
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS102_5.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    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      L      27           -
LGA    -       -      I      28           -
LGA    -       -      C      29           -
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    H      64      M      45          1.865
LGA    H      65      L      46          0.939
LGA    H      66      E      47          1.919
LGA    -       -      S      48           -
LGA    -       -      E      49           -
LGA    H      67      A      50          0.469
LGA    H      68      R      51          1.603
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    1.47     0.00      7.816     0.318

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.531592 * X  +   0.533176 * Y  +  -0.658128 * Z  + -32.246124
  Y_new =  -0.806318 * X  +   0.080643 * Y  +  -0.585959 * Z  +  87.558929
  Z_new =  -0.259346 * X  +   0.842152 * Y  +   0.472779 * Z  +  69.747574 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.059247   -2.082345  [ DEG:    60.6904   -119.3096 ]
  Theta =   0.262345    2.879247  [ DEG:    15.0313    164.9687 ]
  Phi   =  -0.987922    2.153670  [ DEG:   -56.6038    123.3962 ]
 
# 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_5                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS102_5.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   1.47    0.00   7.816
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS102_5
PFRMAT TS
TARGET T0348
MODEL 5
PARENT 2afb_A
ATOM      1  N   HIS    64       1.423  33.009  55.993  1.00  1.00
ATOM      2  CA  HIS    64       2.179  31.849  55.399  1.00  1.00
ATOM      3  C   HIS    64       1.361  30.531  55.440  1.00  1.00
ATOM      4  O   HIS    64       0.268  30.488  56.018  1.00  1.00
ATOM      5  CB  HIS    64       3.533  31.690  56.114  1.00  1.00
ATOM      6  N   HIS    65       1.895  29.469  54.825  1.00  1.00
ATOM      7  CA  HIS    65       1.204  28.161  54.716  1.00  1.00
ATOM      8  C   HIS    65       1.985  27.019  55.404  1.00  1.00
ATOM      9  O   HIS    65       3.208  27.007  55.338  1.00  1.00
ATOM     10  CB  HIS    65       1.059  27.767  53.237  1.00  1.00
ATOM     11  N   HIS    66       1.292  26.042  56.002  1.00  1.00
ATOM     12  CA  HIS    66       1.930  24.760  56.371  1.00  1.00
ATOM     13  C   HIS    66       2.552  24.107  55.121  1.00  1.00
ATOM     14  O   HIS    66       1.969  24.157  54.049  1.00  1.00
ATOM     15  CB  HIS    66       0.924  23.780  57.005  1.00  1.00
ATOM     16  N   HIS    67       3.729  23.503  55.257  1.00  1.00
ATOM     17  CA  HIS    67       4.326  22.744  54.169  1.00  1.00
ATOM     18  C   HIS    67       4.506  21.316  54.606  1.00  1.00
ATOM     19  O   HIS    67       5.333  21.055  55.447  1.00  1.00
ATOM     20  CB  HIS    67       5.689  23.322  53.773  1.00  1.00
ATOM     21  N   HIS    68       3.787  20.379  54.004  1.00  1.00
ATOM     22  CA  HIS    68       3.905  18.971  54.381  1.00  1.00
ATOM     23  C   HIS    68       5.173  18.419  53.767  1.00  1.00
ATOM     24  O   HIS    68       5.115  17.617  52.864  1.00  1.00
ATOM     25  CB  HIS    68       2.655  18.171  53.983  1.00  1.00
TER
END
