
#######################################################
#                                                     #
#                        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 T0378TS247_2-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS247_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.

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

 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
#      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          1.798
LGA    L      84      M      44          0.747
LGA    M      85      L      45          0.419
LGA    A      86      V      46          0.465
LGA    V      87      G      47          0.777
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          2.222
LGA    D      89      L      84          1.554
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    1.32     0.00      7.441     0.494

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.375212 * X  +  -0.925108 * Y  +   0.058230 * Z  +   5.570076
  Y_new =  -0.875101 * X  +   0.374242 * Y  +   0.306825 * Z  +  20.560246
  Z_new =  -0.305639 * X  +   0.064168 * Y  +  -0.949983 * Z  +  56.576012 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.074149   -0.067444  [ DEG:   176.1357     -3.8643 ]
  Theta =   0.310609    2.830984  [ DEG:    17.7966    162.2034 ]
  Phi   =  -1.975851    1.165742  [ DEG:  -113.2079     66.7921 ]
 
# 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: T0378TS247_2-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS247_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   1.32    0.00   7.441
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS247_2-D1
PFRMAT TS
TARGET T0378
MODEL  2
PARENT 1zjr_A 1gz0_A 1gz0_B 1gz0_C 1gz0_D 1gz0_F 1gz0_H 1v2x_A 1x7p_A 1ipa_A
ATOM      1  N   PRO    83       5.570  20.560  56.576  1.00 0.00         0
ATOM      2  CA  PRO    83       5.655  21.006  55.196  1.00 0.00         0
ATOM      3  C   PRO    83       4.319  21.678  54.913  1.00 0.00         0
ATOM      4  O   PRO    83       3.283  21.014  54.986  1.00 0.00         0
ATOM      5  CB  PRO    83       5.880  19.717  54.404  1.00 0.00         0
ATOM      6  CG  PRO    83       6.502  18.779  55.384  1.00 0.00         0
ATOM      7  CD  PRO    83       5.852  19.071  56.708  1.00 0.00         0
ATOM      8  N   LEU    84       4.332  22.971  54.597  1.00 0.00         0
ATOM      9  CA  LEU    84       3.101  23.695  54.328  1.00 0.00         0
ATOM     10  C   LEU    84       2.822  23.660  52.834  1.00 0.00         0
ATOM     11  O   LEU    84       3.643  24.085  52.020  1.00 0.00         0
ATOM     12  CB  LEU    84       3.227  25.151  54.782  1.00 0.00         0
ATOM     13  CG  LEU    84       2.009  26.045  54.535  1.00 0.00         0
ATOM     14  CD1 LEU    84       0.816  25.567  55.348  1.00 0.00         0
ATOM     15  CD2 LEU    84       2.309  27.483  54.931  1.00 0.00         0
ATOM     16  N   MET    85       1.647  23.144  52.478  1.00 0.00         0
ATOM     17  CA  MET    85       1.255  23.056  51.083  1.00 0.00         0
ATOM     18  C   MET    85       0.640  24.365  50.607  1.00 0.00         0
ATOM     19  O   MET    85      -0.182  24.986  51.286  1.00 0.00         0
ATOM     20  CB  MET    85       0.224  21.943  50.885  1.00 0.00         0
ATOM     21  CG  MET    85       0.740  20.552  51.218  1.00 0.00         0
ATOM     22  SD  MET    85       2.167  20.083  50.221  1.00 0.00         0
ATOM     23  CE  MET    85       1.416  19.941  48.601  1.00 0.00         0
ATOM     24  N   ALA    86       1.052  24.785  49.412  1.00 0.00         0
ATOM     25  CA  ALA    86       0.492  25.960  48.766  1.00 0.00         0
ATOM     26  C   ALA    86      -0.221  25.554  47.483  1.00 0.00         0
ATOM     27  O   ALA    86       0.028  24.467  46.956  1.00 0.00         0
ATOM     28  CB  ALA    86       1.594  26.951  48.423  1.00 0.00         0
ATOM     29  N   VAL    87      -1.109  26.428  46.983  1.00 0.00         0
ATOM     30  CA  VAL    87      -1.871  26.243  45.743  1.00 0.00         0
ATOM     31  C   VAL    87      -1.129  25.594  44.571  1.00 0.00         0
ATOM     32  O   VAL    87      -1.668  24.737  43.862  1.00 0.00         0
ATOM     33  CB  VAL    87      -2.377  27.586  45.185  1.00 0.00         0
ATOM     34  CG1 VAL    87      -1.209  28.444  44.721  1.00 0.00         0
ATOM     35  CG2 VAL    87      -3.304  27.356  44.002  1.00 0.00         0
ATOM     36  N   PHE    88       0.123  26.012  44.369  1.00 0.00         0
ATOM     37  CA  PHE    88       0.975  25.498  43.310  1.00 0.00         0
ATOM     38  C   PHE    88       1.290  24.012  43.474  1.00 0.00         0
ATOM     39  O   PHE    88       1.332  23.258  42.500  1.00 0.00         0
ATOM     40  CB  PHE    88       2.311  26.244  43.286  1.00 0.00         0
ATOM     41  CG  PHE    88       3.254  25.765  42.221  1.00 0.00         0
ATOM     42  CD1 PHE    88       3.095  26.164  40.906  1.00 0.00         0
ATOM     43  CD2 PHE    88       4.302  24.915  42.534  1.00 0.00         0
ATOM     44  CE1 PHE    88       3.964  25.723  39.925  1.00 0.00         0
ATOM     45  CE2 PHE    88       5.170  24.475  41.553  1.00 0.00         0
ATOM     46  CZ  PHE    88       5.004  24.875  40.254  1.00 0.00         0
ATOM     47  N   ASP    89       1.515  23.568  44.714  1.00 0.00         0
ATOM     48  CA  ASP    89       1.961  22.204  44.961  1.00 0.00         0
ATOM     49  C   ASP    89       0.813  21.208  45.058  1.00 0.00         0
ATOM     50  O   ASP    89       1.019  20.027  45.334  1.00 0.00         0
ATOM     51  CB  ASP    89       2.736  22.123  46.278  1.00 0.00         0
ATOM     52  CG  ASP    89       4.007  22.950  46.256  1.00 0.00         0
ATOM     53  OD1 ASP    89       4.775  22.833  45.279  1.00 0.00         0
ATOM     54  OD2 ASP    89       4.234  23.715  47.217  1.00 0.00         0
TER
END
