ATOM     11  N   HIS   115       1.033  -8.322   0.939  1.00  1.00
ATOM     12  CA  HIS   115       0.452  -8.438   2.275  1.00  1.00
ATOM     13  C   HIS   115       1.607  -8.718   3.218  1.00  1.00
ATOM     14  O   HIS   115       2.208  -9.791   3.153  1.00  1.00
ATOM     15  CB  HIS   115      -0.605  -9.550   2.355  1.00  1.00
ATOM     16  N   HIS   116       1.966  -7.698   4.021  1.00  1.00
ATOM     17  CA  HIS   116       3.166  -7.726   4.901  1.00  1.00
ATOM     18  C   HIS   116       3.293  -9.025   5.734  1.00  1.00
ATOM     19  O   HIS   116       4.388  -9.558   5.863  1.00  1.00
ATOM     20  CB  HIS   116       3.112  -6.475   5.814  1.00  1.00
ATOM     21  N   HIS   117       2.178  -9.519   6.267  1.00  1.00
ATOM     22  CA  HIS   117       2.236 -10.688   7.137  1.00  1.00
ATOM     23  C   HIS   117       2.194 -12.001   6.351  1.00  1.00
ATOM     24  O   HIS   117       2.374 -13.056   6.946  1.00  1.00
ATOM     25  CB  HIS   117       1.151 -10.631   8.213  1.00  1.00
TER
END
