
#######################################################
#                                                     #
#                        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   12 (   12),  selected   12 , name T0321TS464_5_2-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS464_5_2-D1.T0321_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    -       -      W       2           -
LGA    -       -      E       3           -
LGA    -       -      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      D       6           -
LGA    -       -      A       7           -
LGA    E       3      M       8          2.021
LGA    I       4      I       9          1.633
LGA    Y       5      N      10          0.146
LGA    D       6      G      11          1.936
LGA    A       7      I      12          2.610
LGA    -       -      P      13           -
LGA    -       -      E      14           -
LGA    -       -      D      15           -
LGA    -       -      F      16           -
LGA    -       -      L      17           -
LGA    -       -      V      18           -
LGA    -       -      D      19           -
LGA    -       -      E      20           -
LGA    -       -      L      21           -
LGA    -       -      V      22           -
LGA    -       -      C      23           -
LGA    -       -      G      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      H      27           -
LGA    -       -      S      28           -
LGA    -       -      V      29           -
LGA    -       -      I      30           -
LGA    -       -      R      31           -
LGA    -       -      S      32           -
LGA    -       -      G      33           -
LGA    -       -      N      34           -
LGA    -       -      G      35           -
LGA    -       -      V      36           -
LGA    -       -      G      37           -
LGA    -       -      L      38           -
LGA    -       -      G      39           -
LGA    -       -      P      40           -
LGA    -       -      N      41           -
LGA    -       -      R      42           -
LGA    -       -      P      43           -
LGA    -       -      F      44           -
LGA    -       -      E      45           -
LGA    -       -      T      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      P      49           -
LGA    -       -      M      50           -
LGA    -       -      L      51           -
LGA    -       -      T      52           -
LGA    -       -      Q      53           -
LGA    -       -      N      54           -
LGA    -       -      L      55           -
LGA    -       -      L      56           -
LGA    -       -      G      57           -
LGA    V      18      L      58          1.428
LGA    D      19      P      59          1.695
LGA    E      20      L      60          1.616
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    L      21      A      63          0.586
LGA    V      22      A      64          2.051
LGA    -       -      G      65           -
LGA    C      23      C      66          1.484
LGA    G      24      V      67          2.586
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      W      70           -
LGA    -       -      N      71           -
LGA    -       -      Y      72           -
LGA    -       -      V      73           -
LGA    -       -      E      74           -
LGA    -       -      A      75           -
LGA    -       -      S      76           -
LGA    -       -      I      77           -
LGA    -       -      G      78           -
LGA    -       -      L      79           -
LGA    -       -      A      80           -
LGA    -       -      A      81           -
LGA    -       -      I      82           -
LGA    -       -      N      83           -
LGA    -       -      A      84           -
LGA    -       -      Y      85           -
LGA    -       -      Y      86           -
LGA    -       -      N      87           -
LGA    -       -      N      88           -
LGA    -       -      P      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      A      92           -
LGA    -       -      R      93           -
LGA    -       -      E      94           -
LGA    -       -      H      95           -
LGA    -       -      G      96           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   12   96    5.0     12    1.79    16.67     11.317     0.636

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.701717 * X  +  -0.049847 * Y  +  -0.710710 * Z  +  78.952835
  Y_new =  -0.702204 * X  +   0.217010 * Y  +   0.678098 * Z  +  58.620785
  Z_new =   0.120430 * X  +   0.974896 * Y  +  -0.187283 * Z  +  22.411976 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.760590   -1.381003  [ DEG:   100.8744    -79.1256 ]
  Theta =  -0.120723   -3.020870  [ DEG:    -6.9169   -173.0831 ]
  Phi   =  -2.355848    0.785745  [ DEG:  -134.9801     45.0199 ]
 
# 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: T0321TS464_5_2-D1                             
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_5_2-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12   96   5.0   12   1.79   16.67  11.317
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      1  CA  GLU     3      -9.159  41.332  66.708  1.00  0.00
ATOM      2  CA  ILE     4     -11.767  43.093  64.553  1.00  0.00
ATOM      3  CA  TYR     5     -13.863  40.006  63.753  1.00  0.00
ATOM      4  CA  ASP     6     -13.284  38.522  67.225  1.00  0.00
ATOM      5  CA  ALA     7     -14.046  41.776  68.966  1.00  0.00
ATOM      6  CA  VAL    18     -20.459  53.817  61.444  1.00  0.00
ATOM      7  CA  ASP    19     -18.691  52.616  64.603  1.00  0.00
ATOM      8  CA  GLU    20     -15.207  51.702  63.419  1.00  0.00
ATOM      9  CA  LEU    21     -13.063  51.701  60.342  1.00  0.00
ATOM     10  CA  VAL    22     -10.700  49.117  59.072  1.00  0.00
ATOM     11  CA  CYS    23      -8.115  50.712  56.795  1.00  0.00
ATOM     12  CA  GLY    24      -5.706  48.162  55.363  1.00  0.00
TER
END
