
#######################################################
#                                                     #
#                        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 T0378TS102_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS102_5-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.

# WARNING! The change of the distance cutoff DIST 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    L      84      R      14          1.839
LGA    M      85      E      15          0.977
LGA    A      86      R      16          1.371
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    V      87      R      19          1.082
LGA    F      88      L      20          0.957
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    -       -      R      43           -
LGA    -       -      M      44           -
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
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    -       -      P      83           -
LGA    -       -      L      84           -
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)    5   89    5.0      5    1.29     0.00      5.445     0.360

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.441595 * X  +   0.895027 * Y  +  -0.062612 * Z  +  -2.709127
  Y_new =  -0.490771 * X  +  -0.182541 * Y  +   0.851952 * Z  +  -0.433294
  Z_new =   0.751091 * X  +   0.406946 * Y  +   0.519862 * Z  +   7.650427 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.664162   -2.477431  [ DEG:    38.0537   -141.9463 ]
  Theta =  -0.849714   -2.291879  [ DEG:   -48.6850   -131.3150 ]
  Phi   =  -2.303500    0.838093  [ DEG:  -131.9808     48.0192 ]
 
# 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: T0378TS102_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS102_5-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   89   5.0    5   1.29    0.00   5.445
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS102_5-D1
PFRMAT TS
TARGET T0378
MODEL 5
PARENT 2ha8_A
ATOM      1  N   LEU    84      16.333  26.053  44.825  1.00  1.00
ATOM      2  CA  LEU    84      17.447  26.941  45.260  1.00  1.00
ATOM      3  C   LEU    84      17.536  27.014  46.776  1.00  1.00
ATOM      4  O   LEU    84      16.568  27.376  47.459  1.00  1.00
ATOM      5  CB  LEU    84      17.301  28.341  44.659  1.00  1.00
ATOM      6  N   MET    85      18.714  26.671  47.287  1.00  1.00
ATOM      7  CA  MET    85      18.955  26.609  48.720  1.00  1.00
ATOM      8  C   MET    85      18.996  25.174  49.213  1.00  1.00
ATOM      9  O   MET    85      18.065  24.401  48.973  1.00  1.00
ATOM     10  CB  MET    85      17.797  27.331  49.435  1.00  1.00
ATOM     11  N   ALA    86      20.078  24.825  49.896  1.00  1.00
ATOM     12  CA  ALA    86      20.227  23.504  50.477  1.00  1.00
ATOM     13  C   ALA    86      19.957  23.565  51.979  1.00  1.00
ATOM     14  O   ALA    86      20.640  24.288  52.699  1.00  1.00
ATOM     15  CB  ALA    86      21.636  22.981  50.224  1.00  1.00
ATOM     16  N   VAL    87      18.982  22.786  52.437  1.00  1.00
ATOM     17  CA  VAL    87      18.645  22.733  53.857  1.00  1.00
ATOM     18  C   VAL    87      19.692  21.983  54.668  1.00  1.00
ATOM     19  O   VAL    87      20.295  21.007  54.201  1.00  1.00
ATOM     20  CB  VAL    87      17.276  22.095  54.064  1.00  1.00
ATOM     21  N   PHE    88      19.907  22.443  55.893  1.00  1.00
ATOM     22  CA  PHE    88      20.754  21.733  56.834  1.00  1.00
ATOM     23  C   PHE    88      20.157  20.324  57.042  1.00  1.00
ATOM     24  O   PHE    88      18.937  20.167  57.102  1.00  1.00
ATOM     25  CB  PHE    88      20.843  22.514  58.172  1.00  1.00
TER
END
