
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS302_5-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.

#      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          1.778
LGA    L      84      M      44          0.699
LGA    M      85      L      45          0.735
LGA    A      86      V      46          0.634
LGA    V      87      G      47          0.650
LGA    -       -      T      48           -
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    F      88      P      83          2.259
LGA    D      89      L      84          1.744
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    1.37     0.00      7.441     0.476

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.318622 * X  +   0.906156 * Y  +  -0.278138 * Z  + -75.868828
  Y_new =   0.937085 * X  +   0.256963 * Y  +  -0.236309 * Z  + -28.961655
  Z_new =  -0.142662 * X  +  -0.335932 * Y  +  -0.931019 * Z  +  84.171310 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.795310    0.346283  [ DEG:  -160.1595     19.8405 ]
  Theta =   0.143150    2.998442  [ DEG:     8.2019    171.7981 ]
  Phi   =   1.898547   -1.243046  [ DEG:   108.7787    -71.2213 ]
 
# 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_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS302_5-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   1.37    0.00   7.441
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS302_5-D1
PFRMAT TS
TARGET T0378
MODEL  5
PARENT 1gz0_D
ATOM   1000  N   PRO    83       5.044  19.963  56.345  1.00  0.00
ATOM   1000  CA  PRO    83       5.394  20.798  55.212  1.00  0.00
ATOM   1000  C   PRO    83       4.170  21.606  54.935  1.00  0.00
ATOM   1000  O   PRO    83       3.082  21.161  55.292  1.00  0.00
ATOM   1000  CB  PRO    83       5.645  19.821  54.045  1.00  0.00
ATOM   1000  CG  PRO    83       4.994  18.460  54.457  1.00  0.00
ATOM   1000  CD  PRO    83       4.685  18.587  55.970  1.00  0.00
ATOM   1000  N   LEU    84       4.309  22.748  54.259  1.00  0.00
ATOM   1000  CA  LEU    84       3.185  23.636  54.167  1.00  0.00
ATOM   1000  C   LEU    84       3.074  23.606  52.700  1.00  0.00
ATOM   1000  O   LEU    84       4.082  23.402  52.023  1.00  0.00
ATOM   1000  CB  LEU    84       3.343  25.092  54.660  1.00  0.00
ATOM   1000  CG  LEU    84       2.712  25.412  56.048  1.00  0.00
ATOM   1000  CD1 LEU    84       2.542  26.932  56.236  1.00  0.00
ATOM   1000  CD2 LEU    84       1.382  24.680  56.352  1.00  0.00
ATOM   1000  N   MET    85       1.846  23.759  52.193  1.00  0.00
ATOM   1000  CA  MET    85       1.560  23.375  50.849  1.00  0.00
ATOM   1000  C   MET    85       0.765  24.538  50.439  1.00  0.00
ATOM   1000  O   MET    85      -0.088  25.013  51.193  1.00  0.00
ATOM   1000  CB  MET    85       0.745  22.093  50.632  1.00  0.00
ATOM   1000  CG  MET    85       1.549  20.831  50.943  1.00  0.00
ATOM   1000  SD  MET    85       3.045  20.601  49.929  1.00  0.00
ATOM   1000  CE  MET    85       3.629  19.146  50.839  1.00  0.00
ATOM   1000  N   ALA    86       1.085  25.035  49.242  1.00  0.00
ATOM   1000  CA  ALA    86       0.441  26.173  48.676  1.00  0.00
ATOM   1000  C   ALA    86      -0.350  25.555  47.583  1.00  0.00
ATOM   1000  O   ALA    86      -0.260  24.349  47.357  1.00  0.00
ATOM   1000  CB  ALA    86       1.407  27.199  48.057  1.00  0.00
ATOM   1000  N   VAL    87      -1.149  26.376  46.872  1.00  0.00
ATOM   1000  CA  VAL    87      -1.966  25.958  45.766  1.00  0.00
ATOM   1000  C   VAL    87      -1.147  25.249  44.719  1.00  0.00
ATOM   1000  O   VAL    87      -1.606  24.283  44.109  1.00  0.00
ATOM   1000  CB  VAL    87      -2.759  27.118  45.194  1.00  0.00
ATOM   1000  CG1 VAL    87      -1.842  28.252  44.675  1.00  0.00
ATOM   1000  CG2 VAL    87      -3.781  26.619  44.153  1.00  0.00
ATOM   1000  N   PHE    88       0.123  25.648  44.553  1.00  0.00
ATOM   1000  CA  PHE    88       0.869  25.338  43.361  1.00  0.00
ATOM   1000  C   PHE    88       1.448  23.973  43.638  1.00  0.00
ATOM   1000  O   PHE    88       1.914  23.278  42.737  1.00  0.00
ATOM   1000  CB  PHE    88       2.010  26.359  43.124  1.00  0.00
ATOM   1000  CG  PHE    88       2.937  26.003  41.998  1.00  0.00
ATOM   1000  CD1 PHE    88       2.528  26.137  40.692  1.00  0.00
ATOM   1000  CD2 PHE    88       4.198  25.489  42.248  1.00  0.00
ATOM   1000  CE1 PHE    88       3.335  25.754  39.650  1.00  0.00
ATOM   1000  CE2 PHE    88       5.005  25.108  41.197  1.00  0.00
ATOM   1000  CZ  PHE    88       4.624  25.342  39.900  1.00  0.00
ATOM   1000  N   ASP    89       1.368  23.534  44.906  1.00  0.00
ATOM   1000  CA  ASP    89       2.086  22.383  45.355  1.00  0.00
ATOM   1000  C   ASP    89       1.107  21.271  45.343  1.00  0.00
ATOM   1000  O   ASP    89       1.503  20.139  45.606  1.00  0.00
ATOM   1000  CB  ASP    89       2.562  22.415  46.818  1.00  0.00
ATOM   1000  CG  ASP    89       3.697  23.404  46.982  1.00  0.00
ATOM   1000  OD1 ASP    89       4.321  23.793  45.959  1.00  0.00
ATOM   1000  OD2 ASP    89       3.938  23.811  48.149  1.00  0.00
TER
END
