
#######################################################
#                                                     #
#                        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    5 (    5),  selected    5 , name T0320TS464_4_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS464_4_2-D2.T0320_D2.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    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    I     272      N     233          1.161
LGA    S     273      P     234          2.349
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    V     274      R     237          0.684
LGA    V     275      K     238          1.424
LGA    D     276      D     239          0.787
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   73    5.0      5    1.41    20.00      6.543     0.331

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.191128 * X  +  -0.293278 * Y  +  -0.936727 * Z  +  38.641563
  Y_new =  -0.673432 * X  +  -0.655113 * Y  +   0.342514 * Z  + 108.307999
  Z_new =  -0.714114 * X  +   0.696286 * Y  +  -0.072293 * Z  + -13.071722 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.674252   -1.467341  [ DEG:    95.9276    -84.0724 ]
  Theta =   0.795358    2.346235  [ DEG:    45.5707    134.4293 ]
  Phi   =  -1.847336    1.294257  [ DEG:  -105.8446     74.1554 ]
 
# 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: T0320TS464_4_2-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_4_2-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   73   5.0    5   1.41   20.00   6.543
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_4_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM     29  CA  ILE   272      19.156  14.060   4.750  1.00  0.00
ATOM     30  CA  SER   273      16.603  12.511   2.373  1.00  0.00
ATOM     31  CA  VAL   274      15.730  12.785  -1.322  1.00  0.00
ATOM     32  CA  VAL   275      12.419  11.773  -2.871  1.00  0.00
ATOM     33  CA  ASP   276      12.672  11.386  -6.644  1.00  0.00
TER
END
