
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS247_1-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          1.821
LGA    L      84      M      44          0.745
LGA    M      85      L      45          0.391
LGA    A      86      V      46          0.449
LGA    V      87      G      47          0.814
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          2.182
LGA    D      89      L      84          1.497
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 =  -0.308819 * X  +  -0.946811 * Y  +   0.090442 * Z  +   5.621220
  Y_new =  -0.881954 * X  +   0.320662 * Y  +   0.345446 * Z  +  20.600643
  Z_new =  -0.356074 * X  +   0.026915 * Y  +  -0.934070 * Z  +  56.547604 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.112786   -0.028807  [ DEG:   178.3495     -1.6505 ]
  Theta =   0.364063    2.777530  [ DEG:    20.8593    159.1407 ]
  Phi   =  -1.907607    1.233986  [ DEG:  -109.2978     70.7022 ]
 
# 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_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS247_1-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_1-D1
PFRMAT TS
TARGET T0378
MODEL  1
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       5.621  20.601  56.548  1.00 0.00         0
ATOM      2  CA  PRO    83       5.753  21.102  55.191  1.00 0.00         0
ATOM      3  C   PRO    83       4.395  21.709  54.866  1.00 0.00         0
ATOM      4  O   PRO    83       3.398  20.987  54.850  1.00 0.00         0
ATOM      5  CB  PRO    83       6.091  19.858  54.368  1.00 0.00         0
ATOM      6  CG  PRO    83       6.713  18.919  55.347  1.00 0.00         0
ATOM      7  CD  PRO    83       5.980  19.125  56.643  1.00 0.00         0
ATOM      8  N   LEU    84       4.357  23.014  54.609  1.00 0.00         0
ATOM      9  CA  LEU    84       3.105  23.697  54.322  1.00 0.00         0
ATOM     10  C   LEU    84       2.793  23.607  52.836  1.00 0.00         0
ATOM     11  O   LEU    84       3.568  24.062  51.996  1.00 0.00         0
ATOM     12  CB  LEU    84       3.197  25.173  54.715  1.00 0.00         0
ATOM     13  CG  LEU    84       1.956  26.026  54.441  1.00 0.00         0
ATOM     14  CD1 LEU    84       0.782  25.551  55.284  1.00 0.00         0
ATOM     15  CD2 LEU    84       2.223  27.485  54.775  1.00 0.00         0
ATOM     16  N   MET    85       1.643  23.012  52.519  1.00 0.00         0
ATOM     17  CA  MET    85       1.185  22.934  51.142  1.00 0.00         0
ATOM     18  C   MET    85       0.576  24.257  50.688  1.00 0.00         0
ATOM     19  O   MET    85      -0.174  24.916  51.414  1.00 0.00         0
ATOM     20  CB  MET    85       0.120  21.845  50.993  1.00 0.00         0
ATOM     21  CG  MET    85       0.619  20.443  51.302  1.00 0.00         0
ATOM     22  SD  MET    85       1.988  19.941  50.239  1.00 0.00         0
ATOM     23  CE  MET    85       1.160  19.818  48.656  1.00 0.00         0
ATOM     24  N   ALA    86       0.914  24.642  49.458  1.00 0.00         0
ATOM     25  CA  ALA    86       0.410  25.854  48.835  1.00 0.00         0
ATOM     26  C   ALA    86      -0.227  25.527  47.488  1.00 0.00         0
ATOM     27  O   ALA    86      -0.060  24.416  46.982  1.00 0.00         0
ATOM     28  CB  ALA    86       1.543  26.845  48.609  1.00 0.00         0
ATOM     29  N   VAL    87      -0.958  26.486  46.899  1.00 0.00         0
ATOM     30  CA  VAL    87      -1.740  26.308  45.667  1.00 0.00         0
ATOM     31  C   VAL    87      -0.965  25.639  44.531  1.00 0.00         0
ATOM     32  O   VAL    87      -1.453  24.705  43.890  1.00 0.00         0
ATOM     33  CB  VAL    87      -2.231  27.657  45.110  1.00 0.00         0
ATOM     34  CG1 VAL    87      -2.851  27.472  43.734  1.00 0.00         0
ATOM     35  CG2 VAL    87      -3.278  28.264  46.032  1.00 0.00         0
ATOM     36  N   PHE    88       0.257  26.112  44.270  1.00 0.00         0
ATOM     37  CA  PHE    88       1.114  25.553  43.229  1.00 0.00         0
ATOM     38  C   PHE    88       1.574  24.116  43.468  1.00 0.00         0
ATOM     39  O   PHE    88       2.057  23.451  42.550  1.00 0.00         0
ATOM     40  CB  PHE    88       2.390  26.384  43.081  1.00 0.00         0
ATOM     41  CG  PHE    88       2.173  27.717  42.424  1.00 0.00         0
ATOM     42  CD1 PHE    88       2.108  28.875  43.178  1.00 0.00         0
ATOM     43  CD2 PHE    88       2.034  27.812  41.050  1.00 0.00         0
ATOM     44  CE1 PHE    88       1.907  30.101  42.572  1.00 0.00         0
ATOM     45  CE2 PHE    88       1.834  29.038  40.444  1.00 0.00         0
ATOM     46  CZ  PHE    88       1.771  30.180  41.199  1.00 0.00         0
ATOM     47  N   ASP    89       1.434  23.608  44.699  1.00 0.00         0
ATOM     48  CA  ASP    89       1.742  22.213  45.002  1.00 0.00         0
ATOM     49  C   ASP    89       0.612  21.273  44.607  1.00 0.00         0
ATOM     50  O   ASP    89       0.808  20.056  44.602  1.00 0.00         0
ATOM     51  CB  ASP    89       1.989  22.033  46.500  1.00 0.00         0
ATOM     52  CG  ASP    89       3.300  22.643  46.954  1.00 0.00         0
ATOM     53  OD1 ASP    89       4.141  22.956  46.083  1.00 0.00         0
ATOM     54  OD2 ASP    89       3.488  22.807  48.177  1.00 0.00         0
TER
END
