
#######################################################
#                                                     #
#                        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   18 (   18),  selected   18 , name T0372TS464_4_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS464_4_2-D1.T0372_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    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    K       5      L      62          3.160
LGA    D       6      A      63          1.998
LGA    I       7      Y      64          1.537
LGA    T       8      M      65          1.707
LGA    L       9      M      66          0.939
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    A     102      L      77          3.038
LGA    D     103      R      78          3.498
LGA    -       -      K      79           -
LGA    L     104      L      80          1.215
LGA    E     105      I      81          1.288
LGA    A     106      E      82          1.361
LGA    I     107      D      83          0.735
LGA    L     108      A      84          2.111
LGA    P     109      D      85          5.929
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    E     110      N      90          2.404
LGA    R     111      F      91          3.955
LGA    F     112      C      92          1.361
LGA    I     113      M      93          1.919
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    F     114      V      96          3.185
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18  126    5.0     18    2.62     5.56     10.432     0.661

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.803716 * X  +  -0.455786 * Y  +  -0.382493 * Z  +  -1.334575
  Y_new =  -0.418288 * X  +  -0.889979 * Y  +   0.181584 * Z  + 144.668091
  Z_new =  -0.423174 * X  +   0.014050 * Y  +  -0.905940 * Z  +  79.916786 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.126085   -0.015508  [ DEG:   179.1115     -0.8885 ]
  Theta =   0.436945    2.704647  [ DEG:    25.0351    154.9649 ]
  Phi   =  -0.479868    2.661724  [ DEG:   -27.4944    152.5056 ]
 
# 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: T0372TS464_4_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_4_2-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18  126   5.0   18   2.62    5.56  10.432
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM      1  CA  LYS     5      39.172  45.371  -6.903  1.00  0.00
ATOM      2  CA  ASP     6      36.600  46.053  -4.200  1.00  0.00
ATOM      3  CA  ILE     7      35.606  49.267  -2.488  1.00  0.00
ATOM      4  CA  THR     8      34.184  49.993   0.958  1.00  0.00
ATOM      5  CA  LEU     9      32.813  53.504   1.603  1.00  0.00
ATOM      6  CA  ALA   102      32.744  59.446  -8.293  1.00  0.00
ATOM      7  CA  ASP   103      36.357  58.967  -7.231  1.00  0.00
ATOM      8  CA  LEU   104      35.792  55.314  -6.256  1.00  0.00
ATOM      9  CA  GLU   105      34.344  54.807  -9.716  1.00  0.00
ATOM     10  CA  ALA   106      37.779  55.429 -11.240  1.00  0.00
ATOM     11  CA  ILE   107      39.224  52.178  -9.921  1.00  0.00
ATOM     12  CA  LEU   108      36.279  50.277 -11.417  1.00  0.00
ATOM     13  CA  PRO   109      35.645  47.971  -8.462  1.00  0.00
ATOM     14  CA  GLU   110      33.867  44.676  -9.092  1.00  0.00
ATOM     15  CA  ARG   111      31.950  45.346  -5.913  1.00  0.00
ATOM     16  CA  PHE   112      31.222  48.524  -4.010  1.00  0.00
ATOM     17  CA  ILE   113      29.866  48.373  -0.495  1.00  0.00
ATOM     18  CA  PHE   114      28.716  51.486   1.346  1.00  0.00
TER
END
