
#######################################################
#                                                     #
#                        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    7 (   54),  selected    7 , name T0378TS302_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS302_4-D1.T0378_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 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    -       -      S      12           -
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    P      83      R      43          2.372
LGA    L      84      M      44          0.891
LGA    M      85      L      45          0.549
LGA    A      86      V      46          1.260
LGA    V      87      G      47          2.048
LGA    F      88      T      48          3.925
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    D      89      L      84          1.508
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    7   89    5.0      7    2.08     0.00      6.953     0.322

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.333911 * X  +   0.938522 * Y  +  -0.087630 * Z  + -105.501266
  Y_new =   0.019808 * X  +   0.085959 * Y  +   0.996102 * Z  +  -2.121931
  Z_new =   0.942396 * X  +  -0.334345 * Y  +   0.010112 * Z  +  21.876879 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.540560    1.601033  [ DEG:   -88.2676     91.7324 ]
  Theta =  -1.229723   -1.911869  [ DEG:   -70.4580   -109.5420 ]
  Phi   =   0.059251   -3.082342  [ DEG:     3.3948   -176.6052 ]
 
# 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: T0378TS302_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS302_4-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    7   89   5.0    7   2.08    0.00   6.953
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS302_4-D1
PFRMAT TS
TARGET T0378
MODEL  4
PARENT 1gz0_C
ATOM   1000  N   PRO    83       6.264  20.708  55.931  1.00  0.00
ATOM   1000  CA  PRO    83       5.953  21.417  54.706  1.00  0.00
ATOM   1000  C   PRO    83       4.592  21.997  54.912  1.00  0.00
ATOM   1000  O   PRO    83       3.903  21.582  55.846  1.00  0.00
ATOM   1000  CB  PRO    83       5.872  20.324  53.624  1.00  0.00
ATOM   1000  CG  PRO    83       5.594  18.986  54.383  1.00  0.00
ATOM   1000  CD  PRO    83       5.896  19.284  55.875  1.00  0.00
ATOM   1000  N   LEU    84       4.179  22.929  54.040  1.00  0.00
ATOM   1000  CA  LEU    84       2.887  23.514  54.216  1.00  0.00
ATOM   1000  C   LEU    84       2.387  23.739  52.841  1.00  0.00
ATOM   1000  O   LEU    84       2.746  24.719  52.192  1.00  0.00
ATOM   1000  CB  LEU    84       2.861  24.836  55.005  1.00  0.00
ATOM   1000  CG  LEU    84       1.444  25.325  55.403  1.00  0.00
ATOM   1000  CD1 LEU    84       0.671  26.030  54.267  1.00  0.00
ATOM   1000  CD2 LEU    84       0.580  24.232  56.071  1.00  0.00
ATOM   1000  N   MET    85       1.534  22.825  52.379  1.00  0.00
ATOM   1000  CA  MET    85       1.073  22.849  51.030  1.00  0.00
ATOM   1000  C   MET    85       0.091  23.970  50.926  1.00  0.00
ATOM   1000  O   MET    85      -0.889  24.062  51.669  1.00  0.00
ATOM   1000  CB  MET    85       0.341  21.568  50.698  1.00  0.00
ATOM   1000  CG  MET    85       1.185  20.345  50.345  1.00  0.00
ATOM   1000  SD  MET    85       2.124  19.673  51.755  1.00  0.00
ATOM   1000  CE  MET    85       3.060  18.462  50.782  1.00  0.00
ATOM   1000  N   ALA    86       0.367  24.852  49.959  1.00  0.00
ATOM   1000  CA  ALA    86      -0.418  26.025  49.720  1.00  0.00
ATOM   1000  C   ALA    86      -1.308  25.611  48.592  1.00  0.00
ATOM   1000  O   ALA    86      -1.134  24.517  48.062  1.00  0.00
ATOM   1000  CB  ALA    86       0.429  27.225  49.260  1.00  0.00
ATOM   1000  N   VAL    87      -2.275  26.483  48.194  1.00  0.00
ATOM   1000  CA  VAL    87      -3.185  26.268  47.091  1.00  0.00
ATOM   1000  C   VAL    87      -2.540  25.660  45.891  1.00  0.00
ATOM   1000  O   VAL    87      -3.108  24.768  45.261  1.00  0.00
ATOM   1000  CB  VAL    87      -3.967  27.522  46.652  1.00  0.00
ATOM   1000  CG1 VAL    87      -3.086  28.756  46.431  1.00  0.00
ATOM   1000  CG2 VAL    87      -4.837  27.283  45.388  1.00  0.00
ATOM   1000  N   PHE    88      -1.333  26.131  45.558  1.00  0.00
ATOM   1000  CA  PHE    88      -0.772  25.919  44.266  1.00  0.00
ATOM   1000  C   PHE    88      -0.101  24.565  44.273  1.00  0.00
ATOM   1000  O   PHE    88       0.097  23.959  43.224  1.00  0.00
ATOM   1000  CB  PHE    88       0.236  27.035  43.909  1.00  0.00
ATOM   1000  CG  PHE    88       0.865  26.872  42.558  1.00  0.00
ATOM   1000  CD1 PHE    88       0.271  26.206  41.504  1.00  0.00
ATOM   1000  CD2 PHE    88       2.110  27.415  42.337  1.00  0.00
ATOM   1000  CE1 PHE    88       0.999  25.854  40.402  1.00  0.00
ATOM   1000  CE2 PHE    88       2.732  27.279  41.120  1.00  0.00
ATOM   1000  CZ  PHE    88       2.209  26.456  40.149  1.00  0.00
ATOM   1000  N   ASP    89       0.224  24.007  45.451  1.00  0.00
ATOM   1000  CA  ASP    89       1.000  22.786  45.466  1.00  0.00
ATOM   1000  C   ASP    89       0.075  21.657  45.213  1.00  0.00
ATOM   1000  O   ASP    89       0.513  20.551  44.899  1.00  0.00
ATOM   1000  CB  ASP    89       1.658  22.442  46.811  1.00  0.00
ATOM   1000  CG  ASP    89       2.869  23.334  47.033  1.00  0.00
ATOM   1000  OD1 ASP    89       3.343  24.002  46.074  1.00  0.00
ATOM   1000  OD2 ASP    89       3.329  23.377  48.204  1.00  0.00
TER
END
