
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS102_5.T0335.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    H      81      M       1          0.595
LGA    H      82      I       2          0.534
LGA    H      83      S       3          0.678
LGA    -       -      N       4           -
LGA    -       -      A       5           -
LGA    -       -      K       6           -
LGA    H      84      I       7          1.062
LGA    H      85      A       8          0.691
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    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    -       -      I      22           -
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    0.74     0.00     11.717     0.599

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.508012 * X  +  -0.782756 * Y  +  -0.359468 * Z  +  40.142918
  Y_new =   0.263832 * X  +   0.255865 * Y  +  -0.930014 * Z  + -19.440460
  Z_new =   0.819949 * X  +  -0.567298 * Y  +   0.076534 * Z  + -69.529099 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.436697    1.704896  [ DEG:   -82.3166     97.6834 ]
  Theta =  -0.961321   -2.180271  [ DEG:   -55.0797   -124.9203 ]
  Phi   =   2.662591   -0.479002  [ DEG:   152.5552    -27.4448 ]
 
# 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_5                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS102_5.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   0.74    0.00  11.717
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS102_5
PFRMAT TS
TARGET T0335
MODEL 5
PARENT 2afb_A
ATOM      1  N   HIS    81       4.165  -4.741 -16.728  1.00  1.00
ATOM      2  CA  HIS    81       3.593  -4.304 -15.404  1.00  1.00
ATOM      3  C   HIS    81       3.197  -5.508 -14.508  1.00  1.00
ATOM      4  O   HIS    81       3.264  -6.664 -14.945  1.00  1.00
ATOM      5  CB  HIS    81       2.394  -3.366 -15.640  1.00  1.00
ATOM      6  N   HIS    82       2.795  -5.228 -13.263  1.00  1.00
ATOM      7  CA  HIS    82       2.453  -6.272 -12.266  1.00  1.00
ATOM      8  C   HIS    82       0.986  -6.182 -11.793  1.00  1.00
ATOM      9  O   HIS    82       0.474  -5.080 -11.639  1.00  1.00
ATOM     10  CB  HIS    82       3.331  -6.107 -11.014  1.00  1.00
ATOM     11  N   HIS    83       0.336  -7.317 -11.507  1.00  1.00
ATOM     12  CA  HIS    83      -0.923  -7.311 -10.732  1.00  1.00
ATOM     13  C   HIS    83      -0.696  -6.623  -9.372  1.00  1.00
ATOM     14  O   HIS    83       0.343  -6.810  -8.756  1.00  1.00
ATOM     15  CB  HIS    83      -1.458  -8.736 -10.493  1.00  1.00
ATOM     16  N   HIS    84      -1.657  -5.829  -8.908  1.00  1.00
ATOM     17  CA  HIS    84      -1.591  -5.249  -7.577  1.00  1.00
ATOM     18  C   HIS    84      -2.772  -5.721  -6.774  1.00  1.00
ATOM     19  O   HIS    84      -3.877  -5.324  -7.060  1.00  1.00
ATOM     20  CB  HIS    84      -1.607  -3.718  -7.639  1.00  1.00
ATOM     21  N   HIS    85      -2.551  -6.513  -5.735  1.00  1.00
ATOM     22  CA  HIS    85      -3.651  -7.016  -4.915  1.00  1.00
ATOM     23  C   HIS    85      -4.101  -5.904  -3.992  1.00  1.00
ATOM     24  O   HIS    85      -3.893  -5.975  -2.803  1.00  1.00
ATOM     25  CB  HIS    85      -3.255  -8.293  -4.157  1.00  1.00
TER
END
