
#######################################################
#                                                     #
#                        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   19 (  159),  selected   19 , name T0386TS349_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   19 , name T0386_D2.pdb
# PARAMETERS: T0386TS349_4-D2.T0386_D2.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18       220 - 237         4.77     6.02
  LCS_AVERAGE:     22.09

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       225 - 237         1.54     8.73
  LCS_AVERAGE:     13.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       225 - 234         0.75     8.20
  LCS_AVERAGE:      8.71

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   81
LCS_GDT     N     219     N     219      3    3   16     0    3    3    3    4    6    8    8    9    9   13   13   14   15   17   17   18   19   19   19 
LCS_GDT     P     220     P     220      4    4   18     3    3    4    4    4    6    8   10   10   11   13   14   15   16   18   18   18   19   19   19 
LCS_GDT     E     221     E     221      4    6   18     3    3    4    4    6    6    8   10   12   13   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     K     222     K     222      4    6   18     4    4    5    6    6    8   10   11   12   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     I     223     I     223      4    6   18     4    4    5    6    6    7    9   11   12   13   14   16   17   17   18   18   18   19   19   19 
LCS_GDT     R     224     R     224      4    6   18     4    4    5    6    6    6    9   11   12   14   14   15   17   17   18   18   18   19   19   19 
LCS_GDT     L     225     L     225     10   13   18     6    9   10   11   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     L     226     L     226     10   13   18     6    9   10   11   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     K     227     K     227     10   13   18     6    9   10   11   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     E     228     E     228     10   13   18     6    9   10   11   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     F     229     F     229     10   13   18     6    9   10   11   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     M     230     M     230     10   13   18     6    9   10   11   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     H     231     H     231     10   13   18     5    9   10   11   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     T     232     T     232     10   13   18     5    9   10   11   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     M     233     M     233     10   13   18     5    9   10   11   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     K     234     K     234     10   13   18     5    9   10   11   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     N     235     N     235      4   13   18     3    4    4    7   10   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     T     236     T     236      4   13   18     3    4    8   11   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_GDT     G     237     G     237      3   13   18     3    3    3    7   12   13   13   13   13   14   15   16   17   17   18   18   18   19   19   19 
LCS_AVERAGE  LCS_A:  14.60  (   8.71   13.00   22.09 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      6      9     10     11     12     13     13     13     13     14     15     16     17     17     18     18     18     19     19     19 
GDT PERCENT_CA   7.41  11.11  12.35  13.58  14.81  16.05  16.05  16.05  16.05  17.28  18.52  19.75  20.99  20.99  22.22  22.22  22.22  23.46  23.46  23.46
GDT RMS_LOCAL    0.21   0.68   0.75   1.12   1.32   1.54   1.54   1.54   1.54   2.45   3.59   3.94   4.09   4.09   4.77   4.77   4.77   5.54   5.54   5.54
GDT RMS_ALL_CA   7.92   8.10   8.20   8.54   8.59   8.73   8.73   8.73   8.73   8.24   6.64   6.35   6.40   6.40   6.02   6.02   6.02   5.54   5.54   5.54

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         24.025
LGA    P     220      P     220         17.815
LGA    E     221      E     221         13.989
LGA    K     222      K     222         10.267
LGA    I     223      I     223         12.363
LGA    R     224      R     224          8.297
LGA    L     225      L     225          1.434
LGA    L     226      L     226          0.635
LGA    K     227      K     227          1.148
LGA    E     228      E     228          1.555
LGA    F     229      F     229          1.226
LGA    M     230      M     230          0.831
LGA    H     231      H     231          1.504
LGA    T     232      T     232          0.633
LGA    M     233      M     233          0.742
LGA    K     234      K     234          1.625
LGA    N     235      N     235          2.925
LGA    T     236      T     236          1.746
LGA    G     237      G     237          2.253

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   81    4.0     13    1.54    15.741    15.351     0.792

LGA_LOCAL      RMSD =  1.542  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.731  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  5.544  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.621627 * X  +   0.518072 * Y  +   0.587521 * Z  + -19.006458
  Y_new =  -0.609993 * X  +   0.150380 * Y  +  -0.778007 * Z  +  53.035717
  Z_new =  -0.491415 * X  +  -0.842014 * Y  +   0.222540 * Z  + 125.328362 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.312410    1.829183  [ DEG:   -75.1955    104.8045 ]
  Theta =   0.513713    2.627879  [ DEG:    29.4336    150.5664 ]
  Phi   =  -2.365641    0.775952  [ DEG:  -135.5412     44.4588 ]
 
# 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: T0386TS349_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS349_4-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19   81   4.0   13   1.54  15.351     5.54
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS349_4-D2
PFRMAT TS
TARGET T0386
MODEL  4  REFINED
PARENT 2G03_A
ATOM   1478  N   ASN   219      11.522  74.043  88.920  1.00  0.00
ATOM   1479  CA  ASN   219      12.047  72.656  89.004  1.00  0.00
ATOM   1480  C   ASN   219      10.998  71.477  88.742  1.00  0.00
ATOM   1481  O   ASN   219      10.303  71.140  89.698  1.00  0.00
ATOM   1482  CB  ASN   219      12.639  72.507  90.446  1.00  0.00
ATOM   1483  CG  ASN   219      13.882  73.366  90.757  1.00  0.00
ATOM   1484  OD1 ASN   219      13.966  73.967  91.838  1.00  0.00
ATOM   1485  ND2 ASN   219      14.787  73.518  89.799  1.00  0.00
ATOM   1486  N   PRO   220      10.872  70.775  87.576  1.00  0.00
ATOM   1487  CA  PRO   220      10.023  69.677  87.443  1.00  0.00
ATOM   1488  C   PRO   220      10.614  68.365  88.012  1.00  0.00
ATOM   1489  O   PRO   220      11.785  68.034  87.808  1.00  0.00
ATOM   1490  CB  PRO   220       9.694  69.402  85.961  1.00  0.00
ATOM   1491  CG  PRO   220      11.004  69.964  85.361  1.00  0.00
ATOM   1492  CD  PRO   220      11.360  71.172  86.215  1.00  0.00
ATOM   1493  N   GLU   221       9.677  67.509  88.380  1.00  0.00
ATOM   1494  CA  GLU   221       9.838  66.146  88.851  1.00  0.00
ATOM   1495  C   GLU   221       9.733  65.153  87.643  1.00  0.00
ATOM   1496  O   GLU   221      10.216  64.040  87.812  1.00  0.00
ATOM   1497  CB  GLU   221       8.741  65.854  89.919  1.00  0.00
ATOM   1498  CG  GLU   221       7.615  64.915  89.460  1.00  0.00
ATOM   1499  CD  GLU   221       6.741  64.519  90.608  1.00  0.00
ATOM   1500  OE1 GLU   221       6.607  65.464  91.486  1.00  0.00
ATOM   1501  OE2 GLU   221       6.239  63.428  90.735  1.00  0.00
ATOM   1502  N   LYS   222       9.201  65.551  86.461  1.00  0.00
ATOM   1503  CA  LYS   222       9.146  64.760  85.261  1.00  0.00
ATOM   1504  C   LYS   222      10.537  64.896  84.543  1.00  0.00
ATOM   1505  O   LYS   222      10.686  65.554  83.505  1.00  0.00
ATOM   1506  CB  LYS   222       8.061  65.292  84.332  1.00  0.00
ATOM   1507  CG  LYS   222       6.693  65.121  84.861  1.00  0.00
ATOM   1508  CD  LYS   222       5.658  65.058  83.749  1.00  0.00
ATOM   1509  CE  LYS   222       4.278  64.987  84.397  1.00  0.00
ATOM   1510  NZ  LYS   222       3.224  64.834  83.404  1.00  0.00
ATOM   1511  N   ILE   223      11.523  64.208  85.154  1.00  0.00
ATOM   1512  CA  ILE   223      12.920  64.136  84.737  1.00  0.00
ATOM   1513  C   ILE   223      13.033  63.592  83.278  1.00  0.00
ATOM   1514  O   ILE   223      13.917  64.035  82.563  1.00  0.00
ATOM   1515  CB  ILE   223      13.805  63.306  85.697  1.00  0.00
ATOM   1516  CG1 ILE   223      13.214  61.957  86.086  1.00  0.00
ATOM   1517  CG2 ILE   223      13.951  64.125  87.021  1.00  0.00
ATOM   1518  CD1 ILE   223      14.270  60.897  86.241  1.00  0.00
ATOM   1519  N   ARG   224      12.245  62.588  82.876  1.00  0.00
ATOM   1520  CA  ARG   224      12.288  61.955  81.548  1.00  0.00
ATOM   1521  C   ARG   224      11.183  62.393  80.593  1.00  0.00
ATOM   1522  O   ARG   224      11.166  61.810  79.493  1.00  0.00
ATOM   1523  CB  ARG   224      12.214  60.454  81.771  1.00  0.00
ATOM   1524  CG  ARG   224      13.372  59.497  81.743  1.00  0.00
ATOM   1525  CD  ARG   224      12.815  58.110  81.442  1.00  0.00
ATOM   1526  NE  ARG   224      12.367  58.077  80.051  1.00  0.00
ATOM   1527  CZ  ARG   224      11.282  57.415  79.561  1.00  0.00
ATOM   1528  NH1 ARG   224      11.124  57.598  78.257  1.00  0.00
ATOM   1529  NH2 ARG   224      10.360  56.716  80.280  1.00  0.00
ATOM   1530  N   LEU   225      10.561  63.551  80.761  1.00  0.00
ATOM   1531  CA  LEU   225       9.472  63.870  79.858  1.00  0.00
ATOM   1532  C   LEU   225      10.061  64.411  78.525  1.00  0.00
ATOM   1533  O   LEU   225      10.778  65.423  78.524  1.00  0.00
ATOM   1534  CB  LEU   225       8.411  64.795  80.566  1.00  0.00
ATOM   1535  CG  LEU   225       7.231  65.138  79.668  1.00  0.00
ATOM   1536  CD1 LEU   225       6.094  65.471  80.616  1.00  0.00
ATOM   1537  CD2 LEU   225       7.485  66.426  78.893  1.00  0.00
ATOM   1538  N   LEU   226       9.537  63.859  77.422  1.00  0.00
ATOM   1539  CA  LEU   226      10.035  64.225  76.111  1.00  0.00
ATOM   1540  C   LEU   226       9.900  65.765  75.780  1.00  0.00
ATOM   1541  O   LEU   226      10.871  66.281  75.225  1.00  0.00
ATOM   1542  CB  LEU   226       9.369  63.274  75.138  1.00  0.00
ATOM   1543  CG  LEU   226       7.847  63.466  74.970  1.00  0.00
ATOM   1544  CD1 LEU   226       7.440  64.638  74.078  1.00  0.00
ATOM   1545  CD2 LEU   226       7.251  62.212  74.298  1.00  0.00
ATOM   1546  N   LYS   227       8.743  66.423  75.977  1.00  0.00
ATOM   1547  CA  LYS   227       8.515  67.864  75.733  1.00  0.00
ATOM   1548  C   LYS   227       9.499  68.727  76.601  1.00  0.00
ATOM   1549  O   LYS   227       9.887  69.788  76.110  1.00  0.00
ATOM   1550  CB  LYS   227       7.037  68.243  76.027  1.00  0.00
ATOM   1551  CG  LYS   227       6.757  69.660  75.473  1.00  0.00
ATOM   1552  CD  LYS   227       5.343  70.083  75.834  1.00  0.00
ATOM   1553  CE  LYS   227       4.999  71.445  75.182  1.00  0.00
ATOM   1554  NZ  LYS   227       3.582  71.753  75.570  1.00  0.00
ATOM   1555  N   GLU   228       9.647  68.455  77.911  1.00  0.00
ATOM   1556  CA  GLU   228      10.584  69.151  78.755  1.00  0.00
ATOM   1557  C   GLU   228      12.013  69.059  78.251  1.00  0.00
ATOM   1558  O   GLU   228      12.558  70.099  78.058  1.00  0.00
ATOM   1559  CB  GLU   228      10.546  68.536  80.125  1.00  0.00
ATOM   1560  CG  GLU   228       9.292  68.695  80.896  1.00  0.00
ATOM   1561  CD  GLU   228       9.244  68.191  82.332  1.00  0.00
ATOM   1562  OE1 GLU   228       8.102  67.828  82.724  1.00  0.00
ATOM   1563  OE2 GLU   228      10.411  68.299  82.925  1.00  0.00
ATOM   1564  N   PHE   229      12.615  67.870  78.102  1.00  0.00
ATOM   1565  CA  PHE   229      13.980  67.704  77.554  1.00  0.00
ATOM   1566  C   PHE   229      14.102  68.387  76.133  1.00  0.00
ATOM   1567  O   PHE   229      15.173  68.985  75.886  1.00  0.00
ATOM   1568  CB  PHE   229      14.409  66.207  77.533  1.00  0.00
ATOM   1569  CG  PHE   229      14.949  65.733  78.862  1.00  0.00
ATOM   1570  CD1 PHE   229      15.544  64.434  78.855  1.00  0.00
ATOM   1571  CD2 PHE   229      14.938  66.429  80.047  1.00  0.00
ATOM   1572  CE1 PHE   229      16.086  63.915  80.022  1.00  0.00
ATOM   1573  CE2 PHE   229      15.500  65.948  81.199  1.00  0.00
ATOM   1574  CZ  PHE   229      16.072  64.663  81.187  1.00  0.00
ATOM   1575  N   MET   230      13.170  68.183  75.166  1.00  0.00
ATOM   1576  CA  MET   230      13.262  68.843  73.824  1.00  0.00
ATOM   1577  C   MET   230      13.152  70.374  73.929  1.00  0.00
ATOM   1578  O   MET   230      14.008  71.021  73.370  1.00  0.00
ATOM   1579  CB  MET   230      12.246  68.214  72.869  1.00  0.00
ATOM   1580  CG  MET   230      12.509  66.768  72.584  1.00  0.00
ATOM   1581  SD  MET   230      14.136  66.487  71.891  1.00  0.00
ATOM   1582  CE  MET   230      14.141  64.767  71.438  1.00  0.00
ATOM   1583  N   HIS   231      12.065  70.892  74.445  1.00  0.00
ATOM   1584  CA  HIS   231      11.878  72.339  74.592  1.00  0.00
ATOM   1585  C   HIS   231      13.041  72.893  75.479  1.00  0.00
ATOM   1586  O   HIS   231      13.315  74.065  75.314  1.00  0.00
ATOM   1587  CB  HIS   231      10.495  72.692  75.141  1.00  0.00
ATOM   1588  CG  HIS   231       9.414  72.395  74.169  1.00  0.00
ATOM   1589  ND1 HIS   231       8.881  73.375  73.356  1.00  0.00
ATOM   1590  CD2 HIS   231       8.758  71.227  73.904  1.00  0.00
ATOM   1591  CE1 HIS   231       7.910  72.797  72.633  1.00  0.00
ATOM   1592  NE2 HIS   231       7.827  71.505  72.937  1.00  0.00
ATOM   1593  N   THR   232      13.492  72.209  76.571  1.00  0.00
ATOM   1594  CA  THR   232      14.632  72.647  77.365  1.00  0.00
ATOM   1595  C   THR   232      15.856  72.879  76.424  1.00  0.00
ATOM   1596  O   THR   232      16.550  73.834  76.681  1.00  0.00
ATOM   1597  CB  THR   232      14.963  71.718  78.597  1.00  0.00
ATOM   1598  OG1 THR   232      15.523  70.419  78.130  1.00  0.00
ATOM   1599  CG2 THR   232      13.909  71.751  79.627  1.00  0.00
ATOM   1600  N   MET   233      16.344  71.864  75.691  1.00  0.00
ATOM   1601  CA  MET   233      17.433  71.949  74.750  1.00  0.00
ATOM   1602  C   MET   233      17.254  73.159  73.782  1.00  0.00
ATOM   1603  O   MET   233      18.295  73.628  73.322  1.00  0.00
ATOM   1604  CB  MET   233      17.414  70.625  73.989  1.00  0.00
ATOM   1605  CG  MET   233      17.866  69.467  74.823  1.00  0.00
ATOM   1606  SD  MET   233      17.658  67.998  73.701  1.00  0.00
ATOM   1607  CE  MET   233      16.965  66.791  74.867  1.00  0.00
ATOM   1608  N   LYS   234      16.078  73.283  73.119  1.00  0.00
ATOM   1609  CA  LYS   234      15.798  74.427  72.270  1.00  0.00
ATOM   1610  C   LYS   234      16.055  75.740  73.068  1.00  0.00
ATOM   1611  O   LYS   234      16.626  76.666  72.460  1.00  0.00
ATOM   1612  CB  LYS   234      14.351  74.366  71.800  1.00  0.00
ATOM   1613  CG  LYS   234      14.072  73.469  70.644  1.00  0.00
ATOM   1614  CD  LYS   234      12.712  73.811  70.051  1.00  0.00
ATOM   1615  CE  LYS   234      12.815  75.039  69.152  1.00  0.00
ATOM   1616  NZ  LYS   234      13.601  74.620  67.937  1.00  0.00
ATOM   1617  N   ASN   235      15.457  75.928  74.260  1.00  0.00
ATOM   1618  CA  ASN   235      15.673  77.038  75.132  1.00  0.00
ATOM   1619  C   ASN   235      17.183  77.206  75.472  1.00  0.00
ATOM   1620  O   ASN   235      17.655  78.349  75.329  1.00  0.00
ATOM   1621  CB  ASN   235      14.774  76.939  76.348  1.00  0.00
ATOM   1622  CG  ASN   235      14.791  78.121  77.262  1.00  0.00
ATOM   1623  OD1 ASN   235      15.716  78.367  78.056  1.00  0.00
ATOM   1624  ND2 ASN   235      13.691  78.791  77.286  1.00  0.00
ATOM   1625  N   THR   236      17.889  76.193  76.015  1.00  0.00
ATOM   1626  CA  THR   236      19.303  76.261  76.295  1.00  0.00
ATOM   1627  C   THR   236      20.153  76.639  75.034  1.00  0.00
ATOM   1628  O   THR   236      21.041  77.489  75.206  1.00  0.00
ATOM   1629  CB  THR   236      19.671  74.929  77.040  1.00  0.00
ATOM   1630  OG1 THR   236      19.398  73.724  76.317  1.00  0.00
ATOM   1631  CG2 THR   236      18.863  74.857  78.416  1.00  0.00
ATOM   1632  N   GLY   237      19.942  76.037  73.850  1.00  0.00
ATOM   1633  CA  GLY   237      20.662  76.409  72.634  1.00  0.00
ATOM   1634  C   GLY   237      20.247  77.838  72.219  1.00  0.00
ATOM   1635  O   GLY   237      21.007  78.558  71.582  1.00  0.00
ATOM   1636  OXT GLY   237      19.077  78.182  72.499  1.00  0.00
TER
END
