
#######################################################
#                                                     #
#                        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 T0335TS599_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS599_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          4.277
LGA    K       6      K       6          3.280
LGA    I       7      I       7          2.719
LGA    A       8      A       8          2.231
LGA    R       9      R       9          2.200
LGA    I      10      I      10          1.619
LGA    N      11      N      11          1.009
LGA    E      12      E      12          0.798
LGA    L      13      L      13          1.229
LGA    A      14      A      14          1.004
LGA    A      15      A      15          1.673
LGA    K      16      K      16          1.783
LGA    A      17      A      17          0.772
LGA    K      18      K      18          1.948
LGA    A      19      A      19          3.843
LGA    G      20      G      20          3.228
LGA    V      21      V      21          0.769
LGA    I      22      I      22          1.099
LGA    T      23      T      23          1.169
LGA    E      24      E      24          2.160
LGA    E      25      E      25          2.721
LGA    E      26      E      26          1.761
LGA    K      27      K      27          1.143
LGA    A      28      A      28          2.159
LGA    E      29      E      29          2.051
LGA    Q      30      Q      30          1.097
LGA    Q      31      Q      31          1.237
LGA    K      32      K      32          1.574
LGA    L      33      L      33          1.624
LGA    R      34      R      34          1.176
LGA    Q      35      Q      35          0.985
LGA    E      36      E      36          1.482
LGA    Y      37      Y      37          2.903
LGA    L      38      L      38          3.172
LGA    K      39      K      39          2.702
LGA    G      40      G      40          4.147

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     36    2.19   100.00     87.846     1.573

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.196256 * X  +  -0.979732 * Y  +  -0.040120 * Z  +   5.313961
  Y_new =   0.776632 * X  +   0.180289 * Y  +  -0.603605 * Z  +  -3.647227
  Z_new =   0.598604 * X  +   0.087302 * Y  +   0.796273 * Z  + -18.437799 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.109202   -3.032390  [ DEG:     6.2568   -173.7432 ]
  Theta =  -0.641758   -2.499835  [ DEG:   -36.7700   -143.2300 ]
  Phi   =   1.323277   -1.818316  [ DEG:    75.8182   -104.1818 ]
 
# 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: T0335TS599_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS599_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   2.19  100.00  87.846
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS599_4-D1
PFRMAT TS                                                                       
TARGET T0335                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      5  CA  ALA     5      -1.694  -8.643  -9.055  1.00  0.00              
ATOM      6  CA  LYS     6       0.123  -5.666  -7.562  1.00  0.00              
ATOM      7  CA  ILE     7      -2.864  -3.432  -8.185  1.00  0.00              
ATOM      8  CA  ALA     8      -5.199  -5.934  -6.505  1.00  0.00              
ATOM      9  CA  ARG     9      -2.888  -6.270  -3.515  1.00  0.00              
ATOM     10  CA  ILE    10      -2.605  -2.544  -3.031  1.00  0.00              
ATOM     11  CA  ASN    11      -6.336  -2.201  -3.152  1.00  0.00              
ATOM     12  CA  GLU    12      -6.824  -4.885  -0.572  1.00  0.00              
ATOM     13  CA  LEU    13      -4.300  -3.258   1.785  1.00  0.00              
ATOM     14  CA  ALA    14      -5.971   0.135   1.367  1.00  0.00              
ATOM     15  CA  ALA    15      -9.317  -1.412   2.314  1.00  0.00              
ATOM     16  CA  LYS    16      -7.722  -3.131   5.360  1.00  0.00              
ATOM     17  CA  ALA    17      -6.181   0.171   6.400  1.00  0.00              
ATOM     18  CA  LYS    18      -9.483   2.000   6.044  1.00  0.00              
ATOM     19  CA  ALA    19     -11.233  -0.536   8.239  1.00  0.00              
ATOM     20  CA  GLY    20      -8.579  -0.298  10.911  1.00  0.00              
ATOM     21  CA  VAL    21      -8.125   3.471  10.772  1.00  0.00              
ATOM     22  CA  ILE    22      -4.597   3.514   9.560  1.00  0.00              
ATOM     23  CA  THR    23      -2.139   5.667  11.400  1.00  0.00              
ATOM     24  CA  GLU    24       0.114   8.157   9.730  1.00  0.00              
ATOM     25  CA  GLU    25       3.025   5.658  10.016  1.00  0.00              
ATOM     26  CA  GLU    26       0.977   2.954   8.322  1.00  0.00              
ATOM     27  CA  LYS    27       0.085   5.396   5.495  1.00  0.00              
ATOM     28  CA  ALA    28       3.748   6.337   4.974  1.00  0.00              
ATOM     29  CA  GLU    29       4.757   2.651   4.836  1.00  0.00              
ATOM     30  CA  GLN    30       2.006   1.942   2.286  1.00  0.00              
ATOM     31  CA  GLN    31       3.130   4.800   0.108  1.00  0.00              
ATOM     32  CA  LYS    32       6.769   3.581   0.207  1.00  0.00              
ATOM     33  CA  LEU    33       5.727   0.033  -0.664  1.00  0.00              
ATOM     34  CA  ARG    34       3.640   1.215  -3.583  1.00  0.00              
ATOM     35  CA  GLN    35       6.485   3.295  -4.944  1.00  0.00              
ATOM     36  CA  GLU    36       8.941   0.375  -4.703  1.00  0.00              
ATOM     37  CA  TYR    37       6.557  -2.038  -6.433  1.00  0.00              
ATOM     38  CA  LEU    38       5.889   0.438  -9.181  1.00  0.00              
ATOM     39  CA  LYS    39       9.648   1.014  -9.735  1.00  0.00              
ATOM     40  CA  GLY    40      10.251  -2.744  -9.810  1.00  0.00              
TER                                                                             
END
