
#######################################################
#                                                     #
#                        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   20 (  170),  selected   20 , name T0386TS298_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   20 , name T0386_D2.pdb
# PARAMETERS: T0386TS298_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:    20       219 - 238         3.84     3.84
  LCS_AVERAGE:     24.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       222 - 237         1.41     4.94
  LCS_AVERAGE:     17.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       222 - 234         0.86     5.08
  LCS_AVERAGE:     11.91

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    4   20     0    3    3    5    5    6    6    8   11   11   14   18   20   20   20   20   20   20   20   20 
LCS_GDT     P     220     P     220      3    4   20     0    3    3    5    5    6    6    8   11   12   16   19   20   20   20   20   20   20   20   20 
LCS_GDT     E     221     E     221      3   14   20     3    3    3    5    5    6   12   14   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     K     222     K     222     13   16   20     7   11   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     I     223     I     223     13   16   20     7   11   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     R     224     R     224     13   16   20     7   11   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     L     225     L     225     13   16   20     7   11   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     L     226     L     226     13   16   20     7   11   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     K     227     K     227     13   16   20     7   11   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     E     228     E     228     13   16   20     7   11   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     F     229     F     229     13   16   20     7   11   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     M     230     M     230     13   16   20     7   11   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     H     231     H     231     13   16   20     7   11   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     T     232     T     232     13   16   20     4   11   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     M     233     M     233     13   16   20     4    9   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     K     234     K     234     13   16   20     4   10   13   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     N     235     N     235      4   16   20     3    4    4    8   12   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     T     236     T     236      4   16   20     3    8   11   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     G     237     G     237      4   16   20     3    4   10   15   15   16   16   16   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     R     238     R     238      3    5   20     3    3    3    5    5    8   10   11   14   15   18   19   20   20   20   20   20   20   20   20 
LCS_AVERAGE  LCS_A:  18.02  (  11.91   17.47   24.69 )

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      7     11     13     15     15     16     16     16     17     17     18     19     20     20     20     20     20     20     20     20 
GDT PERCENT_CA   8.64  13.58  16.05  18.52  18.52  19.75  19.75  19.75  20.99  20.99  22.22  23.46  24.69  24.69  24.69  24.69  24.69  24.69  24.69  24.69
GDT RMS_LOCAL    0.28   0.62   0.86   1.20   1.20   1.41   1.41   1.41   2.08   2.08   2.57   3.35   3.84   3.84   3.84   3.84   3.84   3.84   3.84   3.84
GDT RMS_ALL_CA   5.22   4.97   5.08   4.90   4.90   4.94   4.94   4.94   4.62   4.62   4.52   4.05   3.84   3.84   3.84   3.84   3.84   3.84   3.84   3.84

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         13.677
LGA    P     220      P     220         12.193
LGA    E     221      E     221          7.167
LGA    K     222      K     222          1.225
LGA    I     223      I     223          1.066
LGA    R     224      R     224          1.518
LGA    L     225      L     225          1.308
LGA    L     226      L     226          0.650
LGA    K     227      K     227          0.693
LGA    E     228      E     228          1.113
LGA    F     229      F     229          0.999
LGA    M     230      M     230          1.089
LGA    H     231      H     231          1.306
LGA    T     232      T     232          0.548
LGA    M     233      M     233          1.317
LGA    K     234      K     234          1.689
LGA    N     235      N     235          3.013
LGA    T     236      T     236          1.559
LGA    G     237      G     237          1.693
LGA    R     238      R     238          8.313

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20   81    4.0     16    1.41    19.136    19.198     1.058

LGA_LOCAL      RMSD =  1.413  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.940  Number of atoms =   20 
Std_ALL_ATOMS  RMSD =  3.835  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.980464 * X  +  -0.132341 * Y  +   0.145523 * Z  +  12.862714
  Y_new =  -0.196102 * X  +   0.715328 * Y  +  -0.670708 * Z  +  18.265781
  Z_new =  -0.015334 * X  +  -0.686142 * Y  +  -0.727306 * Z  + 114.305428 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.385309    0.756284  [ DEG:  -136.6681     43.3319 ]
  Theta =   0.015335    3.126258  [ DEG:     0.8786    179.1214 ]
  Phi   =  -2.944188    0.197405  [ DEG:  -168.6895     11.3105 ]
 
# 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: T0386TS298_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS298_4-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20   81   4.0   16   1.41  19.198     3.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS298_4-D2
PFRMAT TS
TARGET T0386
MODEL  4  REFINED
PARENT 2G03_A
ATOM   1478  N   ASN   219      15.466  58.011  82.266  1.00  0.00
ATOM   1479  CA  ASN   219      14.322  57.133  81.863  1.00  0.00
ATOM   1480  C   ASN   219      13.835  57.400  80.335  1.00  0.00
ATOM   1481  O   ASN   219      13.634  58.569  80.037  1.00  0.00
ATOM   1482  CB  ASN   219      13.166  57.187  82.903  1.00  0.00
ATOM   1483  CG  ASN   219      12.004  56.294  82.491  1.00  0.00
ATOM   1484  OD1 ASN   219      12.163  55.130  82.300  1.00  0.00
ATOM   1485  ND2 ASN   219      10.807  56.982  82.440  1.00  0.00
ATOM   1486  N   PRO   220      13.425  56.393  79.447  1.00  0.00
ATOM   1487  CA  PRO   220      13.179  56.614  77.997  1.00  0.00
ATOM   1488  C   PRO   220      11.767  56.918  77.230  1.00  0.00
ATOM   1489  O   PRO   220      11.920  57.685  76.270  1.00  0.00
ATOM   1490  CB  PRO   220      13.868  55.371  77.410  1.00  0.00
ATOM   1491  CG  PRO   220      14.113  54.255  78.560  1.00  0.00
ATOM   1492  CD  PRO   220      13.856  54.979  79.864  1.00  0.00
ATOM   1493  N   GLU   221      10.499  56.485  77.508  1.00  0.00
ATOM   1494  CA  GLU   221       9.416  56.738  76.502  1.00  0.00
ATOM   1495  C   GLU   221       8.188  57.659  76.898  1.00  0.00
ATOM   1496  O   GLU   221       7.341  57.854  76.011  1.00  0.00
ATOM   1497  CB  GLU   221       8.864  55.344  76.157  1.00  0.00
ATOM   1498  CG  GLU   221       8.165  54.611  77.345  1.00  0.00
ATOM   1499  CD  GLU   221       9.055  53.519  77.964  1.00  0.00
ATOM   1500  OE1 GLU   221       8.769  52.296  77.786  1.00  0.00
ATOM   1501  OE2 GLU   221      10.043  53.806  78.696  1.00  0.00
ATOM   1502  N   LYS   222       8.190  58.378  78.018  1.00  0.00
ATOM   1503  CA  LYS   222       7.033  59.192  78.404  1.00  0.00
ATOM   1504  C   LYS   222       6.908  60.449  77.484  1.00  0.00
ATOM   1505  O   LYS   222       7.910  61.107  77.195  1.00  0.00
ATOM   1506  CB  LYS   222       7.124  59.561  79.891  1.00  0.00
ATOM   1507  CG  LYS   222       5.899  60.367  80.364  1.00  0.00
ATOM   1508  CD  LYS   222       4.639  59.504  80.481  1.00  0.00
ATOM   1509  CE  LYS   222       3.439  60.279  81.030  1.00  0.00
ATOM   1510  NZ  LYS   222       2.192  59.504  81.003  1.00  0.00
ATOM   1511  N   ILE   223       5.710  60.669  76.904  1.00  0.00
ATOM   1512  CA  ILE   223       5.397  61.865  76.090  1.00  0.00
ATOM   1513  C   ILE   223       5.934  63.167  76.814  1.00  0.00
ATOM   1514  O   ILE   223       6.504  63.991  76.101  1.00  0.00
ATOM   1515  CB  ILE   223       3.909  61.884  75.830  1.00  0.00
ATOM   1516  CG1 ILE   223       3.540  62.989  74.801  1.00  0.00
ATOM   1517  CG2 ILE   223       3.041  61.992  77.134  1.00  0.00
ATOM   1518  CD1 ILE   223       3.003  64.384  75.252  1.00  0.00
ATOM   1519  N   ARG   224       5.510  63.478  78.053  1.00  0.00
ATOM   1520  CA  ARG   224       6.004  64.614  78.858  1.00  0.00
ATOM   1521  C   ARG   224       7.565  64.613  78.926  1.00  0.00
ATOM   1522  O   ARG   224       8.119  65.705  78.830  1.00  0.00
ATOM   1523  CB  ARG   224       5.353  64.570  80.252  1.00  0.00
ATOM   1524  CG  ARG   224       5.833  65.645  81.221  1.00  0.00
ATOM   1525  CD  ARG   224       5.190  65.522  82.614  1.00  0.00
ATOM   1526  NE  ARG   224       5.734  66.546  83.516  1.00  0.00
ATOM   1527  CZ  ARG   224       6.291  66.276  84.712  1.00  0.00
ATOM   1528  NH1 ARG   224       6.389  65.003  85.139  1.00  0.00
ATOM   1529  NH2 ARG   224       6.771  67.275  85.476  1.00  0.00
ATOM   1530  N   LEU   225       8.232  63.522  79.352  1.00  0.00
ATOM   1531  CA  LEU   225       9.693  63.400  79.348  1.00  0.00
ATOM   1532  C   LEU   225      10.346  63.780  77.962  1.00  0.00
ATOM   1533  O   LEU   225      11.509  64.156  78.007  1.00  0.00
ATOM   1534  CB  LEU   225       9.972  61.924  79.677  1.00  0.00
ATOM   1535  CG  LEU   225       9.776  61.391  81.093  1.00  0.00
ATOM   1536  CD1 LEU   225      10.343  59.971  81.204  1.00  0.00
ATOM   1537  CD2 LEU   225      10.464  62.277  82.135  1.00  0.00
ATOM   1538  N   LEU   226       9.780  63.380  76.804  1.00  0.00
ATOM   1539  CA  LEU   226      10.294  63.597  75.455  1.00  0.00
ATOM   1540  C   LEU   226      10.001  65.081  75.000  1.00  0.00
ATOM   1541  O   LEU   226      10.956  65.696  74.531  1.00  0.00
ATOM   1542  CB  LEU   226       9.519  62.628  74.586  1.00  0.00
ATOM   1543  CG  LEU   226       9.857  61.167  74.602  1.00  0.00
ATOM   1544  CD1 LEU   226       8.960  60.409  73.631  1.00  0.00
ATOM   1545  CD2 LEU   226      11.261  60.943  74.122  1.00  0.00
ATOM   1546  N   LYS   227       8.762  65.626  75.118  1.00  0.00
ATOM   1547  CA  LYS   227       8.383  66.993  74.804  1.00  0.00
ATOM   1548  C   LYS   227       8.983  68.035  75.801  1.00  0.00
ATOM   1549  O   LYS   227       9.347  69.114  75.295  1.00  0.00
ATOM   1550  CB  LYS   227       6.889  67.050  74.692  1.00  0.00
ATOM   1551  CG  LYS   227       6.179  66.311  73.628  1.00  0.00
ATOM   1552  CD  LYS   227       4.671  66.545  73.629  1.00  0.00
ATOM   1553  CE  LYS   227       4.267  67.945  73.248  1.00  0.00
ATOM   1554  NZ  LYS   227       4.662  68.244  71.832  1.00  0.00
ATOM   1555  N   GLU   228       8.713  67.966  77.127  1.00  0.00
ATOM   1556  CA  GLU   228       9.387  68.899  78.026  1.00  0.00
ATOM   1557  C   GLU   228      10.900  68.874  77.656  1.00  0.00
ATOM   1558  O   GLU   228      11.399  69.954  77.345  1.00  0.00
ATOM   1559  CB  GLU   228       9.260  68.538  79.502  1.00  0.00
ATOM   1560  CG  GLU   228       7.930  68.500  80.147  1.00  0.00
ATOM   1561  CD  GLU   228       7.226  69.737  79.859  1.00  0.00
ATOM   1562  OE1 GLU   228       6.278  69.859  79.069  1.00  0.00
ATOM   1563  OE2 GLU   228       7.838  70.752  80.535  1.00  0.00
ATOM   1564  N   PHE   229      11.606  67.707  77.637  1.00  0.00
ATOM   1565  CA  PHE   229      13.012  67.544  77.203  1.00  0.00
ATOM   1566  C   PHE   229      13.357  68.364  75.942  1.00  0.00
ATOM   1567  O   PHE   229      14.460  68.909  75.923  1.00  0.00
ATOM   1568  CB  PHE   229      13.199  66.047  76.830  1.00  0.00
ATOM   1569  CG  PHE   229      14.494  65.830  76.002  1.00  0.00
ATOM   1570  CD1 PHE   229      15.747  66.122  76.519  1.00  0.00
ATOM   1571  CD2 PHE   229      14.374  65.333  74.721  1.00  0.00
ATOM   1572  CE1 PHE   229      16.871  65.909  75.753  1.00  0.00
ATOM   1573  CE2 PHE   229      15.510  65.123  73.960  1.00  0.00
ATOM   1574  CZ  PHE   229      16.760  65.410  74.474  1.00  0.00
ATOM   1575  N   MET   230      12.591  68.209  74.824  1.00  0.00
ATOM   1576  CA  MET   230      12.774  68.918  73.587  1.00  0.00
ATOM   1577  C   MET   230      12.785  70.443  73.862  1.00  0.00
ATOM   1578  O   MET   230      13.605  71.096  73.214  1.00  0.00
ATOM   1579  CB  MET   230      11.691  68.496  72.549  1.00  0.00
ATOM   1580  CG  MET   230      12.010  67.051  72.050  1.00  0.00
ATOM   1581  SD  MET   230      10.868  66.623  70.758  1.00  0.00
ATOM   1582  CE  MET   230       9.276  66.753  71.597  1.00  0.00
ATOM   1583  N   HIS   231      11.714  71.043  74.429  1.00  0.00
ATOM   1584  CA  HIS   231      11.647  72.458  74.818  1.00  0.00
ATOM   1585  C   HIS   231      12.934  72.859  75.616  1.00  0.00
ATOM   1586  O   HIS   231      13.423  73.951  75.323  1.00  0.00
ATOM   1587  CB  HIS   231      10.395  72.692  75.635  1.00  0.00
ATOM   1588  CG  HIS   231       9.129  72.781  74.904  1.00  0.00
ATOM   1589  ND1 HIS   231       7.932  72.815  75.540  1.00  0.00
ATOM   1590  CD2 HIS   231       8.824  72.877  73.619  1.00  0.00
ATOM   1591  CE1 HIS   231       6.939  72.965  74.714  1.00  0.00
ATOM   1592  NE2 HIS   231       7.471  73.002  73.500  1.00  0.00
ATOM   1593  N   THR   232      13.275  72.199  76.762  1.00  0.00
ATOM   1594  CA  THR   232      14.499  72.486  77.504  1.00  0.00
ATOM   1595  C   THR   232      15.737  72.524  76.534  1.00  0.00
ATOM   1596  O   THR   232      16.604  73.378  76.767  1.00  0.00
ATOM   1597  CB  THR   232      14.677  71.638  78.810  1.00  0.00
ATOM   1598  OG1 THR   232      15.994  71.263  79.266  1.00  0.00
ATOM   1599  CG2 THR   232      13.606  70.637  79.066  1.00  0.00
ATOM   1600  N   MET   233      15.990  71.481  75.731  1.00  0.00
ATOM   1601  CA  MET   233      17.031  71.391  74.711  1.00  0.00
ATOM   1602  C   MET   233      17.133  72.656  73.825  1.00  0.00
ATOM   1603  O   MET   233      18.242  73.180  73.735  1.00  0.00
ATOM   1604  CB  MET   233      16.671  70.144  73.870  1.00  0.00
ATOM   1605  CG  MET   233      17.878  69.823  72.908  1.00  0.00
ATOM   1606  SD  MET   233      17.307  70.485  71.296  1.00  0.00
ATOM   1607  CE  MET   233      16.901  68.955  70.418  1.00  0.00
ATOM   1608  N   LYS   234      16.052  73.152  73.175  1.00  0.00
ATOM   1609  CA  LYS   234      16.051  74.390  72.406  1.00  0.00
ATOM   1610  C   LYS   234      16.466  75.600  73.306  1.00  0.00
ATOM   1611  O   LYS   234      17.250  76.430  72.824  1.00  0.00
ATOM   1612  CB  LYS   234      14.640  74.591  71.897  1.00  0.00
ATOM   1613  CG  LYS   234      14.298  74.127  70.532  1.00  0.00
ATOM   1614  CD  LYS   234      15.069  72.959  69.995  1.00  0.00
ATOM   1615  CE  LYS   234      14.716  72.709  68.511  1.00  0.00
ATOM   1616  NZ  LYS   234      15.835  71.945  67.891  1.00  0.00
ATOM   1617  N   ASN   235      15.776  75.869  74.428  1.00  0.00
ATOM   1618  CA  ASN   235      16.083  76.901  75.407  1.00  0.00
ATOM   1619  C   ASN   235      17.600  77.009  75.726  1.00  0.00
ATOM   1620  O   ASN   235      18.029  78.156  75.871  1.00  0.00
ATOM   1621  CB  ASN   235      15.275  76.615  76.690  1.00  0.00
ATOM   1622  CG  ASN   235      15.581  77.494  77.905  1.00  0.00
ATOM   1623  OD1 ASN   235      16.759  77.632  78.327  1.00  0.00
ATOM   1624  ND2 ASN   235      14.548  78.031  78.545  1.00  0.00
ATOM   1625  N   THR   236      18.383  75.896  75.854  1.00  0.00
ATOM   1626  CA  THR   236      19.824  75.968  76.115  1.00  0.00
ATOM   1627  C   THR   236      20.583  76.958  75.152  1.00  0.00
ATOM   1628  O   THR   236      21.266  77.844  75.689  1.00  0.00
ATOM   1629  CB  THR   236      20.478  74.559  76.111  1.00  0.00
ATOM   1630  OG1 THR   236      19.844  73.575  76.982  1.00  0.00
ATOM   1631  CG2 THR   236      21.923  74.721  76.707  1.00  0.00
ATOM   1632  N   GLY   237      20.399  76.917  73.810  1.00  0.00
ATOM   1633  CA  GLY   237      21.157  77.790  72.920  1.00  0.00
ATOM   1634  C   GLY   237      20.784  79.286  73.033  1.00  0.00
ATOM   1635  O   GLY   237      21.722  80.116  73.044  1.00  0.00
ATOM   1636  N   ARG   238      19.561  79.613  72.737  1.00  0.00
ATOM   1637  CA  ARG   238      19.172  81.039  72.721  1.00  0.00
ATOM   1638  C   ARG   238      18.106  81.329  73.821  1.00  0.00
ATOM   1639  O   ARG   238      18.443  81.741  74.926  1.00  0.00
ATOM   1640  CB  ARG   238      18.724  81.326  71.265  1.00  0.00
ATOM   1641  CG  ARG   238      17.358  80.751  70.920  1.00  0.00
ATOM   1642  CD  ARG   238      17.220  79.376  71.478  1.00  0.00
ATOM   1643  NE  ARG   238      16.088  78.649  70.909  1.00  0.00
ATOM   1644  CZ  ARG   238      14.833  79.116  70.946  1.00  0.00
ATOM   1645  NH1 ARG   238      14.539  80.299  71.482  1.00  0.00
ATOM   1646  NH2 ARG   238      13.871  78.343  70.448  1.00  0.00
ATOM   1647  OXT ARG   238      16.951  80.981  73.540  1.00  0.00
TER
END
