
#######################################################
#                                                     #
#                        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 (  105),  selected   12 , name T0386TS468_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS468_1-D2.T0386_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     219           -
LGA    -       -      P     220           -
LGA    N     219      E     221          1.578
LGA    P     220      K     222          0.275
LGA    E     221      I     223          0.155
LGA    K     222      R     224          0.311
LGA    I     223      L     225          0.536
LGA    R     224      L     226          0.783
LGA    L     225      K     227          1.076
LGA    L     226      E     228          2.017
LGA    K     227      -       -           -
LGA    E     228      F     229          0.814
LGA    F     229      M     230          0.794
LGA    M     230      H     231          1.261
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    -       -      I     279           -
LGA    -       -      D     280           -
LGA    -       -      H     281           -
LGA    -       -      L     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   12   81    5.0     11    1.03     0.00     13.196     0.972

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.981123 * X  +  -0.158821 * Y  +  -0.110334 * Z  +  17.911554
  Y_new =  -0.090402 * X  +   0.881035 * Y  +  -0.464332 * Z  +  83.886223
  Z_new =   0.170954 * X  +  -0.445593 * Y  +  -0.878762 * Z  +  90.659821 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.672306    0.469287  [ DEG:  -153.1118     26.8881 ]
  Theta =  -0.171798   -2.969795  [ DEG:    -9.8433   -170.1567 ]
  Phi   =  -3.049711    0.091881  [ DEG:  -174.7356      5.2644 ]
 
# 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: T0386TS468_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS468_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12   81   5.0   11   1.03    0.00  13.196
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS468_1-D2
PFRMAT TS
TARGET T0386    
MODEL  1
PARENT n/a
ATOM   1449  N   ASN   219       2.359  59.603  79.304  1.00  0.00
ATOM   1450  CA  ASN   219       3.515  59.695  80.149  1.00  0.00
ATOM   1451  C   ASN   219       4.843  59.702  79.381  1.00  0.00
ATOM   1452  O   ASN   219       5.720  60.540  79.657  1.00  0.00
ATOM   1453  CB  ASN   219       3.570  58.508  81.113  1.00  0.00
ATOM   1454  CG  ASN   219       2.527  58.599  82.209  1.00  0.00
ATOM   1455  OD1 ASN   219       2.017  59.679  82.505  1.00  0.00
ATOM   1456  ND2 ASN   219       2.209  57.462  82.817  1.00  0.00
ATOM   1457  N   PRO   220       4.990  58.784  78.418  1.00  0.00
ATOM   1458  CA  PRO   220       6.217  58.668  77.617  1.00  0.00
ATOM   1459  C   PRO   220       6.408  59.823  76.628  1.00  0.00
ATOM   1460  O   PRO   220       7.536  60.307  76.423  1.00  0.00
ATOM   1461  CB  PRO   220       6.045  57.345  76.867  1.00  0.00
ATOM   1462  CG  PRO   220       5.080  56.567  77.697  1.00  0.00
ATOM   1463  CD  PRO   220       4.132  57.574  78.286  1.00  0.00
ATOM   1464  N   GLU   221       5.333  60.274  75.988  1.00  0.00
ATOM   1465  CA  GLU   221       5.485  61.418  75.092  1.00  0.00
ATOM   1466  C   GLU   221       5.730  62.641  75.989  1.00  0.00
ATOM   1467  O   GLU   221       6.477  63.541  75.636  1.00  0.00
ATOM   1468  CB  GLU   221       4.220  61.613  74.254  1.00  0.00
ATOM   1469  CG  GLU   221       3.996  60.534  73.208  1.00  0.00
ATOM   1470  CD  GLU   221       2.690  60.709  72.460  1.00  0.00
ATOM   1471  OE1 GLU   221       1.929  61.638  72.802  1.00  0.00
ATOM   1472  OE2 GLU   221       2.426  59.916  71.530  1.00  0.00
ATOM   1473  N   LYS   222       5.115  62.643  77.164  1.00  0.00
ATOM   1474  CA  LYS   222       5.295  63.733  78.118  1.00  0.00
ATOM   1475  C   LYS   222       6.761  63.821  78.523  1.00  0.00
ATOM   1476  O   LYS   222       7.315  64.928  78.597  1.00  0.00
ATOM   1477  CB  LYS   222       4.450  63.493  79.371  1.00  0.00
ATOM   1478  CG  LYS   222       4.541  64.605  80.404  1.00  0.00
ATOM   1479  CD  LYS   222       3.619  64.340  81.582  1.00  0.00
ATOM   1480  CE  LYS   222       3.732  65.437  82.628  1.00  0.00
ATOM   1481  NZ  LYS   222       2.845  65.184  83.797  1.00  0.00
ATOM   1482  N   ILE   223       7.405  62.670  78.758  1.00  0.00
ATOM   1483  CA  ILE   223       8.824  62.652  79.149  1.00  0.00
ATOM   1484  C   ILE   223       9.700  63.225  78.038  1.00  0.00
ATOM   1485  O   ILE   223      10.630  63.985  78.293  1.00  0.00
ATOM   1486  CB  ILE   223       9.311  61.219  79.438  1.00  0.00
ATOM   1487  CG1 ILE   223       8.618  60.662  80.683  1.00  0.00
ATOM   1488  CG2 ILE   223      10.813  61.205  79.675  1.00  0.00
ATOM   1489  CD1 ILE   223       8.811  59.174  80.874  1.00  0.00
ATOM   1490  N   ARG   224       9.614  62.600  76.854  1.00  0.00
ATOM   1491  CA  ARG   224      10.549  62.981  75.781  1.00  0.00
ATOM   1492  C   ARG   224      10.372  64.418  75.324  1.00  0.00
ATOM   1493  O   ARG   224      11.349  65.125  75.062  1.00  0.00
ATOM   1494  CB  ARG   224      10.348  62.090  74.555  1.00  0.00
ATOM   1495  CG  ARG   224      11.266  62.421  73.389  1.00  0.00
ATOM   1496  CD  ARG   224      12.724  62.200  73.756  1.00  0.00
ATOM   1497  NE  ARG   224      13.618  62.460  72.629  1.00  0.00
ATOM   1498  CZ  ARG   224      14.941  62.533  72.725  1.00  0.00
ATOM   1499  NH1 ARG   224      15.673  62.773  71.647  1.00  0.00
ATOM   1500  NH2 ARG   224      15.530  62.364  73.903  1.00  0.00
ATOM   1501  N   LEU   225       9.125  64.899  75.211  1.00  0.00
ATOM   1502  CA  LEU   225       8.910  66.272  74.783  1.00  0.00
ATOM   1503  C   LEU   225       8.814  67.277  75.922  1.00  0.00
ATOM   1504  O   LEU   225       9.599  68.225  76.005  1.00  0.00
ATOM   1505  CB  LEU   225       7.604  66.389  73.993  1.00  0.00
ATOM   1506  CG  LEU   225       7.532  65.603  72.683  1.00  0.00
ATOM   1507  CD1 LEU   225       6.143  65.702  72.072  1.00  0.00
ATOM   1508  CD2 LEU   225       8.534  66.146  71.674  1.00  0.00
ATOM   1509  N   LEU   226       7.842  67.095  76.834  1.00  0.00
ATOM   1510  CA  LEU   226       7.622  68.081  77.901  1.00  0.00
ATOM   1511  C   LEU   226       8.844  68.262  78.773  1.00  0.00
ATOM   1512  O   LEU   226       9.372  69.365  78.941  1.00  0.00
ATOM   1513  CB  LEU   226       6.470  67.641  78.807  1.00  0.00
ATOM   1514  CG  LEU   226       6.162  68.549  80.001  1.00  0.00
ATOM   1515  CD1 LEU   226       5.724  69.927  79.529  1.00  0.00
ATOM   1516  CD2 LEU   226       5.047  67.959  80.850  1.00  0.00
ATOM   1517  N   LYS   227       9.322  67.142  79.357  1.00  0.00
ATOM   1518  CA  LYS   227      10.546  67.259  80.195  1.00  0.00
ATOM   1519  C   LYS   227      11.828  67.403  79.396  1.00  0.00
ATOM   1520  O   LYS   227      12.647  68.281  79.682  1.00  0.00
ATOM   1521  CB  LYS   227      10.714  66.018  81.074  1.00  0.00
ATOM   1522  CG  LYS   227      11.917  66.075  82.003  1.00  0.00
ATOM   1523  CD  LYS   227      11.935  64.890  82.955  1.00  0.00
ATOM   1524  CE  LYS   227      13.101  64.979  83.925  1.00  0.00
ATOM   1525  NZ  LYS   227      13.112  63.841  84.886  1.00  0.00
ATOM   1526  N   GLU   228      12.059  66.560  78.372  1.00  0.00
ATOM   1527  CA  GLU   228      13.443  66.651  77.812  1.00  0.00
ATOM   1528  C   GLU   228      13.626  67.725  76.738  1.00  0.00
ATOM   1529  O   GLU   228      14.760  68.142  76.492  1.00  0.00
ATOM   1530  CB  GLU   228      13.848  65.325  77.166  1.00  0.00
ATOM   1531  CG  GLU   228      13.954  64.165  78.142  1.00  0.00
ATOM   1532  CD  GLU   228      14.350  62.868  77.466  1.00  0.00
ATOM   1533  OE1 GLU   228      14.565  62.881  76.235  1.00  0.00
ATOM   1534  OE2 GLU   228      14.444  61.838  78.164  1.00  0.00
ATOM   1535  N   PHE   229      12.583  68.275  76.118  1.00  0.00
ATOM   1536  CA  PHE   229      12.826  69.251  75.067  1.00  0.00
ATOM   1537  C   PHE   229      12.607  70.645  75.630  1.00  0.00
ATOM   1538  O   PHE   229      13.206  71.612  75.158  1.00  0.00
ATOM   1539  CB  PHE   229      11.870  69.024  73.895  1.00  0.00
ATOM   1540  CG  PHE   229      12.096  67.730  73.169  1.00  0.00
ATOM   1541  CD1 PHE   229      13.272  67.020  73.341  1.00  0.00
ATOM   1542  CD2 PHE   229      11.134  67.220  72.314  1.00  0.00
ATOM   1543  CE1 PHE   229      13.480  65.827  72.672  1.00  0.00
ATOM   1544  CE2 PHE   229      11.342  66.029  71.646  1.00  0.00
ATOM   1545  CZ  PHE   229      12.510  65.333  71.823  1.00  0.00
ATOM   1546  N   MET   230      11.755  70.741  76.648  1.00  0.00
ATOM   1547  CA  MET   230      11.454  72.022  77.269  1.00  0.00
ATOM   1548  C   MET   230      12.558  72.435  78.242  1.00  0.00
ATOM   1549  O   MET   230      13.032  71.584  79.032  1.00  0.00
ATOM   1550  CB  MET   230      10.139  71.945  78.046  1.00  0.00
ATOM   1551  CG  MET   230       8.915  71.713  77.175  1.00  0.00
ATOM   1552  SD  MET   230       8.631  73.055  76.004  1.00  0.00
ATOM   1553  CE  MET   230       8.052  74.346  77.103  1.00  0.00
TER
END
