
#######################################################
#                                                     #
#                        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_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   20 , name T0386_D2.pdb
# PARAMETERS: T0386TS298_2-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         3.83     3.83
  LCS_AVERAGE:     24.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       222 - 237         1.45     4.91
  LCS_AVERAGE:     17.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       222 - 234         0.88     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      0    4   20     0    0    3    4    5    5    6    8   12   13   14   17   17   20   20   20   20   20   20   20 
LCS_GDT     P     220     P     220      3    4   20     3    3    3    4    5    5    6    9   12   13   17   19   19   20   20   20   20   20   20   20 
LCS_GDT     E     221     E     221      3   14   20     3    3    3    4    5    5    6   13   17   17   18   19   19   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   19   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   19   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   19   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   19   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   19   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   19   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   19   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   19   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   19   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   19   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   19   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   19   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   19   20   20   20   20   20   20   20 
LCS_GDT     N     235     N     235      5   16   20     3    4    5   10   12   16   16   16   17   17   18   19   19   20   20   20   20   20   20   20 
LCS_GDT     T     236     T     236      5   16   20     3    7   10   15   15   16   16   16   17   17   18   19   19   20   20   20   20   20   20   20 
LCS_GDT     G     237     G     237      5   16   20     3    5   11   15   15   16   16   16   17   17   18   19   19   20   20   20   20   20   20   20 
LCS_GDT     R     238     R     238      3    5   20     3    3    3    5    5    8   12   13   14   15   18   19   19   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     19     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  23.46  24.69  24.69  24.69  24.69  24.69  24.69  24.69
GDT RMS_LOCAL    0.30   0.63   0.88   1.24   1.24   1.45   1.45   1.45   2.10   2.10   2.60   3.32   3.32   3.83   3.83   3.83   3.83   3.83   3.83   3.83
GDT RMS_ALL_CA   4.97   4.95   5.08   4.87   4.87   4.91   4.91   4.91   4.62   4.62   4.53   4.07   4.07   3.83   3.83   3.83   3.83   3.83   3.83   3.83

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         13.818
LGA    P     220      P     220         11.701
LGA    E     221      E     221          7.211
LGA    K     222      K     222          0.990
LGA    I     223      I     223          1.198
LGA    R     224      R     224          1.609
LGA    L     225      L     225          1.371
LGA    L     226      L     226          0.645
LGA    K     227      K     227          0.595
LGA    E     228      E     228          1.221
LGA    F     229      F     229          1.120
LGA    M     230      M     230          1.202
LGA    H     231      H     231          1.230
LGA    T     232      T     232          0.496
LGA    M     233      M     233          1.342
LGA    K     234      K     234          1.787
LGA    N     235      N     235          3.019
LGA    T     236      T     236          1.594
LGA    G     237      G     237          1.817
LGA    R     238      R     238          8.349

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20   81    4.0     16    1.45    19.136    19.160     1.033

LGA_LOCAL      RMSD =  1.448  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.915  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 =  -0.985069 * X  +  -0.124197 * Y  +   0.119223 * Z  +  12.048988
  Y_new =  -0.172127 * X  +   0.723965 * Y  +  -0.668017 * Z  +  18.039665
  Z_new =  -0.003348 * X  +  -0.678565 * Y  +  -0.734533 * Z  + 113.758354 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.395780    0.745812  [ DEG:  -137.2681     42.7319 ]
  Theta =   0.003348    3.138245  [ DEG:     0.1918    179.8082 ]
  Phi   =  -2.968603    0.172990  [ DEG:  -170.0884      9.9116 ]
 
# 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_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS298_2-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   1.45  19.160     3.83
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS298_2-D2
PFRMAT TS
TARGET T0386
MODEL  2  REFINED
PARENT 2G03_A
ATOM   1470  N   ASN   219      15.807  58.011  81.898  1.00  0.00
ATOM   1471  CA  ASN   219      14.646  57.047  81.621  1.00  0.00
ATOM   1472  C   ASN   219      13.869  57.163  80.190  1.00  0.00
ATOM   1473  O   ASN   219      13.899  58.285  79.688  1.00  0.00
ATOM   1474  CB  ASN   219      13.573  57.245  82.733  1.00  0.00
ATOM   1475  CG  ASN   219      12.537  56.110  82.989  1.00  0.00
ATOM   1476  OD1 ASN   219      12.883  54.976  83.306  1.00  0.00
ATOM   1477  ND2 ASN   219      11.248  56.449  82.804  1.00  0.00
ATOM   1478  N   PRO   220      13.168  56.139  79.503  1.00  0.00
ATOM   1479  CA  PRO   220      12.559  56.217  78.099  1.00  0.00
ATOM   1480  C   PRO   220      11.103  56.902  77.803  1.00  0.00
ATOM   1481  O   PRO   220      11.043  58.118  77.986  1.00  0.00
ATOM   1482  CB  PRO   220      12.585  54.818  77.505  1.00  0.00
ATOM   1483  CG  PRO   220      12.252  53.992  78.792  1.00  0.00
ATOM   1484  CD  PRO   220      12.971  54.723  79.919  1.00  0.00
ATOM   1485  N   GLU   221      10.415  56.279  76.762  1.00  0.00
ATOM   1486  CA  GLU   221       9.197  56.675  75.995  1.00  0.00
ATOM   1487  C   GLU   221       8.113  57.636  76.576  1.00  0.00
ATOM   1488  O   GLU   221       7.267  58.051  75.758  1.00  0.00
ATOM   1489  CB  GLU   221       8.482  55.348  75.682  1.00  0.00
ATOM   1490  CG  GLU   221       9.422  54.165  75.421  1.00  0.00
ATOM   1491  CD  GLU   221       9.075  52.829  74.860  1.00  0.00
ATOM   1492  OE1 GLU   221       9.907  51.921  74.790  1.00  0.00
ATOM   1493  OE2 GLU   221       7.885  52.713  74.472  1.00  0.00
ATOM   1494  N   LYS   222       8.123  58.105  77.824  1.00  0.00
ATOM   1495  CA  LYS   222       6.999  59.007  78.226  1.00  0.00
ATOM   1496  C   LYS   222       6.873  60.299  77.345  1.00  0.00
ATOM   1497  O   LYS   222       7.870  60.969  77.074  1.00  0.00
ATOM   1498  CB  LYS   222       7.218  59.415  79.694  1.00  0.00
ATOM   1499  CG  LYS   222       6.053  60.269  80.251  1.00  0.00
ATOM   1500  CD  LYS   222       4.763  59.469  80.458  1.00  0.00
ATOM   1501  CE  LYS   222       3.638  60.311  81.065  1.00  0.00
ATOM   1502  NZ  LYS   222       2.354  59.599  81.127  1.00  0.00
ATOM   1503  N   ILE   223       5.631  60.648  76.951  1.00  0.00
ATOM   1504  CA  ILE   223       5.275  61.872  76.209  1.00  0.00
ATOM   1505  C   ILE   223       5.779  63.174  76.953  1.00  0.00
ATOM   1506  O   ILE   223       6.276  64.045  76.243  1.00  0.00
ATOM   1507  CB  ILE   223       3.745  61.830  75.923  1.00  0.00
ATOM   1508  CG1 ILE   223       3.360  62.967  74.956  1.00  0.00
ATOM   1509  CG2 ILE   223       2.917  61.872  77.257  1.00  0.00
ATOM   1510  CD1 ILE   223       2.758  64.318  75.458  1.00  0.00
ATOM   1511  N   ARG   224       5.531  63.374  78.262  1.00  0.00
ATOM   1512  CA  ARG   224       6.037  64.510  79.058  1.00  0.00
ATOM   1513  C   ARG   224       7.598  64.557  79.026  1.00  0.00
ATOM   1514  O   ARG   224       8.120  65.660  78.878  1.00  0.00
ATOM   1515  CB  ARG   224       5.436  64.357  80.458  1.00  0.00
ATOM   1516  CG  ARG   224       5.215  65.706  81.108  1.00  0.00
ATOM   1517  CD  ARG   224       4.432  65.553  82.356  1.00  0.00
ATOM   1518  NE  ARG   224       2.978  65.508  82.161  1.00  0.00
ATOM   1519  CZ  ARG   224       2.220  65.470  83.289  1.00  0.00
ATOM   1520  NH1 ARG   224       2.735  65.494  84.523  1.00  0.00
ATOM   1521  NH2 ARG   224       0.893  65.398  83.177  1.00  0.00
ATOM   1522  N   LEU   225       8.306  63.472  79.409  1.00  0.00
ATOM   1523  CA  LEU   225       9.764  63.387  79.332  1.00  0.00
ATOM   1524  C   LEU   225      10.294  63.878  77.930  1.00  0.00
ATOM   1525  O   LEU   225      10.915  64.929  77.900  1.00  0.00
ATOM   1526  CB  LEU   225      10.089  61.900  79.554  1.00  0.00
ATOM   1527  CG  LEU   225      10.016  61.290  80.942  1.00  0.00
ATOM   1528  CD1 LEU   225      10.638  59.889  80.934  1.00  0.00
ATOM   1529  CD2 LEU   225      10.745  62.143  81.984  1.00  0.00
ATOM   1530  N   LEU   226       9.909  63.229  76.816  1.00  0.00
ATOM   1531  CA  LEU   226      10.227  63.595  75.458  1.00  0.00
ATOM   1532  C   LEU   226       9.893  65.096  75.118  1.00  0.00
ATOM   1533  O   LEU   226      10.800  65.733  74.573  1.00  0.00
ATOM   1534  CB  LEU   226       9.482  62.680  74.528  1.00  0.00
ATOM   1535  CG  LEU   226       9.878  61.239  74.384  1.00  0.00
ATOM   1536  CD1 LEU   226       8.939  60.526  73.418  1.00  0.00
ATOM   1537  CD2 LEU   226      11.242  61.158  73.766  1.00  0.00
ATOM   1538  N   LYS   227       8.620  65.572  75.198  1.00  0.00
ATOM   1539  CA  LYS   227       8.252  66.925  74.871  1.00  0.00
ATOM   1540  C   LYS   227       8.917  68.018  75.766  1.00  0.00
ATOM   1541  O   LYS   227       9.278  69.048  75.182  1.00  0.00
ATOM   1542  CB  LYS   227       6.739  67.121  74.827  1.00  0.00
ATOM   1543  CG  LYS   227       5.948  66.270  73.885  1.00  0.00
ATOM   1544  CD  LYS   227       4.453  66.569  73.959  1.00  0.00
ATOM   1545  CE  LYS   227       4.078  67.948  73.482  1.00  0.00
ATOM   1546  NZ  LYS   227       4.390  68.107  72.023  1.00  0.00
ATOM   1547  N   GLU   228       8.659  68.048  77.106  1.00  0.00
ATOM   1548  CA  GLU   228       9.339  69.015  77.992  1.00  0.00
ATOM   1549  C   GLU   228      10.835  69.076  77.647  1.00  0.00
ATOM   1550  O   GLU   228      11.388  70.159  77.779  1.00  0.00
ATOM   1551  CB  GLU   228       9.200  68.666  79.455  1.00  0.00
ATOM   1552  CG  GLU   228       7.873  68.556  80.109  1.00  0.00
ATOM   1553  CD  GLU   228       7.111  69.760  79.825  1.00  0.00
ATOM   1554  OE1 GLU   228       6.164  69.842  79.029  1.00  0.00
ATOM   1555  OE2 GLU   228       7.668  70.799  80.512  1.00  0.00
ATOM   1556  N   PHE   229      11.551  67.920  77.576  1.00  0.00
ATOM   1557  CA  PHE   229      12.948  67.783  77.175  1.00  0.00
ATOM   1558  C   PHE   229      13.289  68.547  75.853  1.00  0.00
ATOM   1559  O   PHE   229      14.327  69.142  75.812  1.00  0.00
ATOM   1560  CB  PHE   229      13.378  66.307  76.970  1.00  0.00
ATOM   1561  CG  PHE   229      14.436  65.988  75.873  1.00  0.00
ATOM   1562  CD1 PHE   229      15.771  66.387  76.004  1.00  0.00
ATOM   1563  CD2 PHE   229      14.036  65.413  74.674  1.00  0.00
ATOM   1564  CE1 PHE   229      16.681  66.236  74.974  1.00  0.00
ATOM   1565  CE2 PHE   229      14.952  65.264  73.649  1.00  0.00
ATOM   1566  CZ  PHE   229      16.262  65.676  73.793  1.00  0.00
ATOM   1567  N   MET   230      12.620  68.253  74.696  1.00  0.00
ATOM   1568  CA  MET   230      12.838  69.001  73.475  1.00  0.00
ATOM   1569  C   MET   230      12.831  70.533  73.802  1.00  0.00
ATOM   1570  O   MET   230      13.555  71.235  73.095  1.00  0.00
ATOM   1571  CB  MET   230      11.828  68.569  72.387  1.00  0.00
ATOM   1572  CG  MET   230      12.200  67.164  71.857  1.00  0.00
ATOM   1573  SD  MET   230      11.140  66.758  70.490  1.00  0.00
ATOM   1574  CE  MET   230       9.503  66.824  71.244  1.00  0.00
ATOM   1575  N   HIS   231      11.767  71.064  74.434  1.00  0.00
ATOM   1576  CA  HIS   231      11.652  72.444  74.895  1.00  0.00
ATOM   1577  C   HIS   231      12.946  72.867  75.663  1.00  0.00
ATOM   1578  O   HIS   231      13.442  73.958  75.358  1.00  0.00
ATOM   1579  CB  HIS   231      10.351  72.554  75.708  1.00  0.00
ATOM   1580  CG  HIS   231      10.158  73.905  76.331  1.00  0.00
ATOM   1581  ND1 HIS   231       8.969  74.168  76.971  1.00  0.00
ATOM   1582  CD2 HIS   231      10.915  75.081  76.288  1.00  0.00
ATOM   1583  CE1 HIS   231       9.079  75.450  77.410  1.00  0.00
ATOM   1584  NE2 HIS   231      10.212  76.004  76.995  1.00  0.00
ATOM   1585  N   THR   232      13.359  72.197  76.768  1.00  0.00
ATOM   1586  CA  THR   232      14.601  72.508  77.494  1.00  0.00
ATOM   1587  C   THR   232      15.858  72.470  76.541  1.00  0.00
ATOM   1588  O   THR   232      16.740  73.285  76.770  1.00  0.00
ATOM   1589  CB  THR   232      14.581  71.665  78.817  1.00  0.00
ATOM   1590  OG1 THR   232      14.535  70.241  78.595  1.00  0.00
ATOM   1591  CG2 THR   232      13.349  72.071  79.702  1.00  0.00
ATOM   1592  N   MET   233      16.007  71.489  75.657  1.00  0.00
ATOM   1593  CA  MET   233      17.068  71.371  74.637  1.00  0.00
ATOM   1594  C   MET   233      17.105  72.661  73.746  1.00  0.00
ATOM   1595  O   MET   233      18.226  73.119  73.505  1.00  0.00
ATOM   1596  CB  MET   233      16.697  70.088  73.814  1.00  0.00
ATOM   1597  CG  MET   233      17.912  69.802  72.852  1.00  0.00
ATOM   1598  SD  MET   233      17.316  70.431  71.235  1.00  0.00
ATOM   1599  CE  MET   233      16.931  68.883  70.382  1.00  0.00
ATOM   1600  N   LYS   234      16.016  73.027  73.046  1.00  0.00
ATOM   1601  CA  LYS   234      15.985  74.282  72.289  1.00  0.00
ATOM   1602  C   LYS   234      16.451  75.487  73.155  1.00  0.00
ATOM   1603  O   LYS   234      17.091  76.387  72.598  1.00  0.00
ATOM   1604  CB  LYS   234      14.589  74.569  71.790  1.00  0.00
ATOM   1605  CG  LYS   234      14.199  74.090  70.441  1.00  0.00
ATOM   1606  CD  LYS   234      14.925  72.907  69.877  1.00  0.00
ATOM   1607  CE  LYS   234      14.536  72.681  68.397  1.00  0.00
ATOM   1608  NZ  LYS   234      15.620  71.893  67.748  1.00  0.00
ATOM   1609  N   ASN   235      15.856  75.660  74.338  1.00  0.00
ATOM   1610  CA  ASN   235      16.128  76.698  75.274  1.00  0.00
ATOM   1611  C   ASN   235      17.607  76.770  75.771  1.00  0.00
ATOM   1612  O   ASN   235      18.019  77.900  76.079  1.00  0.00
ATOM   1613  CB  ASN   235      15.221  76.498  76.498  1.00  0.00
ATOM   1614  CG  ASN   235      15.430  77.410  77.710  1.00  0.00
ATOM   1615  OD1 ASN   235      16.572  77.524  78.226  1.00  0.00
ATOM   1616  ND2 ASN   235      14.365  78.000  78.244  1.00  0.00
ATOM   1617  N   THR   236      18.456  75.726  75.626  1.00  0.00
ATOM   1618  CA  THR   236      19.848  75.888  76.100  1.00  0.00
ATOM   1619  C   THR   236      20.558  77.076  75.347  1.00  0.00
ATOM   1620  O   THR   236      21.111  77.935  76.052  1.00  0.00
ATOM   1621  CB  THR   236      20.664  74.553  76.124  1.00  0.00
ATOM   1622  OG1 THR   236      21.653  74.409  75.057  1.00  0.00
ATOM   1623  CG2 THR   236      19.815  73.257  75.974  1.00  0.00
ATOM   1624  N   GLY   237      20.680  77.069  74.001  1.00  0.00
ATOM   1625  CA  GLY   237      21.311  78.122  73.173  1.00  0.00
ATOM   1626  C   GLY   237      20.569  79.495  73.179  1.00  0.00
ATOM   1627  O   GLY   237      21.295  80.494  73.098  1.00  0.00
ATOM   1628  N   ARG   238      19.296  79.491  72.780  1.00  0.00
ATOM   1629  CA  ARG   238      18.433  80.656  72.753  1.00  0.00
ATOM   1630  C   ARG   238      16.941  80.218  72.856  1.00  0.00
ATOM   1631  O   ARG   238      16.282  80.474  73.875  1.00  0.00
ATOM   1632  CB  ARG   238      18.797  81.399  71.460  1.00  0.00
ATOM   1633  CG  ARG   238      18.462  80.653  70.190  1.00  0.00
ATOM   1634  CD  ARG   238      18.889  81.613  69.057  1.00  0.00
ATOM   1635  NE  ARG   238      18.369  80.889  67.897  1.00  0.00
ATOM   1636  CZ  ARG   238      18.285  81.473  66.660  1.00  0.00
ATOM   1637  NH1 ARG   238      18.554  82.776  66.457  1.00  0.00
ATOM   1638  NH2 ARG   238      17.994  80.574  65.653  1.00  0.00
ATOM   1639  OXT ARG   238      16.523  79.471  71.984  1.00  0.00
TER
END
