
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS247_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.

#      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          1.666
LGA    L      84      M      44          0.512
LGA    M      85      L      45          0.751
LGA    A      86      V      46          0.762
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          2.093
LGA    D      89      L      84          1.708
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    1.31     0.00      7.441     0.495

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.404635 * X  +  -0.882191 * Y  +   0.240854 * Z  +   5.110568
  Y_new =  -0.677374 * X  +   0.466080 * Y  +   0.569153 * Z  +  19.776186
  Z_new =  -0.614358 * X  +   0.067151 * Y  +  -0.786165 * Z  +  56.502987 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.056384   -0.085209  [ DEG:   175.1179     -4.8821 ]
  Theta =   0.661572    2.480021  [ DEG:    37.9053    142.0947 ]
  Phi   =  -2.109271    1.032322  [ DEG:  -120.8523     59.1477 ]
 
# 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_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS247_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   1.31    0.00   7.441
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS247_4-D1
PFRMAT TS
TARGET T0378
MODEL  4
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       5.111  19.776  56.503  1.00 0.00         0
ATOM      2  CA  PRO    83       5.460  20.603  55.361  1.00 0.00         0
ATOM      3  C   PRO    83       4.260  21.515  55.146  1.00 0.00         0
ATOM      4  O   PRO    83       3.152  21.136  55.544  1.00 0.00         0
ATOM      5  CB  PRO    83       5.684  19.596  54.231  1.00 0.00         0
ATOM      6  CG  PRO    83       6.019  18.321  54.928  1.00 0.00         0
ATOM      7  CD  PRO    83       5.188  18.297  56.178  1.00 0.00         0
ATOM      8  N   LEU    84       4.450  22.685  54.537  1.00 0.00         0
ATOM      9  CA  LEU    84       3.365  23.627  54.301  1.00 0.00         0
ATOM     10  C   LEU    84       3.098  23.697  52.806  1.00 0.00         0
ATOM     11  O   LEU    84       4.037  23.830  52.014  1.00 0.00         0
ATOM     12  CB  LEU    84       3.741  25.017  54.815  1.00 0.00         0
ATOM     13  CG  LEU    84       4.050  25.128  56.310  1.00 0.00         0
ATOM     14  CD1 LEU    84       4.491  26.539  56.666  1.00 0.00         0
ATOM     15  CD2 LEU    84       2.820  24.790  57.139  1.00 0.00         0
ATOM     16  N   MET    85       1.829  23.610  52.391  1.00 0.00         0
ATOM     17  CA  MET    85       1.505  23.513  50.974  1.00 0.00         0
ATOM     18  C   MET    85       0.683  24.688  50.471  1.00 0.00         0
ATOM     19  O   MET    85      -0.313  25.083  51.081  1.00 0.00         0
ATOM     20  CB  MET    85       0.696  22.244  50.695  1.00 0.00         0
ATOM     21  CG  MET    85       0.284  22.078  49.242  1.00 0.00         0
ATOM     22  SD  MET    85      -0.572  20.521  48.935  1.00 0.00         0
ATOM     23  CE  MET    85      -2.116  20.808  49.796  1.00 0.00         0
ATOM     24  N   ALA    86       1.108  25.256  49.341  1.00 0.00         0
ATOM     25  CA  ALA    86       0.322  26.253  48.631  1.00 0.00         0
ATOM     26  C   ALA    86      -0.381  25.625  47.429  1.00 0.00         0
ATOM     27  O   ALA    86      -0.062  24.498  47.048  1.00 0.00         0
ATOM     28  CB  ALA    86       1.216  27.377  48.132  1.00 0.00         0
ATOM     29  N   VAL    87      -1.341  26.338  46.819  1.00 0.00         0
ATOM     30  CA  VAL    87      -2.065  25.911  45.617  1.00 0.00         0
ATOM     31  C   VAL    87      -1.223  25.257  44.513  1.00 0.00         0
ATOM     32  O   VAL    87      -1.615  24.241  43.932  1.00 0.00         0
ATOM     33  CB  VAL    87      -2.763  27.098  44.927  1.00 0.00         0
ATOM     34  CG1 VAL    87      -1.734  28.064  44.358  1.00 0.00         0
ATOM     35  CG2 VAL    87      -3.644  26.609  43.787  1.00 0.00         0
ATOM     36  N   PHE    88      -0.057  25.835  44.212  1.00 0.00         0
ATOM     37  CA  PHE    88       0.853  25.325  43.191  1.00 0.00         0
ATOM     38  C   PHE    88       1.458  23.967  43.534  1.00 0.00         0
ATOM     39  O   PHE    88       1.860  23.201  42.659  1.00 0.00         0
ATOM     40  CB  PHE    88       2.023  26.290  42.986  1.00 0.00         0
ATOM     41  CG  PHE    88       1.648  27.552  42.264  1.00 0.00         0
ATOM     42  CD1 PHE    88       1.453  28.733  42.959  1.00 0.00         0
ATOM     43  CD2 PHE    88       1.491  27.559  40.889  1.00 0.00         0
ATOM     44  CE1 PHE    88       1.108  29.894  42.293  1.00 0.00         0
ATOM     45  CE2 PHE    88       1.146  28.720  40.223  1.00 0.00         0
ATOM     46  CZ  PHE    88       0.954  29.884  40.919  1.00 0.00         0
ATOM     47  N   ASP    89       1.523  23.661  44.833  1.00 0.00         0
ATOM     48  CA  ASP    89       2.130  22.430  45.312  1.00 0.00         0
ATOM     49  C   ASP    89       1.130  21.282  45.356  1.00 0.00         0
ATOM     50  O   ASP    89       1.527  20.141  45.592  1.00 0.00         0
ATOM     51  CB  ASP    89       2.681  22.620  46.727  1.00 0.00         0
ATOM     52  CG  ASP    89       3.807  23.633  46.782  1.00 0.00         0
ATOM     53  OD1 ASP    89       4.728  23.545  45.944  1.00 0.00         0
ATOM     54  OD2 ASP    89       3.767  24.516  47.664  1.00 0.00         0
TER
END
