
#######################################################
#                                                     #
#                        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 T0378TS247_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS247_3-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          1.787
LGA    L      84      M      44          0.732
LGA    M      85      L      45          0.408
LGA    A      86      V      46          0.468
LGA    V      87      G      47          0.790
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          2.185
LGA    D      89      L      84          1.542
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    1.30     0.00      7.441     0.499

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.357094 * X  +  -0.930676 * Y  +   0.079540 * Z  +   5.561766
  Y_new =  -0.870356 * X  +   0.362439 * Y  +   0.333344 * Z  +  20.526619
  Z_new =  -0.339064 * X  +   0.049806 * Y  +  -0.939444 * Z  +  56.572296 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.088625   -0.052967  [ DEG:   176.9652     -3.0348 ]
  Theta =   0.345921    2.795671  [ DEG:    19.8198    160.1802 ]
  Phi   =  -1.960137    1.181456  [ DEG:  -112.3076     67.6924 ]
 
# 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: T0378TS247_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS247_3-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   1.30    0.00   7.441
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS247_3-D1
PFRMAT TS
TARGET T0378
MODEL  3
PARENT 1zjr_A 1gz0_A 1gz0_B 1gz0_C 1gz0_D 1gz0_F 1gz0_H 1v2x_A 1x7p_A 1ipa_A
ATOM      1  N   PRO    83       5.562  20.527  56.572  1.00 0.00         0
ATOM      2  CA  PRO    83       5.677  21.010  55.210  1.00 0.00         0
ATOM      3  C   PRO    83       4.336  21.671  54.927  1.00 0.00         0
ATOM      4  O   PRO    83       3.308  20.996  54.994  1.00 0.00         0
ATOM      5  CB  PRO    83       5.938  19.745  54.390  1.00 0.00         0
ATOM      6  CG  PRO    83       6.544  18.788  55.361  1.00 0.00         0
ATOM      7  CD  PRO    83       5.857  19.036  56.674  1.00 0.00         0
ATOM      8  N   LEU    84       4.342  22.965  54.615  1.00 0.00         0
ATOM      9  CA  LEU    84       3.108  23.684  54.343  1.00 0.00         0
ATOM     10  C   LEU    84       2.824  23.641  52.850  1.00 0.00         0
ATOM     11  O   LEU    84       3.647  24.050  52.031  1.00 0.00         0
ATOM     12  CB  LEU    84       3.228  25.143  54.788  1.00 0.00         0
ATOM     13  CG  LEU    84       2.009  26.031  54.536  1.00 0.00         0
ATOM     14  CD1 LEU    84       0.819  25.555  55.353  1.00 0.00         0
ATOM     15  CD2 LEU    84       2.304  27.473  54.923  1.00 0.00         0
ATOM     16  N   MET    85       1.641  23.137  52.500  1.00 0.00         0
ATOM     17  CA  MET    85       1.243  23.054  51.106  1.00 0.00         0
ATOM     18  C   MET    85       0.637  24.369  50.631  1.00 0.00         0
ATOM     19  O   MET    85      -0.153  25.014  51.325  1.00 0.00         0
ATOM     20  CB  MET    85       0.200  21.951  50.912  1.00 0.00         0
ATOM     21  CG  MET    85       0.704  20.556  51.241  1.00 0.00         0
ATOM     22  SD  MET    85       2.122  20.073  50.238  1.00 0.00         0
ATOM     23  CE  MET    85       1.364  19.939  48.621  1.00 0.00         0
ATOM     24  N   ALA    86       1.023  24.764  49.419  1.00 0.00         0
ATOM     25  CA  ALA    86       0.471  25.943  48.773  1.00 0.00         0
ATOM     26  C   ALA    86      -0.216  25.552  47.471  1.00 0.00         0
ATOM     27  O   ALA    86       0.053  24.479  46.925  1.00 0.00         0
ATOM     28  CB  ALA    86       1.574  26.943  48.462  1.00 0.00         0
ATOM     29  N   VAL    87      -1.103  26.429  46.978  1.00 0.00         0
ATOM     30  CA  VAL    87      -1.859  26.261  45.733  1.00 0.00         0
ATOM     31  C   VAL    87      -1.118  25.641  44.541  1.00 0.00         0
ATOM     32  O   VAL    87      -1.669  24.806  43.818  1.00 0.00         0
ATOM     33  CB  VAL    87      -2.374  27.611  45.200  1.00 0.00         0
ATOM     34  CG1 VAL    87      -1.214  28.486  44.756  1.00 0.00         0
ATOM     35  CG2 VAL    87      -3.296  27.396  44.010  1.00 0.00         0
ATOM     36  N   PHE    88       0.139  26.045  44.326  1.00 0.00         0
ATOM     37  CA  PHE    88       0.983  25.503  43.270  1.00 0.00         0
ATOM     38  C   PHE    88       1.291  24.014  43.450  1.00 0.00         0
ATOM     39  O   PHE    88       1.335  23.253  42.482  1.00 0.00         0
ATOM     40  CB  PHE    88       2.326  26.235  43.229  1.00 0.00         0
ATOM     41  CG  PHE    88       3.260  25.729  42.168  1.00 0.00         0
ATOM     42  CD1 PHE    88       3.100  26.106  40.846  1.00 0.00         0
ATOM     43  CD2 PHE    88       4.300  24.875  42.491  1.00 0.00         0
ATOM     44  CE1 PHE    88       3.959  25.640  39.870  1.00 0.00         0
ATOM     45  CE2 PHE    88       5.160  24.409  41.515  1.00 0.00         0
ATOM     46  CZ  PHE    88       4.993  24.789  40.209  1.00 0.00         0
ATOM     47  N   ASP    89       1.510  23.572  44.691  1.00 0.00         0
ATOM     48  CA  ASP    89       1.946  22.206  44.952  1.00 0.00         0
ATOM     49  C   ASP    89       0.802  21.202  45.022  1.00 0.00         0
ATOM     50  O   ASP    89       1.017  20.017  45.286  1.00 0.00         0
ATOM     51  CB  ASP    89       2.687  22.126  46.288  1.00 0.00         0
ATOM     52  CG  ASP    89       4.052  22.782  46.237  1.00 0.00         0
ATOM     53  OD1 ASP    89       4.544  23.046  45.121  1.00 0.00         0
ATOM     54  OD2 ASP    89       4.630  23.034  47.315  1.00 0.00         0
TER
END
