
#######################################################
#                                                     #
#                        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   36 (   36),  selected   36 , name T0335TS393_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS393_4-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          1.723
LGA    K       6      K       6          1.747
LGA    I       7      I       7          1.254
LGA    A       8      A       8          1.119
LGA    R       9      R       9          2.081
LGA    I      10      I      10          2.087
LGA    N      11      N      11          1.253
LGA    E      12      E      12          1.746
LGA    L      13      L      13          3.275
LGA    A      14      A      14          2.531
LGA    A      15      A      15          0.921
LGA    K      16      K      16          2.901
LGA    A      17      A      17          4.211
LGA    K      18      K      18          2.226
LGA    A      19      A      19          1.748
LGA    G      20      G      20          3.322
LGA    V      21      V      21          1.889
LGA    I      22      I      22          2.157
LGA    T      23      T      23          1.343
LGA    E      24      E      24          1.452
LGA    E      25      E      25          1.230
LGA    E      26      E      26          1.636
LGA    K      27      K      27          1.443
LGA    A      28      A      28          0.870
LGA    E      29      E      29          0.948
LGA    Q      30      Q      30          1.547
LGA    Q      31      Q      31          1.854
LGA    K      32      K      32          1.718
LGA    L      33      L      33          1.211
LGA    R      34      R      34          1.586
LGA    Q      35      Q      35          1.322
LGA    E      36      E      36          1.476
LGA    Y      37      Y      37          2.254
LGA    L      38      L      38          2.173
LGA    K      39      K      39          2.257
LGA    G      40      G      40          3.024

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     36    2.01   100.00     88.710     1.702

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.124329 * X  +   0.592078 * Y  +   0.796233 * Z  +   4.661878
  Y_new =   0.467480 * X  +  -0.742770 * Y  +   0.479327 * Z  +   1.746711
  Z_new =   0.875217 * X  +   0.312628 * Y  +  -0.369133 * Z  +  -6.697523 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.438885   -0.702707  [ DEG:   139.7379    -40.2621 ]
  Theta =  -1.065884   -2.075709  [ DEG:   -61.0707   -118.9293 ]
  Phi   =   1.310857   -1.830736  [ DEG:    75.1066   -104.8934 ]
 
# 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: T0335TS393_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS393_4-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   36   5.0   36   2.01  100.00  88.710
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS393_4-D1
PFRMAT TS
TARGET T0335
MODEL 4
PARENT N/A
ATOM      5  CA  ALA     5       0.547 -10.493  -6.381  1.00 25.00           C
ATOM      6  CA  LYS     6       1.910  -6.914  -6.385  1.00 25.00           C
ATOM      7  CA  ILE     7      -1.450  -5.609  -7.679  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.287  -7.538  -4.927  1.00 25.00           C
ATOM      9  CA  ARG     9      -0.929  -6.069  -2.291  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.551  -2.548  -3.659  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.333  -3.136  -3.522  1.00 25.00           C
ATOM     12  CA  GLU    12      -5.037  -4.351   0.098  1.00 25.00           C
ATOM     13  CA  LEU    13      -2.998  -1.236   1.001  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.642   0.999  -0.634  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.404  -0.788   1.329  1.00 25.00           C
ATOM     16  CA  LYS    16      -6.440  -0.300   4.581  1.00 25.00           C
ATOM     17  CA  ALA    17      -6.003   3.421   3.787  1.00 25.00           C
ATOM     18  CA  LYS    18      -9.757   3.744   3.109  1.00 25.00           C
ATOM     19  CA  ALA    19     -10.532   2.015   6.437  1.00 25.00           C
ATOM     20  CA  GLY    20     -10.576   4.612   9.263  1.00 25.00           C
ATOM     21  CA  VAL    21      -8.329   2.281  11.365  1.00 25.00           C
ATOM     22  CA  ILE    22      -4.893   2.109   9.650  1.00 25.00           C
ATOM     23  CA  THR    23      -2.034   3.609  11.716  1.00 25.00           C
ATOM     24  CA  GLU    24       0.979   5.874  11.401  1.00 25.00           C
ATOM     25  CA  GLU    25       3.949   3.537  10.783  1.00 25.00           C
ATOM     26  CA  GLU    26       1.630   0.992   9.106  1.00 25.00           C
ATOM     27  CA  LYS    27       0.168   3.750   6.888  1.00 25.00           C
ATOM     28  CA  ALA    28       3.698   4.874   5.917  1.00 25.00           C
ATOM     29  CA  GLU    29       4.636   1.263   5.053  1.00 25.00           C
ATOM     30  CA  GLN    30       1.483   0.930   2.906  1.00 25.00           C
ATOM     31  CA  GLN    31       2.342   4.194   1.095  1.00 25.00           C
ATOM     32  CA  LYS    32       5.900   2.929   0.453  1.00 25.00           C
ATOM     33  CA  LEU    33       4.508  -0.359  -0.933  1.00 25.00           C
ATOM     34  CA  ARG    34       2.136   1.584  -3.228  1.00 25.00           C
ATOM     35  CA  GLN    35       5.054   3.735  -4.464  1.00 25.00           C
ATOM     36  CA  GLU    36       7.115   0.582  -5.158  1.00 25.00           C
ATOM     37  CA  TYR    37       4.184  -0.938  -7.099  1.00 25.00           C
ATOM     38  CA  LEU    38       3.843   2.280  -9.150  1.00 25.00           C
ATOM     39  CA  LYS    39       7.596   2.218  -9.915  1.00 25.00           C
ATOM     40  CA  GLY    40       7.336  -1.441 -11.018  1.00 25.00           C
TER
END
