
#######################################################
#                                                     #
#                        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   12 (   12),  selected   12 , name T0330TS464_3_2-D1
# Molecule2: number of CA atoms  153 ( 1188),  selected  153 , name T0330_D1.pdb
# PARAMETERS: T0330TS464_3_2-D1.T0330_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    -       -      S       2           -
LGA    S       2      R       3          1.377
LGA    R       3      T       4          3.714
LGA    -       -      L       5           -
LGA    -       -      V       6           -
LGA    -       -      L       7           -
LGA    -       -      F       8           -
LGA    -       -      D       9           -
LGA    -       -      I      10           -
LGA    -       -      D      11           -
LGA    -       -      G      12           -
LGA    -       -      T      13           -
LGA    -       -      L      14           -
LGA    -       -      L      15           -
LGA    -       -      K      16           -
LGA    -       -      T      92           -
LGA    -       -      L      93           -
LGA    -       -      L      94           -
LGA    -       -      E      95           -
LGA    -       -      G      96           -
LGA    -       -      V      97           -
LGA    -       -      R      98           -
LGA    -       -      E      99           -
LGA    -       -      L     100           -
LGA    -       -      L     101           -
LGA    -       -      D     102           -
LGA    -       -      A     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      R     107           -
LGA    -       -      S     108           -
LGA    -       -      D     109           -
LGA    -       -      V     110           -
LGA    -       -      L     111           -
LGA    -       -      L     112           -
LGA    -       -      G     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      T     116           -
LGA    -       -      G     117           -
LGA    -       -      N     118           -
LGA    -       -      F     119           -
LGA    -       -      E     120           -
LGA    -       -      A     121           -
LGA    -       -      S     122           -
LGA    -       -      G     123           -
LGA    -       -      R     124           -
LGA    -       -      H     125           -
LGA    -       -      K     126           -
LGA    -       -      L     127           -
LGA    -       -      K     128           -
LGA    -       -      L     129           -
LGA    -       -      P     130           -
LGA    -       -      G     131           -
LGA    -       -      I     132           -
LGA    -       -      D     133           -
LGA    -       -      H     134           -
LGA    -       -      Y     135           -
LGA    -       -      F     136           -
LGA    -       -      P     137           -
LGA    -       -      F     138           -
LGA    -       -      G     139           -
LGA    -       -      A     140           -
LGA    -       -      F     141           -
LGA    -       -      A     142           -
LGA    -       -      D     143           -
LGA    -       -      D     144           -
LGA    -       -      A     145           -
LGA    -       -      L     146           -
LGA    -       -      D     147           -
LGA    -       -      R     148           -
LGA    -       -      N     149           -
LGA    -       -      E     150           -
LGA    -       -      L     151           -
LGA    -       -      P     152           -
LGA    -       -      H     153           -
LGA    -       -      I     154           -
LGA    -       -      A     155           -
LGA    -       -      L     156           -
LGA    -       -      E     157           -
LGA    -       -      R     158           -
LGA    -       -      A     159           -
LGA    -       -      R     160           -
LGA    -       -      R     161           -
LGA    -       -      M     162           -
LGA    -       -      T     163           -
LGA    -       -      G     164           -
LGA    -       -      A     165           -
LGA    -       -      N     166           -
LGA    -       -      Y     167           -
LGA    -       -      S     168           -
LGA    -       -      P     169           -
LGA    -       -      S     170           -
LGA    T       4      Q     171          2.198
LGA    L       5      I     172          1.673
LGA    V       6      V     173          2.238
LGA    L       7      I     174          2.385
LGA    F       8      I     175          2.768
LGA    G      12      G     176          3.392
LGA    T      13      D     177          2.449
LGA    L      14      T     178           -
LGA    -       -      E     179           -
LGA    -       -      H     180           -
LGA    L      15      D     181          3.781
LGA    K      16      I     182          4.586
LGA    -       -      R     183           -
LGA    -       -      C     184           -
LGA    -       -      A     185           -
LGA    -       -      R     186           -
LGA    -       -      E     187           -
LGA    -       -      L     188           -
LGA    -       -      D     189           -
LGA    -       -      A     190           -
LGA    -       -      R     191           -
LGA    -       -      S     192           -
LGA    -       -      I     193           -
LGA    -       -      A     194           -
LGA    -       -      V     195           -
LGA    -       -      A     196           -
LGA    -       -      T     197           -
LGA    -       -      G     198           -
LGA    -       -      N     199           -
LGA    -       -      F     200           -
LGA    -       -      T     201           -
LGA    -       -      M     202           -
LGA    -       -      E     203           -
LGA    -       -      E     204           -
LGA    -       -      L     205           -
LGA    -       -      A     206           -
LGA    -       -      R     207           -
LGA    -       -      H     208           -
LGA    -       -      K     209           -
LGA    -       -      P     210           -
LGA    -       -      G     211           -
LGA    -       -      T     212           -
LGA    -       -      L     213           -
LGA    -       -      F     214           -
LGA    -       -      K     215           -
LGA    -       -      N     216           -
LGA    -       -      F     217           -
LGA    -       -      A     218           -
LGA    -       -      E     219           -
LGA    -       -      T     220           -
LGA    -       -      D     221           -
LGA    -       -      E     222           -
LGA    -       -      V     223           -
LGA    -       -      L     224           -
LGA    -       -      A     225           -
LGA    -       -      S     226           -
LGA    -       -      I     227           -
LGA    -       -      L     228           -
LGA    -       -      T     229           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   12  153    5.0     11    2.93    18.18      5.367     0.363

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.621342 * X  +  -0.158160 * Y  +  -0.767411 * Z  +  94.685341
  Y_new =  -0.780263 * X  +   0.035417 * Y  +   0.624448 * Z  +  74.166649
  Z_new =  -0.071584 * X  +   0.986778 * Y  +  -0.145412 * Z  + -17.416470 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.717104   -1.424489  [ DEG:    98.3828    -81.6172 ]
  Theta =   0.071645    3.069947  [ DEG:     4.1050    175.8950 ]
  Phi   =  -2.243292    0.898301  [ DEG:  -128.5312     51.4688 ]
 
# 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: T0330TS464_3_2-D1                             
REMARK     2: T0330_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS464_3_2-D1.T0330_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12  153   5.0   11   2.93   18.18   5.367
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS464_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0330
PARENT N/A
ATOM      1  CA  SER     2      22.286  56.433  34.004  1.00  0.00
ATOM      2  CA  ARG     3      25.607  54.600  34.329  1.00  0.00
ATOM      3  CA  THR     4      26.573  52.824  31.099  1.00  0.00
ATOM      4  CA  LEU     5      26.497  52.799  27.307  1.00  0.00
ATOM      5  CA  VAL     6      26.739  49.287  25.868  1.00  0.00
ATOM      6  CA  LEU     7      27.054  47.883  22.370  1.00  0.00
ATOM      7  CA  PHE     8      25.783  44.375  21.637  1.00  0.00
ATOM      8  CA  GLY    12      23.044  39.559  20.893  1.00  0.00
ATOM      9  CA  THR    13      26.436  39.435  22.603  1.00  0.00
ATOM     10  CA  LEU    14      27.817  42.272  24.739  1.00  0.00
ATOM     11  CA  LEU    15      30.962  43.638  23.064  1.00  0.00
ATOM     12  CA  LYS    16      31.680  47.032  24.604  1.00  0.00
TER
END
