
#######################################################
#                                                     #
#                        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 (    7),  selected    7 , name T0321TS464_3_2-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS464_3_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    -       -      M       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      G      11           -
LGA    -       -      I      12           -
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    -       -      L      58           -
LGA    -       -      P      59           -
LGA    -       -      L      60           -
LGA    A      84      R      61          1.309
LGA    Y      85      V      62          1.666
LGA    Y      86      A      63          1.941
LGA    -       -      A      64           -
LGA    N      87      G      65          1.352
LGA    N      88      C      66          1.202
LGA    P      89      V      67          1.387
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    Q      90      S      76          3.029
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)    7   96    5.0      7    1.80     0.00      6.666     0.369

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.378868 * X  +  -0.379273 * Y  +  -0.844163 * Z  +  42.022671
  Y_new =  -0.366326 * X  +   0.899121 * Y  +  -0.239555 * Z  +  89.011940
  Z_new =   0.849861 * X  +   0.218479 * Y  +  -0.479586 * Z  +  28.595345 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.714127   -0.427465  [ DEG:   155.5080    -24.4920 ]
  Theta =  -1.015722   -2.125870  [ DEG:   -58.1966   -121.8034 ]
  Phi   =  -2.373024    0.768568  [ DEG:  -135.9643     44.0357 ]
 
# 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_3_2-D1                             
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_3_2-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    7   96   5.0    7   1.80    0.00   6.666
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      1  CA  ALA    84     -14.995  47.929  64.255  1.00  0.00
ATOM      2  CA  TYR    85     -15.745  49.762  61.027  1.00  0.00
ATOM      3  CA  TYR    86     -12.729  50.009  58.743  1.00  0.00
ATOM      4  CA  ASN    87     -11.706  47.376  56.222  1.00  0.00
ATOM      5  CA  ASN    88      -8.561  49.442  55.508  1.00  0.00
ATOM      6  CA  PRO    89      -5.576  49.240  57.838  1.00  0.00
ATOM      7  CA  GLN    90      -5.438  52.002  60.442  1.00  0.00
TER
END
