
#######################################################
#                                                     #
#                        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 T0358TS102_4
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358TS102_4.T0358.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    -       -      G      10           -
LGA    -       -      P      11           -
LGA    -       -      F      12           -
LGA    -       -      T      13           -
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    -       -      T      28           -
LGA    -       -      L      29           -
LGA    -       -      E      30           -
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    -       -      F      37           -
LGA    -       -      R      38           -
LGA    -       -      L      39           -
LGA    -       -      V      40           -
LGA    -       -      V      41           -
LGA    -       -      R      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      V      49           -
LGA    -       -      W      50           -
LGA    -       -      R      51           -
LGA    -       -      A      52           -
LGA    -       -      W      53           -
LGA    -       -      N      54           -
LGA    -       -      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    H      83      G      62          0.927
LGA    H      84      L      63          2.471
LGA    H      85      N      64          2.194
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    H      86      R      68          1.533
LGA    H      87      T      69          0.427
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   66    5.0      5    1.69     0.00      7.117     0.279

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.141229 * X  +  -0.957575 * Y  +   0.251206 * Z  +  -6.868070
  Y_new =  -0.946532 * X  +  -0.204958 * Y  +  -0.249137 * Z  +  65.837845
  Z_new =   0.290054 * X  +  -0.202589 * Y  +  -0.935321 * Z  +  -7.162083 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.928289    0.213304  [ DEG:  -167.7786     12.2214 ]
  Theta =  -0.294284   -2.847309  [ DEG:   -16.8612   -163.1388 ]
  Phi   =  -1.422683    1.718910  [ DEG:   -81.5137     98.4863 ]
 
# 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: T0358TS102_4                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS102_4.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   66   5.0    5   1.69    0.00   7.117
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS102_4
PFRMAT TS
TARGET T0358
MODEL 4
PARENT 2afb_A
ATOM      1  N   HIS    83       1.320   2.661   8.334  1.00  1.00
ATOM      2  CA  HIS    83       1.688   1.313   8.897  1.00  1.00
ATOM      3  C   HIS    83       2.595   0.501   7.935  1.00  1.00
ATOM      4  O   HIS    83       2.848   0.928   6.801  1.00  1.00
ATOM      5  CB  HIS    83       0.410   0.532   9.254  1.00  1.00
ATOM      6  N   HIS    84       3.080  -0.658   8.396  1.00  1.00
ATOM      7  CA  HIS    84       4.016  -1.511   7.624  1.00  1.00
ATOM      8  C   HIS    84       3.435  -2.911   7.327  1.00  1.00
ATOM      9  O   HIS    84       2.752  -3.468   8.178  1.00  1.00
ATOM     10  CB  HIS    84       5.308  -1.731   8.428  1.00  1.00
ATOM     11  N   HIS    85       3.748  -3.500   6.167  1.00  1.00
ATOM     12  CA  HIS    85       3.531  -4.947   5.953  1.00  1.00
ATOM     13  C   HIS    85       4.284  -5.753   7.029  1.00  1.00
ATOM     14  O   HIS    85       5.394  -5.398   7.397  1.00  1.00
ATOM     15  CB  HIS    85       4.008  -5.399   4.559  1.00  1.00
ATOM     16  N   HIS    86       3.683  -6.826   7.535  1.00  1.00
ATOM     17  CA  HIS    86       4.369  -7.722   8.452  1.00  1.00
ATOM     18  C   HIS    86       4.427  -9.098   7.845  1.00  1.00
ATOM     19  O   HIS    86       3.410  -9.739   7.736  1.00  1.00
ATOM     20  CB  HIS    86       3.641  -7.800   9.799  1.00  1.00
ATOM     21  N   HIS    87       5.612  -9.585   7.505  1.00  1.00
ATOM     22  CA  HIS    87       5.745 -10.911   6.904  1.00  1.00
ATOM     23  C   HIS    87       5.615 -11.945   8.002  1.00  1.00
ATOM     24  O   HIS    87       6.575 -12.594   8.345  1.00  1.00
ATOM     25  CB  HIS    87       7.054 -11.046   6.113  1.00  1.00
TER
END
