
#######################################################
#                                                     #
#                        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 T0348TS102_3
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS102_3.T0348.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    -       -      D       2           -
LGA    -       -      A       3           -
LGA    -       -      K       4           -
LGA    -       -      F       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      I       8           -
LGA    -       -      L       9           -
LGA    -       -      V      10           -
LGA    -       -      C      11           -
LGA    -       -      P      12           -
LGA    -       -      L      13           -
LGA    -       -      C      14           -
LGA    -       -      K      15           -
LGA    -       -      G      16           -
LGA    -       -      P      17           -
LGA    -       -      L      18           -
LGA    -       -      V      19           -
LGA    -       -      F      20           -
LGA    -       -      D      21           -
LGA    -       -      K      22           -
LGA    -       -      S      23           -
LGA    -       -      K      24           -
LGA    H      64      D      25          0.912
LGA    H      65      E      26          0.671
LGA    H      66      L      27          0.387
LGA    H      67      I      28          0.871
LGA    H      68      C      29          0.876
LGA    -       -      K      30           -
LGA    -       -      G      31           -
LGA    -       -      D      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      A      35           -
LGA    -       -      F      36           -
LGA    -       -      P      37           -
LGA    -       -      I      38           -
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    -       -      M      44           -
LGA    -       -      M      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    -       -      E      49           -
LGA    -       -      A      50           -
LGA    -       -      R      51           -
LGA    -       -      E      52           -
LGA    -       -      L      53           -
LGA    -       -      A      54           -
LGA    -       -      P      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      E      58           -
LGA    -       -      V      59           -
LGA    -       -      K      60           -
LGA    -       -      L      61           -
LGA    -       -      E      62           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   61    5.0      5    0.77     0.00      8.197     0.575

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.657167 * X  +   0.744652 * Y  +   0.116723 * Z  +  -2.316212
  Y_new =   0.543097 * X  +  -0.575180 * Y  +   0.611730 * Z  +   4.067978
  Z_new =   0.522663 * X  +  -0.338617 * Y  +  -0.782408 * Z  +  96.627777 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.733144    0.408449  [ DEG:  -156.5976     23.4024 ]
  Theta =  -0.549972   -2.591621  [ DEG:   -31.5111   -148.4889 ]
  Phi   =   0.690645   -2.450948  [ DEG:    39.5710   -140.4290 ]
 
# 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: T0348TS102_3                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS102_3.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   61   5.0    5   0.77    0.00   8.197
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS102_3
PFRMAT TS
TARGET T0348
MODEL 3
PARENT 1zko_A
ATOM      1  N   HIS    64      13.185  26.271  45.701  1.00  1.00
ATOM      2  CA  HIS    64      13.498  25.927  47.116  1.00  1.00
ATOM      3  C   HIS    64      12.542  26.627  48.059  1.00  1.00
ATOM      4  O   HIS    64      12.176  27.783  47.845  1.00  1.00
ATOM      5  CB  HIS    64      14.942  26.291  47.451  1.00  1.00
ATOM      6  N   HIS    65      12.153  25.911  49.104  1.00  1.00
ATOM      7  CA  HIS    65      11.135  26.375  50.031  1.00  1.00
ATOM      8  C   HIS    65      11.734  26.642  51.399  1.00  1.00
ATOM      9  O   HIS    65      12.733  26.022  51.771  1.00  1.00
ATOM     10  CB  HIS    65      10.000  25.358  50.092  1.00  1.00
ATOM     11  N   HIS    66      11.142  27.591  52.122  1.00  1.00
ATOM     12  CA  HIS    66      11.634  27.998  53.435  1.00  1.00
ATOM     13  C   HIS    66      11.738  26.805  54.383  1.00  1.00
ATOM     14  O   HIS    66      10.763  26.088  54.610  1.00  1.00
ATOM     15  CB  HIS    66      10.716  29.080  54.013  1.00  1.00
ATOM     16  N   HIS    67      12.933  26.592  54.924  1.00  1.00
ATOM     17  CA  HIS    67      13.167  25.487  55.839  1.00  1.00
ATOM     18  C   HIS    67      12.457  25.729  57.161  1.00  1.00
ATOM     19  O   HIS    67      12.542  26.818  57.719  1.00  1.00
ATOM     20  CB  HIS    67      14.667  25.339  56.082  1.00  1.00
ATOM     21  N   HIS    68      11.750  24.710  57.641  1.00  1.00
ATOM     22  CA  HIS    68      11.189  24.730  58.983  1.00  1.00
ATOM     23  C   HIS    68      12.308  24.543  59.996  1.00  1.00
ATOM     24  O   HIS    68      13.351  23.971  59.682  1.00  1.00
ATOM     25  CB  HIS    68      10.194  23.599  59.185  1.00  1.00
TER
END
