
#######################################################
#                                                     #
#                        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 T0335TS102_1
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS102_1.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      S       3           -
LGA    -       -      N       4           -
LGA    -       -      A       5           -
LGA    -       -      K       6           -
LGA    -       -      I       7           -
LGA    -       -      A       8           -
LGA    -       -      R       9           -
LGA    -       -      I      10           -
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    -       -      L      13           -
LGA    -       -      A      14           -
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    H      81      K      18          0.900
LGA    H      82      A      19          0.622
LGA    H      83      G      20          0.381
LGA    H      84      V      21          1.490
LGA    H      85      I      22          1.670
LGA    -       -      T      23           -
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    -       -      K      27           -
LGA    -       -      A      28           -
LGA    -       -      E      29           -
LGA    -       -      Q      30           -
LGA    -       -      Q      31           -
LGA    -       -      K      32           -
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      Q      35           -
LGA    -       -      E      36           -
LGA    -       -      Y      37           -
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -
LGA    -       -      F      41           -
LGA    -       -      R      42           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   42    5.0      5    1.13     0.00     11.539     0.407

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.347833 * X  +  -0.921554 * Y  +   0.172481 * Z  + 213.146881
  Y_new =  -0.231342 * X  +   0.262643 * Y  +   0.936749 * Z  + -47.969334
  Z_new =  -0.908567 * X  +   0.285930 * Y  +  -0.304550 * Z  + 157.134720 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.387717   -0.753875  [ DEG:   136.8061    -43.1939 ]
  Theta =   1.139840    2.001753  [ DEG:    65.3080    114.6920 ]
  Phi   =  -2.554680    0.586913  [ DEG:  -146.3724     33.6276 ]
 
# 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: T0335TS102_1                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS102_1.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   42   5.0    5   1.13    0.00  11.539
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS102_1
PFRMAT TS
TARGET T0335
MODEL 1
PARENT 1vlv_A
ATOM      1  N   HIS    81      -9.765   4.847   5.739  1.00  1.00
ATOM      2  CA  HIS    81      -9.338   3.738   4.838  1.00  1.00
ATOM      3  C   HIS    81     -10.292   2.558   4.959  1.00  1.00
ATOM      4  O   HIS    81      -9.846   1.417   4.745  1.00  1.00
ATOM      5  CB  HIS    81      -7.928   3.180   5.205  1.00  1.00
ATOM      6  N   HIS    82     -11.580   2.808   5.260  1.00  1.00
ATOM      7  CA  HIS    82     -12.534   1.804   5.868  1.00  1.00
ATOM      8  C   HIS    82     -12.236   1.543   7.362  1.00  1.00
ATOM      9  O   HIS    82     -13.149   1.659   8.181  1.00  1.00
ATOM     10  CB  HIS    82     -12.609   0.462   5.139  1.00  1.00
ATOM     11  N   HIS    83     -11.007   1.119   7.685  1.00  1.00
ATOM     12  CA  HIS    83     -10.445   1.299   9.045  1.00  1.00
ATOM     13  C   HIS    83      -9.260   2.203   8.877  1.00  1.00
ATOM     14  O   HIS    83      -8.244   1.817   8.305  1.00  1.00
ATOM     15  CB  HIS    83     -10.041  -0.008   9.747  1.00  1.00
ATOM     16  N   HIS    84      -9.419   3.432   9.349  1.00  1.00
ATOM     17  CA  HIS    84      -8.354   4.416   9.331  1.00  1.00
ATOM     18  C   HIS    84      -7.160   4.027  10.259  1.00  1.00
ATOM     19  O   HIS    84      -7.355   3.737  11.447  1.00  1.00
ATOM     20  CB  HIS    84      -8.963   5.769   9.727  1.00  1.00
ATOM     21  N   HIS    85      -5.938   4.037   9.712  1.00  1.00
ATOM     22  CA  HIS    85      -4.733   3.745  10.476  1.00  1.00
ATOM     23  C   HIS    85      -4.339   4.960  11.330  1.00  1.00
ATOM     24  O   HIS    85      -4.200   6.068  10.780  1.00  1.00
ATOM     25  CB  HIS    85      -3.553   3.383   9.552  1.00  1.00
TER
END
