
#######################################################
#                                                     #
#                        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   16 (  126),  selected   16 , name T0382TS009_2_1-D1
# Molecule2: number of CA atoms  119 (  920),  selected  119 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_2_1-D1.T0382_D1.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.

# WARNING! The change of the distance cutoff DIST may give you better result.

 ERROR! 0 0 16 119
 ERROR! 0 0 16 119
 ERROR! 0 0 16 119
 ERROR! 0 0 16 119
 ERROR! 0 0 16 119
 ERROR! 0 0 16 119
 ERROR! 0 0 16 119
 ERROR! 0 0 16 119
 ERROR! 0 0 16 119
 ERROR! 0 0 16 119
#      Molecule1      Molecule2       DISTANCE
LGA    L       4      L       4           -
LGA    D       5      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    -       -      T      11           -
LGA    -       -      Q      12           -
LGA    -       -      D      13           -
LGA    -       -      L      14           -
LGA    -       -      V      15           -
LGA    -       -      A      16           -
LGA    -       -      L      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      K      20           -
LGA    -       -      V      21           -
LGA    L       6      T      22           #
LGA    -       -      V      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      D      26           -
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    -       -      Q      33           -
LGA    -       -      I      34           -
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    H       7      F      37          2.766
LGA    Q       8      N      38          1.640
LGA    M       9      R      39          1.757
LGA    T      10      L      40          2.942
LGA    -       -      F      41           -
LGA    T      11      G      42          1.654
LGA    Q      12      V      43          1.880
LGA    D      13      M      44          1.954
LGA    L      14      A      45          3.036
LGA    -       -      E      46           -
LGA    -       -      I      47           -
LGA    V      15      A      48          1.271
LGA    A      16      D      49          1.503
LGA    -       -      E      50           -
LGA    L      17      L      51          1.160
LGA    -       -      K      52           -
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    -       -      D      57           -
LGA    -       -      Q      58           -
LGA    F      18      R      59          2.131
LGA    -       -      T      60           -
LGA    -       -      A      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      S      64           -
LGA    -       -      L      65           -
LGA    -       -      F      66           -
LGA    -       -      E      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      N      70           -
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    -       -      R      74           -
LGA    -       -      L      75           -
LGA    -       -      Q      76           -
LGA    -       -      A      77           -
LGA    -       -      A      78           -
LGA    -       -      K      79           -
LGA    A      19      L      80          2.744
LGA    -       -      T      81           -
LGA    -       -      L      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    -       -      V      87           -
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    -       -      R      90           -
LGA    -       -      E      91           -
LGA    -       -      Q      92           -
LGA    -       -      L      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    -       -      I      96           -
LGA    -       -      V      97           -
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
LGA    -       -      P     103           -
LGA    -       -      Q     104           -
LGA    -       -      A     105           -
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    -       -      C     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    -       -      P     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16  119    5.0     13    2.12     7.69      9.048     0.584

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.517282 * X  +  -0.789824 * Y  +  -0.329541 * Z  +  -5.055288
  Y_new =   0.287458 * X  +   0.523041 * Y  +  -0.802369 * Z  +  25.605122
  Z_new =   0.806094 * X  +   0.320322 * Y  +   0.497601 * Z  +  17.710012 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.571957   -2.569636  [ DEG:    32.7707   -147.2293 ]
  Theta =  -0.937522   -2.204071  [ DEG:   -53.7160   -126.2840 ]
  Phi   =   0.507215   -2.634378  [ DEG:    29.0613   -150.9387 ]
 
# 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: T0382TS009_2_1-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_2_1-D1.T0382_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16  119   5.0   13   2.12    7.69   9.048
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_2_1-D1
REMARK PARENT number 1
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                      
ATOM     24  N   LEU     4      -3.355  30.051  10.485  1.00  0.00              
ATOM     25  CA  LEU     4      -2.556  29.601   9.352  1.00  0.00              
ATOM     26  C   LEU     4      -2.799  30.473   8.125  1.00  0.00              
ATOM     27  O   LEU     4      -2.253  31.571   8.015  1.00  0.00              
ATOM     28  CB  LEU     4      -1.069  29.599   9.711  1.00  0.00              
ATOM     29  CG  LEU     4      -0.376  28.235   9.722  1.00  0.00              
ATOM     30  CD1 LEU     4       1.102  28.380   9.391  1.00  0.00              
ATOM     31  CD2 LEU     4      -1.055  27.279   8.753  1.00  0.00              
ATOM     32  N   ASP     5      -3.622  29.979   7.206  1.00  0.00              
ATOM     33  CA  ASP     5      -3.938  30.713   5.987  1.00  0.00              
ATOM     34  C   ASP     5      -4.910  31.854   6.266  1.00  0.00              
ATOM     35  O   ASP     5      -4.503  32.947   6.659  1.00  0.00              
ATOM     36  CB  ASP     5      -2.661  31.255   5.341  1.00  0.00              
ATOM     37  CG  ASP     5      -2.237  30.454   4.126  1.00  0.00              
ATOM     38  OD1 ASP     5      -2.277  31.006   3.006  1.00  0.00              
ATOM     39  OD2 ASP     5      -1.865  29.274   4.293  1.00  0.00              
ATOM     40  N   LEU     6      -6.197  31.591   6.060  1.00  0.00              
ATOM     41  CA  LEU     6      -7.229  32.596   6.289  1.00  0.00              
ATOM     42  C   LEU     6      -6.805  33.586   7.369  1.00  0.00              
ATOM     43  O   LEU     6      -7.315  34.705   7.432  1.00  0.00              
ATOM     44  CB  LEU     6      -7.551  33.339   4.991  1.00  0.00              
ATOM     45  CG  LEU     6      -9.031  33.426   4.609  1.00  0.00              
ATOM     46  CD1 LEU     6      -9.320  34.724   3.871  1.00  0.00              
ATOM     47  CD2 LEU     6      -9.912  33.297   5.842  1.00  0.00              
ATOM     48  N   HIS     7      -5.871  33.167   8.215  1.00  0.00              
ATOM     49  CA  HIS     7      -5.377  34.016   9.293  1.00  0.00              
ATOM     50  C   HIS     7      -5.128  35.439   8.804  1.00  0.00              
ATOM     51  O   HIS     7      -5.939  36.335   9.036  1.00  0.00              
ATOM     52  CB  HIS     7      -6.364  34.026  10.462  1.00  0.00              
ATOM     53  CG  HIS     7      -5.728  33.763  11.791  1.00  0.00              
ATOM     54  ND1 HIS     7      -4.540  33.077  11.926  1.00  0.00              
ATOM     55  CD2 HIS     7      -6.115  34.093  13.046  1.00  0.00              
ATOM     56  CE1 HIS     7      -4.224  32.997  13.207  1.00  0.00              
ATOM     57  NE2 HIS     7      -5.162  33.605  13.907  1.00  0.00              
ATOM     58  N   GLN     8      -4.003  35.639   8.127  1.00  0.00              
ATOM     59  CA  GLN     8      -3.645  36.952   7.605  1.00  0.00              
ATOM     60  C   GLN     8      -4.279  37.194   6.239  1.00  0.00              
ATOM     61  O   GLN     8      -4.839  38.259   5.984  1.00  0.00              
ATOM     62  CB  GLN     8      -4.068  38.051   8.583  1.00  0.00              
ATOM     63  CG  GLN     8      -3.003  39.107   8.828  1.00  0.00              
ATOM     64  CD  GLN     8      -3.530  40.297   9.607  1.00  0.00              
ATOM     65  OE1 GLN     8      -2.845  41.308   9.751  1.00  0.00              
ATOM     66  NE2 GLN     8      -4.753  40.178  10.110  1.00  0.00              
ATOM     67  N   MET     9      -4.186  36.197   5.365  1.00  0.00              
ATOM     68  CA  MET     9      -4.749  36.300   4.024  1.00  0.00              
ATOM     69  C   MET     9      -5.433  37.647   3.815  1.00  0.00              
ATOM     70  O   MET     9      -5.377  38.219   2.726  1.00  0.00              
ATOM     71  CB  MET     9      -3.662  36.091   2.969  1.00  0.00              
ATOM     72  CG  MET     9      -3.516  34.652   2.503  1.00  0.00              
ATOM     73  SD  MET     9      -1.913  34.324   1.746  1.00  0.00              
ATOM     74  CE  MET     9      -2.060  32.576   1.386  1.00  0.00              
ATOM     75  N   THR    10      -6.077  38.147   4.863  1.00  0.00              
ATOM     76  CA  THR    10      -6.788  39.456   4.795  1.00  0.00              
ATOM     77  C   THR    10      -6.067  40.427   3.866  1.00  0.00              
ATOM     78  O   THR    10      -6.699  41.225   3.174  1.00  0.00              
ATOM     79  CB  THR    10      -8.242  39.285   4.314  1.00  0.00              
ATOM     80  OG1 THR    10      -8.438  37.945   3.846  1.00  0.00              
ATOM     81  CG2 THR    10      -9.214  39.569   5.449  1.00  0.00              
ATOM     82  N   THR    11      -4.740  40.354   3.856  1.00  0.00              
ATOM     83  CA  THR    11      -3.912  41.246   2.994  1.00  0.00             
ATOM     84  C   THR    11      -4.414  41.241   1.554  1.00  0.00             
ATOM     85  O   THR    11      -4.545  42.294   0.929  1.00  0.00             
ATOM     86  CB  THR    11      -3.905  42.693   3.521  1.00  0.00             
ATOM     87  OG1 THR    11      -4.916  42.844   4.526  1.00  0.00             
ATOM     88  CG2 THR    11      -2.549  43.036   4.116  1.00  0.00             
ATOM     89  N   GLN    12      -4.696  40.051   1.034  1.00  0.00             
ATOM     90  CA  GLN    12      -5.184  39.907  -0.332  1.00  0.00             
ATOM     91  C   GLN    12      -6.276  40.928  -0.638  1.00  0.00             
ATOM     92  O   GLN    12      -6.492  41.294  -1.792  1.00  0.00             
ATOM     93  CB  GLN    12      -4.033  40.054  -1.330  1.00  0.00             
ATOM     94  CG  GLN    12      -4.090  39.074  -2.491  1.00  0.00             
ATOM     95  CD  GLN    12      -2.863  39.149  -3.377  1.00  0.00             
ATOM     96  OE1 GLN    12      -2.598  38.240  -4.164  1.00  0.00             
ATOM     97  NE2 GLN    12      -2.109  40.234  -3.251  1.00  0.00             
ATOM     98  N   ASP    13      -6.961  41.383   0.406  1.00  0.00             
ATOM     99  CA  ASP    13      -8.032  42.361   0.252  1.00  0.00             
ATOM    100  C   ASP    13      -8.234  42.731  -1.215  1.00  0.00             
ATOM    101  O   ASP    13      -9.039  43.602  -1.539  1.00  0.00             
ATOM    102  CB  ASP    13      -9.337  41.826   0.843  1.00  0.00             
ATOM    103  CG  ASP    13      -9.829  42.652   2.015  1.00  0.00             
ATOM    104  OD1 ASP    13     -11.043  42.939   2.071  1.00  0.00             
ATOM    105  OD2 ASP    13      -9.000  43.014   2.876  1.00  0.00             
ATOM    106  N   LEU    14      -7.496  42.063  -2.095  1.00  0.00             
ATOM    107  CA  LEU    14      -7.591  42.320  -3.527  1.00  0.00             
ATOM    108  C   LEU    14      -8.685  43.339  -3.832  1.00  0.00             
ATOM    109  O   LEU    14      -9.530  43.116  -4.699  1.00  0.00             
ATOM    110  CB  LEU    14      -6.250  42.810  -4.075  1.00  0.00             
ATOM    111  CG  LEU    14      -5.362  41.753  -4.737  1.00  0.00             
ATOM    112  CD1 LEU    14      -4.934  42.204  -6.124  1.00  0.00             
ATOM    113  CD2 LEU    14      -6.078  40.412  -4.800  1.00  0.00             
ATOM    114  N   VAL    15      -8.663  44.457  -3.114  1.00  0.00             
ATOM    115  CA  VAL    15      -9.674  45.535  -3.311  1.00  0.00             
ATOM    116  C   VAL    15      -9.816  45.893  -4.786  1.00  0.00             
ATOM    117  O   VAL    15     -10.915  46.183  -5.262  1.00  0.00             
ATOM    118  CB  VAL    15     -11.051  45.124  -2.757  1.00  0.00             
ATOM    119  CG1 VAL    15     -11.293  45.768  -1.400  1.00  0.00             
ATOM    120  CG2 VAL    15     -11.159  43.610  -2.663  1.00  0.00             
ATOM    121  N   ALA    16      -8.699  45.874  -5.505  1.00  0.00             
ATOM    122  CA  ALA    16      -8.698  46.198  -6.927  1.00  0.00             
ATOM    123  C   ALA    16     -10.111  46.464  -7.434  1.00  0.00             
ATOM    124  O   ALA    16     -10.489  47.610  -7.677  1.00  0.00             
ATOM    125  CB  ALA    16      -7.809  47.402  -7.196  1.00  0.00             
ATOM    126  N   LEU    17     -10.888  45.396  -7.592  1.00  0.00             
ATOM    127  CA  LEU    17     -12.261  45.513  -8.069  1.00  0.00             
ATOM    128  C   LEU    17     -13.042  46.540  -7.258  1.00  0.00             
ATOM    129  O   LEU    17     -13.261  47.665  -7.708  1.00  0.00             
ATOM    130  CB  LEU    17     -12.281  45.888  -9.553  1.00  0.00             
ATOM    131  CG  LEU    17     -13.062  44.952 -10.478  1.00  0.00             
ATOM    132  CD1 LEU    17     -13.615  45.715 -11.672  1.00  0.00             
ATOM    133  CD2 LEU    17     -14.180  44.254  -9.717  1.00  0.00             
ATOM    134  N   PHE    18     -13.461  46.147  -6.060  1.00  0.00             
ATOM    135  CA  PHE    18     -14.219  47.032  -5.183  1.00  0.00             
ATOM    136  C   PHE    18     -13.296  47.991  -4.438  1.00  0.00             
ATOM    137  O   PHE    18     -12.234  48.361  -4.939  1.00  0.00             
ATOM    138  CB  PHE    18     -15.258  47.817  -5.985  1.00  0.00             
ATOM    139  CG  PHE    18     -16.678  47.511  -5.601  1.00  0.00             
ATOM    140  CD1 PHE    18     -16.964  46.861  -4.413  1.00  0.00             
ATOM    141  CD2 PHE    18     -17.727  47.871  -6.428  1.00  0.00             
ATOM    142  CE1 PHE    18     -18.270  46.579  -4.060  1.00  0.00             
ATOM    143  CE2 PHE    18     -19.032  47.588  -6.076  1.00  0.00             
ATOM    144  CZ  PHE    18     -19.307  46.945  -4.897  1.00  0.00             
ATOM    145  N   ALA    19     -13.710  48.391  -3.240  1.00  0.00             
ATOM    146  CA  ALA    19     -12.923  49.308  -2.424  1.00  0.00             
ATOM    147  C   ALA    19     -12.707  48.749  -1.021  1.00  0.00             
ATOM    148  O   ALA    19     -13.381  47.808  -0.606  1.00  0.00             
ATOM    149  CB  ALA    19     -11.584  49.591  -3.088  1.00  0.00             
TER
END
