
#######################################################
#                                                     #
#                        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   11 (   81),  selected   11 , name T0316TS705_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS705_1-D3.T0316_D3.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     284      -       -           -
LGA    S     285      M     284          2.738
LGA    T     286      S     285          2.184
LGA    S     287      T     286           #
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    -       -      F     333           -
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    L     288      A     339          2.160
LGA    E     289      I     340          1.270
LGA    A     290      T     341          3.951
LGA    S     291      P     342          1.997
LGA    -       -      G     343           -
LGA    Q     292      Q     344          3.374
LGA    V     293      A     345          3.813
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    -       -      L     359           -
LGA    H     294      I     360          3.317
LGA    -       -      D     361           -
LGA    -       -      N     362           -
LGA    -       -      A     363           -
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   11   90    5.0      9    2.89    11.11      6.972     0.301

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.138678 * X  +  -0.972024 * Y  +   0.189575 * Z  +  79.319893
  Y_new =  -0.870823 * X  +   0.028524 * Y  +  -0.490768 * Z  +  48.116039
  Z_new =   0.471631 * X  +  -0.233145 * Y  +  -0.850416 * Z  +  71.928879 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.874013    0.267580  [ DEG:  -164.6688     15.3312 ]
  Theta =  -0.491139   -2.650453  [ DEG:   -28.1402   -151.8598 ]
  Phi   =  -1.728719    1.412873  [ DEG:   -99.0483     80.9517 ]
 
# 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: T0316TS705_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS705_1-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11   90   5.0    9   2.89   11.11   6.972
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS705_1-D3
PFRMAT TS
TARGET T0316
MODEL  1  REFINED
PARENT 1jgt_A
ATOM   2220  N   MET   284      26.430  14.024 -17.138  1.00  0.00              
ATOM   2221  CA  MET   284      26.246  12.872 -16.306  1.00  0.00              
ATOM   2222  C   MET   284      27.513  12.009 -16.174  1.00  0.00              
ATOM   2223  O   MET   284      27.979  11.402 -17.499  1.00  0.00              
ATOM   2224  CB  MET   284      26.841  10.179 -18.216  1.00  0.00              
ATOM   2225  CG  MET   284      27.227   8.881 -17.005  1.00  0.00              
ATOM   2226  SD  MET   284      25.916  13.389 -14.945  1.00  0.00              
ATOM   2227  CE  MET   284      26.776  13.905 -14.231  1.00  0.00              
ATOM   2228  N   SER   285      24.635  13.257 -14.560  1.00  0.00              
ATOM   2229  CA  SER   285      24.170  13.747 -13.298  1.00  0.00              
ATOM   2230  C   SER   285      22.637  13.702 -13.179  1.00  0.00              
ATOM   2231  O   SER   285      22.170  12.376 -13.368  1.00  0.00              
ATOM   2232  CB  SER   285      24.772  12.925 -12.207  1.00  0.00              
ATOM   2233  OG  SER   285      24.888  13.383 -11.072  1.00  0.00              
ATOM   2234  N   THR   286      25.161  11.677 -12.520  1.00  0.00              
ATOM   2235  CA  THR   286      25.730  10.822 -11.520  1.00  0.00              
ATOM   2236  C   THR   286      26.033   9.449 -12.042  1.00  0.00              
ATOM   2237  O   THR   286      24.851   8.839 -12.539  1.00  0.00              
ATOM   2238  CB  THR   286      26.621   8.609 -10.896  1.00  0.00              
ATOM   2239  OG1 THR   286      27.026  11.406 -11.049  1.00  0.00              
ATOM   2240  CG2 THR   286      27.274  11.497  -9.848  1.00  0.00              
ATOM   2241  N   SER   287      27.883  11.832 -11.995  1.00  0.00              
ATOM   2242  CA  SER   287      29.185  12.335 -11.660  1.00  0.00              
ATOM   2243  C   SER   287      30.052  12.621 -12.898  1.00  0.00              
ATOM   2244  O   SER   287      30.312  11.417 -13.603  1.00  0.00              
ATOM   2245  CB  SER   287      29.062  13.618 -10.906  1.00  0.00              
ATOM   2246  OG  SER   287      29.802  13.858  -9.952  1.00  0.00              
ATOM   2247  N   LEU   288      28.101  14.473 -11.296  1.00  0.00              
ATOM   2248  CA  LEU   288      28.006  15.757 -10.671  1.00  0.00              
ATOM   2249  C   LEU   288      26.871  16.629 -11.231  1.00  0.00              
ATOM   2250  O   LEU   288      26.812  17.994 -10.530  1.00  0.00              
ATOM   2251  CB  LEU   288      28.159  18.715 -10.665  1.00  0.00              
ATOM   2252  CG  LEU   288      25.625  18.840 -11.023  1.00  0.00              
ATOM   2253  CD1 LEU   288      27.750  15.559  -9.214  1.00  0.00              
ATOM   2254  CD2 LEU   288      28.309  16.261  -8.374  1.00  0.00              
ATOM   2255  N   GLU   289      26.886  14.588  -8.883  1.00  0.00              
ATOM   2256  CA  GLU   289      26.569  14.333  -7.511  1.00  0.00              
ATOM   2257  C   GLU   289      25.498  13.243  -7.346  1.00  0.00              
ATOM   2258  O   GLU   289      25.004  13.085  -5.907  1.00  0.00              
ATOM   2259  CB  GLU   289      24.043  14.230  -5.622  1.00  0.00              
ATOM   2260  CG  GLU   289      23.723  14.984  -6.579  1.00  0.00              
ATOM   2261  CD  GLU   289      23.612  14.364  -4.446  1.00  0.00              
ATOM   2262  OE1 GLU   289      27.802  13.857  -6.809  1.00  0.00              
ATOM   2263  OE2 GLU   289      28.074  14.256  -5.678  1.00  0.00              
ATOM   2264  N   ALA   290      28.593  12.991  -7.471  1.00  0.00              
ATOM   2265  CA  ALA   290      29.732  12.412  -6.819  1.00  0.00              
ATOM   2266  C   ALA   290      30.482  11.409  -7.713  1.00  0.00              
ATOM   2267  O   ALA   290      30.710  13.475  -6.426  1.00  0.00              
ATOM   2268  CB  ALA   290      31.174  13.504  -5.287  1.00  0.00              
ATOM   2269  N   SER   291      31.029  14.399  -7.350  1.00  0.00              
ATOM   2270  CA  SER   291      31.996  15.411  -7.037  1.00  0.00              
ATOM   2271  C   SER   291      32.316  16.323  -8.234  1.00  0.00              
ATOM   2272  O   SER   291      32.937  15.574  -9.267  1.00  0.00              
ATOM   2273  CB  SER   291      31.426  16.269  -5.959  1.00  0.00              
ATOM   2274  OG  SER   291      32.120  16.671  -5.026  1.00  0.00              
ATOM   2275  N   GLN   292      30.115  16.540  -6.062  1.00  0.00              
ATOM   2276  CA  GLN   292      29.417  17.383  -5.140  1.00  0.00              
ATOM   2277  C   GLN   292      27.931  17.515  -5.523  1.00  0.00              
ATOM   2278  O   GLN   292      27.060  18.237  -4.494  1.00  0.00              
ATOM   2279  CB  GLN   292      26.599  17.222  -3.456  1.00  0.00              
ATOM   2280  CG  GLN   292      27.137  17.158  -2.351  1.00  0.00              
ATOM   2281  CD  GLN   292      25.582  16.396  -3.823  1.00  0.00              
ATOM   2282  OE1 GLN   292      29.490  16.774  -3.783  1.00  0.00              
ATOM   2283  NE2 GLN   292      29.733  17.467  -2.796  1.00  0.00              
ATOM   2284  N   VAL   293      29.299  15.448  -3.690  1.00  0.00              
ATOM   2285  CA  VAL   293      29.319  14.867  -2.385  1.00  0.00              
ATOM   2286  C   VAL   293      28.593  13.554  -2.294  1.00  0.00              
ATOM   2287  O   VAL   293      27.100  13.812  -2.565  1.00  0.00              
ATOM   2288  CB  VAL   293      29.229  12.554  -3.273  1.00  0.00              
ATOM   2289  CG1 VAL   293      30.746  14.658  -2.017  1.00  0.00              
ATOM   2290  CG2 VAL   293      31.498  13.988  -2.718  1.00  0.00              
ATOM   2291  N   HIS   294      31.164  15.264  -0.895  1.00  0.00              
ATOM   2292  CA  HIS   294      32.525  15.133  -0.476  1.00  0.00              
ATOM   2293  C   HIS   294      30.788  16.641   1.951  1.00  0.00              
ATOM   2294  O   HIS   294      32.005  16.003   1.842  1.00  0.00              
ATOM   2295  CB  HIS   294      32.903  16.115   0.646  1.00  0.00              
ATOM   2296  CG  HIS   294      31.071  15.487   3.830  1.00  0.00              
ATOM   2297  ND1 HIS   294      32.161  15.303   2.998  1.00  0.00              
ATOM   2298  CD2 HIS   294      30.274  16.297   3.159  1.00  0.00              
ATOM   2299  CE1 HIS   294      32.716  13.720   0.055  1.00  0.00              
ATOM   2300  NE2 HIS   294      32.251  12.764  -0.622  1.00  0.00              
TER
END
