
#######################################################
#                                                     #
#                        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    7 (   54),  selected    7 , name T0378TS302_2-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS302_2-D1.T0378_D1.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    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    -       -      S      12           -
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    P      83      R      43          1.813
LGA    L      84      M      44          0.812
LGA    M      85      L      45          0.483
LGA    A      86      V      46          0.466
LGA    V      87      G      47          0.671
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    F      88      P      83          2.364
LGA    D      89      L      84          1.571
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    7   89    5.0      7    1.36     0.00      7.441     0.480

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.264058 * X  +   0.963887 * Y  +  -0.034573 * Z  + -83.719368
  Y_new =  -0.084094 * X  +  -0.058716 * Y  +  -0.994726 * Z  +  60.068047
  Z_new =  -0.960834 * X  +  -0.259758 * Y  +   0.096561 * Z  +  90.407654 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.214891    1.926701  [ DEG:   -69.6081    110.3919 ]
  Theta =   1.289995    1.851597  [ DEG:    73.9113    106.0887 ]
  Phi   =  -2.833282    0.308311  [ DEG:  -162.3351     17.6649 ]
 
# 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: T0378TS302_2-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS302_2-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    7   89   5.0    7   1.36    0.00   7.441
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS302_2-D1
PFRMAT TS
TARGET T0378
MODEL  2
PARENT 1gz0_A
ATOM   1000  N   PRO    83       5.517  20.602  56.554  1.00  0.00
ATOM   1000  CA  PRO    83       5.530  21.031  55.169  1.00  0.00
ATOM   1000  C   PRO    83       4.216  21.714  54.931  1.00  0.00
ATOM   1000  O   PRO    83       3.171  21.093  55.124  1.00  0.00
ATOM   1000  CB  PRO    83       5.600  19.720  54.366  1.00  0.00
ATOM   1000  CG  PRO    83       5.032  18.600  55.299  1.00  0.00
ATOM   1000  CD  PRO    83       5.000  19.233  56.717  1.00  0.00
ATOM   1000  N   LEU    84       4.253  22.980  54.497  1.00  0.00
ATOM   1000  CA  LEU    84       3.038  23.712  54.303  1.00  0.00
ATOM   1000  C   LEU    84       2.821  23.719  52.821  1.00  0.00
ATOM   1000  O   LEU    84       3.692  24.166  52.076  1.00  0.00
ATOM   1000  CB  LEU    84       3.126  25.156  54.814  1.00  0.00
ATOM   1000  CG  LEU    84       1.826  25.964  54.633  1.00  0.00
ATOM   1000  CD1 LEU    84       0.618  25.323  55.346  1.00  0.00
ATOM   1000  CD2 LEU    84       2.014  27.425  55.066  1.00  0.00
ATOM   1000  N   MET    85       1.657  23.216  52.368  1.00  0.00
ATOM   1000  CA  MET    85       1.369  23.085  50.969  1.00  0.00
ATOM   1000  C   MET    85       0.722  24.347  50.499  1.00  0.00
ATOM   1000  O   MET    85      -0.156  24.898  51.163  1.00  0.00
ATOM   1000  CB  MET    85       0.422  21.913  50.683  1.00  0.00
ATOM   1000  CG  MET    85       1.042  20.542  50.953  1.00  0.00
ATOM   1000  SD  MET    85       2.426  20.147  49.844  1.00  0.00
ATOM   1000  CE  MET    85       3.792  20.535  50.972  1.00  0.00
ATOM   1000  N   ALA    86       1.141  24.811  49.308  1.00  0.00
ATOM   1000  CA  ALA    86       0.625  26.026  48.736  1.00  0.00
ATOM   1000  C   ALA    86      -0.153  25.548  47.556  1.00  0.00
ATOM   1000  O   ALA    86       0.075  24.427  47.107  1.00  0.00
ATOM   1000  CB  ALA    86       1.704  27.004  48.236  1.00  0.00
ATOM   1000  N   VAL    87      -1.073  26.397  47.027  1.00  0.00
ATOM   1000  CA  VAL    87      -1.914  26.137  45.876  1.00  0.00
ATOM   1000  C   VAL    87      -1.151  25.484  44.760  1.00  0.00
ATOM   1000  O   VAL    87      -1.662  24.591  44.088  1.00  0.00
ATOM   1000  CB  VAL    87      -2.618  27.404  45.375  1.00  0.00
ATOM   1000  CG1 VAL    87      -1.613  28.503  44.979  1.00  0.00
ATOM   1000  CG2 VAL    87      -3.563  27.141  44.180  1.00  0.00
ATOM   1000  N   PHE    88       0.100  25.927  44.560  1.00  0.00
ATOM   1000  CA  PHE    88       0.924  25.537  43.470  1.00  0.00
ATOM   1000  C   PHE    88       1.260  24.068  43.551  1.00  0.00
ATOM   1000  O   PHE    88       1.273  23.404  42.518  1.00  0.00
ATOM   1000  CB  PHE    88       2.234  26.352  43.444  1.00  0.00
ATOM   1000  CG  PHE    88       1.964  27.792  43.085  1.00  0.00
ATOM   1000  CD1 PHE    88       1.894  28.782  44.048  1.00  0.00
ATOM   1000  CD2 PHE    88       1.875  28.173  41.763  1.00  0.00
ATOM   1000  CE1 PHE    88       1.691  30.097  43.696  1.00  0.00
ATOM   1000  CE2 PHE    88       1.684  29.491  41.405  1.00  0.00
ATOM   1000  CZ  PHE    88       1.595  30.460  42.375  1.00  0.00
ATOM   1000  N   ASP    89       1.496  23.502  44.756  1.00  0.00
ATOM   1000  CA  ASP    89       1.995  22.134  44.864  1.00  0.00
ATOM   1000  C   ASP    89       0.792  21.232  45.058  1.00  0.00
ATOM   1000  O   ASP    89       0.872  20.062  45.413  1.00  0.00
ATOM   1000  CB  ASP    89       3.000  21.931  46.027  1.00  0.00
ATOM   1000  CG  ASP    89       3.777  20.589  45.985  1.00  0.00
ATOM   1000  OD1 ASP    89       3.217  19.483  46.186  1.00  0.00
ATOM   1000  OD2 ASP    89       5.018  20.669  45.806  1.00  0.00
TER
END
