
#######################################################
#                                                     #
#                        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 T0351TS102_3
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351TS102_3.T0351.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     113      M       1          0.496
LGA    H     114      I       2          0.255
LGA    H     115      L       3          0.527
LGA    -       -      Y       4           -
LGA    -       -      D       5           -
LGA    H     116      A       6          1.226
LGA    H     117      I       7          0.869
LGA    -       -      M       8           -
LGA    -       -      Y       9           -
LGA    -       -      K      10           -
LGA    -       -      Y      11           -
LGA    -       -      P      12           -
LGA    -       -      N      13           -
LGA    -       -      A      14           -
LGA    -       -      V      15           -
LGA    -       -      S      16           -
LGA    -       -      R      17           -
LGA    -       -      K      18           -
LGA    -       -      D      19           -
LGA    -       -      F      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      R      23           -
LGA    -       -      N      24           -
LGA    -       -      D      25           -
LGA    -       -      G      26           -
LGA    -       -      N      27           -
LGA    -       -      G      28           -
LGA    -       -      S      29           -
LGA    -       -      Y      30           -
LGA    -       -      I      31           -
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    -       -      W      34           -
LGA    -       -      N      35           -
LGA    -       -      L      36           -
LGA    -       -      R      37           -
LGA    -       -      A      38           -
LGA    -       -      P      39           -
LGA    -       -      L      40           -
LGA    -       -      P      41           -
LGA    -       -      T      42           -
LGA    -       -      Q      43           -
LGA    -       -      A      44           -
LGA    -       -      E      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      T      48           -
LGA    -       -      W      49           -
LGA    -       -      W      50           -
LGA    -       -      E      51           -
LGA    -       -      E      52           -
LGA    -       -      L      53           -
LGA    -       -      Q      54           -
LGA    -       -      K      55           -
LGA    -       -      N      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   56    5.0      5    0.75     0.00      8.788     0.585

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.005737 * X  +   0.227006 * Y  +  -0.973876 * Z  +  41.833328
  Y_new =  -0.078616 * X  +  -0.970776 * Y  +  -0.226746 * Z  +  21.754831
  Z_new =  -0.996888 * X  +   0.077863 * Y  +   0.012278 * Z  +   0.724367 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.414404   -1.727189  [ DEG:    81.0394    -98.9606 ]
  Theta =   1.491889    1.649703  [ DEG:    85.4790     94.5210 ]
  Phi   =  -1.497957    1.643636  [ DEG:   -85.8266     94.1734 ]
 
# 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: T0351TS102_3                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351TS102_3.T0351.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   56   5.0    5   0.75    0.00   8.788
REMARK  ---------------------------------------------------------- 
MOLECULE T0351TS102_3
PFRMAT TS
TARGET T0351
MODEL 3
PARENT 1zko_A
ATOM      1  N   HIS   113      -8.350  -5.975   7.008  1.00  1.00
ATOM      2  CA  HIS   113      -7.109  -5.698   6.233  1.00  1.00
ATOM      3  C   HIS   113      -7.023  -4.229   5.872  1.00  1.00
ATOM      4  O   HIS   113      -8.028  -3.600   5.541  1.00  1.00
ATOM      5  CB  HIS   113      -7.056  -6.561   4.975  1.00  1.00
ATOM      6  N   HIS   114      -5.809  -3.701   5.936  1.00  1.00
ATOM      7  CA  HIS   114      -5.567  -2.280   5.758  1.00  1.00
ATOM      8  C   HIS   114      -4.784  -2.024   4.484  1.00  1.00
ATOM      9  O   HIS   114      -4.020  -2.884   4.041  1.00  1.00
ATOM     10  CB  HIS   114      -4.856  -1.726   6.988  1.00  1.00
ATOM     11  N   HIS   115      -5.007  -0.855   3.885  1.00  1.00
ATOM     12  CA  HIS   115      -4.368  -0.485   2.625  1.00  1.00
ATOM     13  C   HIS   115      -2.848  -0.577   2.725  1.00  1.00
ATOM     14  O   HIS   115      -2.231   0.039   3.595  1.00  1.00
ATOM     15  CB  HIS   115      -4.808   0.927   2.224  1.00  1.00
ATOM     16  N   HIS   116      -2.251  -1.363   1.835  1.00  1.00
ATOM     17  CA  HIS   116      -0.808  -1.542   1.826  1.00  1.00
ATOM     18  C   HIS   116      -0.115  -0.267   1.372  1.00  1.00
ATOM     19  O   HIS   116      -0.514   0.335   0.380  1.00  1.00
ATOM     20  CB  HIS   116      -0.445  -2.687   0.883  1.00  1.00
ATOM     21  N   HIS   117       0.910   0.139   2.115  1.00  1.00
ATOM     22  CA  HIS   117       1.785   1.220   1.691  1.00  1.00
ATOM     23  C   HIS   117       2.684   0.724   0.569  1.00  1.00
ATOM     24  O   HIS   117       2.943  -0.473   0.453  1.00  1.00
ATOM     25  CB  HIS   117       2.684   1.684   2.825  1.00  1.00
TER
END
