
#######################################################
#                                                     #
#                        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    6 (   47),  selected    6 , name T0378TS401_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS401_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.

#      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    L      84      S      12          1.355
LGA    M      85      L      13          1.249
LGA    A      86      R      14          1.776
LGA    V      87      E      15          0.234
LGA    F      88      R      16          2.663
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    D      89      R      19          3.113
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    -       -      R      43           -
LGA    -       -      M      44           -
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
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    -       -      P      83           -
LGA    -       -      L      84           -
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)    6   89    5.0      6    1.97     0.00      6.259     0.289

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.822276 * X  +   0.416900 * Y  +   0.387372 * Z  + -39.779991
  Y_new =  -0.442357 * X  +   0.039998 * Y  +   0.895947 * Z  + -66.284004
  Z_new =   0.358026 * X  +  -0.908072 * Y  +   0.217308 * Z  +  52.390411 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.335907    1.805686  [ DEG:   -76.5418    103.4582 ]
  Theta =  -0.366153   -2.775440  [ DEG:   -20.9790   -159.0210 ]
  Phi   =  -0.493558    2.648035  [ DEG:   -28.2788    151.7212 ]
 
# 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: T0378TS401_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS401_1-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6   89   5.0    6   1.97    0.00   6.259
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS401_1-D1
PFRMAT TS
TARGET T0378
MODEL  1 REFINED
PARENT 1zjr_A
ATOM      1  N   LEU    84      16.916  29.909  48.372  1.00 57.54       1SG   2
ATOM      2  CA  LEU    84      16.388  29.962  49.755  1.00 57.54       1SG   3
ATOM      3  CB  LEU    84      14.930  30.463  49.759  1.00 57.54       1SG   4
ATOM      4  CG  LEU    84      14.763  31.932  49.314  1.00 57.54       1SG   5
ATOM      5  CD2 LEU    84      13.364  32.462  49.661  1.00 57.54       1SG   6
ATOM      6  CD1 LEU    84      15.122  32.132  47.833  1.00 57.54       1SG   7
ATOM      7  C   LEU    84      16.432  28.610  50.386  1.00 57.54       1SG   8
ATOM      8  O   LEU    84      17.502  28.088  50.697  1.00 57.54       1SG   9
ATOM      9  N   MET    85      15.250  28.000  50.582  1.00 83.06       1SG  10
ATOM     10  CA  MET    85      15.186  26.709  51.199  1.00 83.06       1SG  11
ATOM     11  CB  MET    85      13.749  26.175  51.331  1.00 83.06       1SG  12
ATOM     12  CG  MET    85      12.854  26.991  52.269  1.00 83.06       1SG  13
ATOM     13  SD  MET    85      13.315  26.918  54.026  1.00 83.06       1SG  14
ATOM     14  CE  MET    85      11.910  27.916  54.601  1.00 83.06       1SG  15
ATOM     15  C   MET    85      15.924  25.768  50.307  1.00 83.06       1SG  16
ATOM     16  O   MET    85      16.666  24.904  50.771  1.00 83.06       1SG  17
ATOM     17  N   ALA    86      15.748  25.936  48.983  1.00 21.90       1SG  18
ATOM     18  CA  ALA    86      16.362  25.056  48.036  1.00 21.90       1SG  19
ATOM     19  CB  ALA    86      16.010  25.406  46.580  1.00 21.90       1SG  20
ATOM     20  C   ALA    86      17.846  25.147  48.175  1.00 21.90       1SG  21
ATOM     21  O   ALA    86      18.544  24.134  48.134  1.00 21.90       1SG  22
ATOM     22  N   VAL    87      18.372  26.370  48.364  1.00 34.71       1SG  23
ATOM     23  CA  VAL    87      19.793  26.508  48.445  1.00 34.71       1SG  24
ATOM     24  CB  VAL    87      20.229  27.919  48.702  1.00 34.71       1SG  25
ATOM     25  CG1 VAL    87      21.755  27.928  48.900  1.00 34.71       1SG  26
ATOM     26  CG2 VAL    87      19.742  28.807  47.544  1.00 34.71       1SG  27
ATOM     27  C   VAL    87      20.276  25.693  49.591  1.00 34.71       1SG  28
ATOM     28  O   VAL    87      21.206  24.910  49.432  1.00 34.71       1SG  29
ATOM     29  N   PHE    88      19.626  25.822  50.761  1.00126.07       1SG  30
ATOM     30  CA  PHE    88      20.044  25.129  51.944  1.00126.07       1SG  31
ATOM     31  CB  PHE    88      19.203  25.495  53.180  1.00126.07       1SG  32
ATOM     32  CG  PHE    88      19.977  25.057  54.376  1.00126.07       1SG  33
ATOM     33  CD1 PHE    88      20.927  25.892  54.921  1.00126.07       1SG  34
ATOM     34  CD2 PHE    88      19.767  23.825  54.952  1.00126.07       1SG  35
ATOM     35  CE1 PHE    88      21.656  25.509  56.021  1.00126.07       1SG  36
ATOM     36  CE2 PHE    88      20.492  23.435  56.054  1.00126.07       1SG  37
ATOM     37  CZ  PHE    88      21.438  24.277  56.589  1.00126.07       1SG  38
ATOM     38  C   PHE    88      19.871  23.672  51.678  1.00126.07       1SG  39
ATOM     39  O   PHE    88      20.673  22.842  52.106  1.00126.07       1SG  40
ATOM     40  N   ASP    89      18.804  23.337  50.936  1.00 74.26       1SG  41
ATOM     41  CA  ASP    89      18.495  21.981  50.607  1.00 74.26       1SG  42
ATOM     42  CB  ASP    89      17.269  21.869  49.685  1.00 74.26       1SG  43
ATOM     43  CG  ASP    89      16.875  20.402  49.549  1.00 74.26       1SG  44
ATOM     44  OD1 ASP    89      17.557  19.536  50.157  1.00 74.26       1SG  45
ATOM     45  OD2 ASP    89      15.875  20.127  48.833  1.00 74.26       1SG  46
ATOM     46  C   ASP    89      19.666  21.434  49.862  1.00 74.26       1SG  47
ATOM     47  O   ASP    89      19.984  20.251  49.977  1.00 74.26       1SG  48
TER
END
