
#######################################################
#                                                     #
#                        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 T0386TS351_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   20 , name T0386_D2.pdb
# PARAMETERS: T0386TS351_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         3.80     3.80
  LCS_AVERAGE:     24.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       222 - 237         1.47     4.88
  LCS_AVERAGE:     17.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       222 - 234         0.88     5.02
  LCS_AVERAGE:     11.67

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    5    5    7    7    9   11   11   14   17   20   20   20   20   20   20   20   20 
LCS_GDT     P     220     P     220      3    4   20     0    3    3    5    5    7    7    9   11   14   17   19   20   20   20   20   20   20   20   20 
LCS_GDT     E     221     E     221      3   14   20     3    3    3    5    5    7   10   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     K     222     K     222     13   16   20     7   10   13   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     I     223     I     223     13   16   20     7   10   13   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     R     224     R     224     13   16   20     7   10   13   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     L     225     L     225     13   16   20     7   10   13   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     L     226     L     226     13   16   20     7   10   13   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     K     227     K     227     13   16   20     7   10   13   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     E     228     E     228     13   16   20     7   10   13   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     F     229     F     229     13   16   20     7   10   13   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     M     230     M     230     13   16   20     7   10   13   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     H     231     H     231     13   16   20     7   10   13   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     T     232     T     232     13   16   20     4   10   13   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     M     233     M     233     13   16   20     4    8   13   15   15   16   16   17   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   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     N     235     N     235      4   16   20     3    3    4    7   12   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     T     236     T     236      4   16   20     3    7   10   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     G     237     G     237      3   16   20     3    3    5   15   15   16   16   17   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     R     238     R     238      3    3   20     3    3    3    5    6    9   12   13   15   17   18   19   20   20   20   20   20   20   20   20 
LCS_AVERAGE  LCS_A:  17.90  (  11.67   17.35   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     10     13     15     15     16     16     17     17     17     18     19     20     20     20     20     20     20     20     20 
GDT PERCENT_CA   8.64  12.35  16.05  18.52  18.52  19.75  19.75  20.99  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    0.27   0.44   0.88   1.23   1.23   1.47   1.47   2.07   2.07   2.07   2.56   3.30   3.80   3.80   3.80   3.80   3.80   3.80   3.80   3.80
GDT RMS_ALL_CA   5.05   5.06   5.02   4.84   4.84   4.88   4.88   4.59   4.59   4.59   4.50   4.04   3.80   3.80   3.80   3.80   3.80   3.80   3.80   3.80

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         10.895
LGA    P     220      P     220          8.432
LGA    E     221      E     221          3.978
LGA    K     222      K     222          3.075
LGA    I     223      I     223          3.390
LGA    R     224      R     224          2.565
LGA    L     225      L     225          1.187
LGA    L     226      L     226          1.873
LGA    K     227      K     227          1.573
LGA    E     228      E     228          1.613
LGA    F     229      F     229          1.191
LGA    M     230      M     230          1.303
LGA    H     231      H     231          1.270
LGA    T     232      T     232          0.803
LGA    M     233      M     233          2.622
LGA    K     234      K     234          2.721
LGA    N     235      N     235          3.819
LGA    T     236      T     236          3.210
LGA    G     237      G     237          2.356
LGA    R     238      R     238          5.704

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20   81    4.0     17    2.07    19.136    19.135     0.785

LGA_LOCAL      RMSD =  2.066  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.036  Number of atoms =   20 
Std_ALL_ATOMS  RMSD =  3.802  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.996007 * X  +   0.013350 * Y  +  -0.088276 * Z  +   1.680102
  Y_new =   0.068763 * X  +   0.745347 * Y  +  -0.663121 * Z  +  18.760355
  Z_new =   0.056944 * X  +  -0.666543 * Y  +  -0.743288 * Z  + 113.601593 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.410576    0.731016  [ DEG:  -138.1159     41.8841 ]
  Theta =  -0.056974   -3.084618  [ DEG:    -3.2644   -176.7356 ]
  Phi   =   3.072664   -0.068929  [ DEG:   176.0507     -3.9493 ]
 
# 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: T0386TS351_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS351_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   17   2.07  19.135     3.80
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS351_2-D2
PFRMAT TS
TARGET T0386
MODEL  2  REFINED
PARENT 2G03_A
ATOM   1470  N   ASN   219      12.149  56.926  82.532  1.00  0.00
ATOM   1471  CA  ASN   219      11.196  56.238  81.524  1.00  0.00
ATOM   1472  C   ASN   219      10.599  56.869  80.147  1.00  0.00
ATOM   1473  O   ASN   219      10.678  58.102  80.039  1.00  0.00
ATOM   1474  CB  ASN   219       9.987  55.788  82.356  1.00  0.00
ATOM   1475  CG  ASN   219      10.286  54.668  83.335  1.00  0.00
ATOM   1476  OD1 ASN   219       9.886  54.707  84.479  1.00  0.00
ATOM   1477  ND2 ASN   219      11.033  53.692  82.886  1.00  0.00
ATOM   1478  N   PRO   220       9.770  56.179  79.170  1.00  0.00
ATOM   1479  CA  PRO   220       9.273  56.639  77.832  1.00  0.00
ATOM   1480  C   PRO   220       7.976  57.516  77.361  1.00  0.00
ATOM   1481  O   PRO   220       8.161  58.720  77.268  1.00  0.00
ATOM   1482  CB  PRO   220       9.249  55.396  76.985  1.00  0.00
ATOM   1483  CG  PRO   220       8.719  54.336  78.072  1.00  0.00
ATOM   1484  CD  PRO   220       9.070  54.925  79.405  1.00  0.00
ATOM   1485  N   GLU   221       6.737  56.970  76.990  1.00  0.00
ATOM   1486  CA  GLU   221       5.533  57.586  76.366  1.00  0.00
ATOM   1487  C   GLU   221       4.884  58.898  76.939  1.00  0.00
ATOM   1488  O   GLU   221       4.026  59.449  76.203  1.00  0.00
ATOM   1489  CB  GLU   221       4.474  56.437  76.260  1.00  0.00
ATOM   1490  CG  GLU   221       4.671  55.469  75.051  1.00  0.00
ATOM   1491  CD  GLU   221       4.566  56.097  73.697  1.00  0.00
ATOM   1492  OE1 GLU   221       3.551  56.170  73.002  1.00  0.00
ATOM   1493  OE2 GLU   221       5.658  56.637  73.381  1.00  0.00
ATOM   1494  N   LYS   222       5.163  59.390  78.091  1.00  0.00
ATOM   1495  CA  LYS   222       4.386  60.584  78.548  1.00  0.00
ATOM   1496  C   LYS   222       4.585  61.856  77.647  1.00  0.00
ATOM   1497  O   LYS   222       5.710  62.203  77.260  1.00  0.00
ATOM   1498  CB  LYS   222       4.749  60.897  80.001  1.00  0.00
ATOM   1499  CG  LYS   222       3.918  62.051  80.593  1.00  0.00
ATOM   1500  CD  LYS   222       2.459  61.660  80.849  1.00  0.00
ATOM   1501  CE  LYS   222       1.650  62.788  81.496  1.00  0.00
ATOM   1502  NZ  LYS   222       0.219  62.480  81.607  1.00  0.00
ATOM   1503  N   ILE   223       3.450  62.416  77.183  1.00  0.00
ATOM   1504  CA  ILE   223       3.442  63.667  76.399  1.00  0.00
ATOM   1505  C   ILE   223       4.225  64.797  77.180  1.00  0.00
ATOM   1506  O   ILE   223       4.911  65.567  76.521  1.00  0.00
ATOM   1507  CB  ILE   223       1.983  64.042  75.971  1.00  0.00
ATOM   1508  CG1 ILE   223       1.150  64.488  77.173  1.00  0.00
ATOM   1509  CG2 ILE   223       1.374  62.919  75.065  1.00  0.00
ATOM   1510  CD1 ILE   223      -0.395  64.475  77.139  1.00  0.00
ATOM   1511  N   ARG   224       4.001  65.036  78.495  1.00  0.00
ATOM   1512  CA  ARG   224       4.729  65.995  79.359  1.00  0.00
ATOM   1513  C   ARG   224       6.274  65.719  79.257  1.00  0.00
ATOM   1514  O   ARG   224       6.980  66.686  78.992  1.00  0.00
ATOM   1515  CB  ARG   224       4.108  65.852  80.774  1.00  0.00
ATOM   1516  CG  ARG   224       2.626  66.293  80.840  1.00  0.00
ATOM   1517  CD  ARG   224       2.322  67.590  80.219  1.00  0.00
ATOM   1518  NE  ARG   224       3.167  68.614  80.878  1.00  0.00
ATOM   1519  CZ  ARG   224       3.416  69.816  80.412  1.00  0.00
ATOM   1520  NH1 ARG   224       2.946  70.332  79.291  1.00  0.00
ATOM   1521  NH2 ARG   224       4.183  70.646  81.167  1.00  0.00
ATOM   1522  N   LEU   225       6.775  64.496  79.485  1.00  0.00
ATOM   1523  CA  LEU   225       8.182  64.108  79.354  1.00  0.00
ATOM   1524  C   LEU   225       8.785  64.527  77.955  1.00  0.00
ATOM   1525  O   LEU   225       9.832  65.160  77.972  1.00  0.00
ATOM   1526  CB  LEU   225       8.186  62.582  79.514  1.00  0.00
ATOM   1527  CG  LEU   225       7.995  61.940  80.879  1.00  0.00
ATOM   1528  CD1 LEU   225       8.294  60.438  80.803  1.00  0.00
ATOM   1529  CD2 LEU   225       8.905  62.567  81.939  1.00  0.00
ATOM   1530  N   LEU   226       8.223  64.040  76.835  1.00  0.00
ATOM   1531  CA  LEU   226       8.611  64.329  75.492  1.00  0.00
ATOM   1532  C   LEU   226       8.611  65.863  75.189  1.00  0.00
ATOM   1533  O   LEU   226       9.623  66.314  74.664  1.00  0.00
ATOM   1534  CB  LEU   226       7.620  63.597  74.600  1.00  0.00
ATOM   1535  CG  LEU   226       7.656  62.120  74.455  1.00  0.00
ATOM   1536  CD1 LEU   226       6.547  61.653  73.521  1.00  0.00
ATOM   1537  CD2 LEU   226       8.941  61.693  73.810  1.00  0.00
ATOM   1538  N   LYS   227       7.479  66.593  75.302  1.00  0.00
ATOM   1539  CA  LYS   227       7.415  68.059  75.028  1.00  0.00
ATOM   1540  C   LYS   227       8.369  68.869  75.947  1.00  0.00
ATOM   1541  O   LYS   227       8.966  69.809  75.402  1.00  0.00
ATOM   1542  CB  LYS   227       5.963  68.513  75.180  1.00  0.00
ATOM   1543  CG  LYS   227       4.947  67.980  74.233  1.00  0.00
ATOM   1544  CD  LYS   227       3.567  68.595  74.457  1.00  0.00
ATOM   1545  CE  LYS   227       3.486  70.059  74.114  1.00  0.00
ATOM   1546  NZ  LYS   227       3.729  70.276  72.649  1.00  0.00
ATOM   1547  N   GLU   228       8.188  68.837  77.295  1.00  0.00
ATOM   1548  CA  GLU   228       9.120  69.583  78.180  1.00  0.00
ATOM   1549  C   GLU   228      10.579  69.237  77.749  1.00  0.00
ATOM   1550  O   GLU   228      11.402  70.154  77.860  1.00  0.00
ATOM   1551  CB  GLU   228       8.964  69.260  79.643  1.00  0.00
ATOM   1552  CG  GLU   228       7.690  69.517  80.352  1.00  0.00
ATOM   1553  CD  GLU   228       7.273  70.880  80.081  1.00  0.00
ATOM   1554  OE1 GLU   228       6.345  71.215  79.329  1.00  0.00
ATOM   1555  OE2 GLU   228       8.125  71.731  80.724  1.00  0.00
ATOM   1556  N   PHE   229      10.961  67.930  77.732  1.00  0.00
ATOM   1557  CA  PHE   229      12.286  67.497  77.249  1.00  0.00
ATOM   1558  C   PHE   229      12.722  68.174  75.942  1.00  0.00
ATOM   1559  O   PHE   229      13.931  68.411  75.842  1.00  0.00
ATOM   1560  CB  PHE   229      12.192  65.999  76.952  1.00  0.00
ATOM   1561  CG  PHE   229      13.024  65.471  75.747  1.00  0.00
ATOM   1562  CD1 PHE   229      14.416  65.387  75.789  1.00  0.00
ATOM   1563  CD2 PHE   229      12.379  65.223  74.529  1.00  0.00
ATOM   1564  CE1 PHE   229      15.126  65.071  74.644  1.00  0.00
ATOM   1565  CE2 PHE   229      13.100  64.909  73.392  1.00  0.00
ATOM   1566  CZ  PHE   229      14.468  64.841  73.454  1.00  0.00
ATOM   1567  N   MET   230      11.955  68.055  74.815  1.00  0.00
ATOM   1568  CA  MET   230      12.258  68.751  73.578  1.00  0.00
ATOM   1569  C   MET   230      12.615  70.229  73.875  1.00  0.00
ATOM   1570  O   MET   230      13.528  70.703  73.208  1.00  0.00
ATOM   1571  CB  MET   230      11.164  68.542  72.536  1.00  0.00
ATOM   1572  CG  MET   230      11.185  67.089  72.001  1.00  0.00
ATOM   1573  SD  MET   230       9.993  66.916  70.694  1.00  0.00
ATOM   1574  CE  MET   230       8.449  67.326  71.531  1.00  0.00
ATOM   1575  N   HIS   231      11.707  71.028  74.488  1.00  0.00
ATOM   1576  CA  HIS   231      11.967  72.415  74.893  1.00  0.00
ATOM   1577  C   HIS   231      13.320  72.530  75.672  1.00  0.00
ATOM   1578  O   HIS   231      13.932  73.579  75.519  1.00  0.00
ATOM   1579  CB  HIS   231      10.778  72.971  75.679  1.00  0.00
ATOM   1580  CG  HIS   231      10.899  74.425  76.057  1.00  0.00
ATOM   1581  ND1 HIS   231      11.545  75.077  77.049  1.00  0.00
ATOM   1582  CD2 HIS   231      10.205  75.361  75.348  1.00  0.00
ATOM   1583  CE1 HIS   231      11.260  76.352  76.952  1.00  0.00
ATOM   1584  NE2 HIS   231      10.439  76.496  75.953  1.00  0.00
ATOM   1585  N   THR   232      13.569  71.734  76.735  1.00  0.00
ATOM   1586  CA  THR   232      14.846  71.706  77.456  1.00  0.00
ATOM   1587  C   THR   232      16.009  71.460  76.433  1.00  0.00
ATOM   1588  O   THR   232      17.059  72.064  76.665  1.00  0.00
ATOM   1589  CB  THR   232      14.884  70.736  78.678  1.00  0.00
ATOM   1590  OG1 THR   232      15.035  69.379  78.378  1.00  0.00
ATOM   1591  CG2 THR   232      13.889  71.154  79.745  1.00  0.00
ATOM   1592  N   MET   233      15.961  70.410  75.610  1.00  0.00
ATOM   1593  CA  MET   233      16.893  70.100  74.553  1.00  0.00
ATOM   1594  C   MET   233      17.205  71.352  73.681  1.00  0.00
ATOM   1595  O   MET   233      18.397  71.604  73.451  1.00  0.00
ATOM   1596  CB  MET   233      16.264  68.900  73.776  1.00  0.00
ATOM   1597  CG  MET   233      17.349  68.388  72.756  1.00  0.00
ATOM   1598  SD  MET   233      16.839  69.131  71.159  1.00  0.00
ATOM   1599  CE  MET   233      16.111  67.699  70.326  1.00  0.00
ATOM   1600  N   LYS   234      16.194  72.006  73.065  1.00  0.00
ATOM   1601  CA  LYS   234      16.399  73.236  72.317  1.00  0.00
ATOM   1602  C   LYS   234      17.164  74.267  73.195  1.00  0.00
ATOM   1603  O   LYS   234      18.037  74.941  72.643  1.00  0.00
ATOM   1604  CB  LYS   234      15.040  73.794  71.939  1.00  0.00
ATOM   1605  CG  LYS   234      14.477  73.456  70.616  1.00  0.00
ATOM   1606  CD  LYS   234      14.908  72.165  69.989  1.00  0.00
ATOM   1607  CE  LYS   234      14.370  72.053  68.544  1.00  0.00
ATOM   1608  NZ  LYS   234      15.223  71.080  67.806  1.00  0.00
ATOM   1609  N   ASN   235      16.643  74.581  74.411  1.00  0.00
ATOM   1610  CA  ASN   235      17.218  75.477  75.399  1.00  0.00
ATOM   1611  C   ASN   235      18.757  75.329  75.567  1.00  0.00
ATOM   1612  O   ASN   235      19.388  76.386  75.617  1.00  0.00
ATOM   1613  CB  ASN   235      16.479  75.254  76.729  1.00  0.00
ATOM   1614  CG  ASN   235      17.043  75.994  77.955  1.00  0.00
ATOM   1615  OD1 ASN   235      18.260  75.912  78.266  1.00  0.00
ATOM   1616  ND2 ASN   235      16.174  76.651  78.717  1.00  0.00
ATOM   1617  N   THR   236      19.321  74.125  75.763  1.00  0.00
ATOM   1618  CA  THR   236      20.781  73.936  75.931  1.00  0.00
ATOM   1619  C   THR   236      21.609  74.713  74.843  1.00  0.00
ATOM   1620  O   THR   236      22.600  75.342  75.247  1.00  0.00
ATOM   1621  CB  THR   236      21.169  72.424  76.016  1.00  0.00
ATOM   1622  OG1 THR   236      21.797  71.840  74.839  1.00  0.00
ATOM   1623  CG2 THR   236      19.992  71.435  76.298  1.00  0.00
ATOM   1624  N   GLY   237      21.425  74.458  73.539  1.00  0.00
ATOM   1625  CA  GLY   237      22.087  75.202  72.463  1.00  0.00
ATOM   1626  C   GLY   237      21.840  76.740  72.541  1.00  0.00
ATOM   1627  O   GLY   237      22.825  77.472  72.442  1.00  0.00
ATOM   1628  N   ARG   238      20.582  77.215  72.495  1.00  0.00
ATOM   1629  CA  ARG   238      20.196  78.633  72.558  1.00  0.00
ATOM   1630  C   ARG   238      18.660  78.715  72.640  1.00  0.00
ATOM   1631  O   ARG   238      18.107  79.214  73.615  1.00  0.00
ATOM   1632  CB  ARG   238      20.761  79.393  71.359  1.00  0.00
ATOM   1633  CG  ARG   238      20.194  78.898  70.017  1.00  0.00
ATOM   1634  CD  ARG   238      20.619  79.817  68.922  1.00  0.00
ATOM   1635  NE  ARG   238      20.103  79.263  67.629  1.00  0.00
ATOM   1636  CZ  ARG   238      20.219  80.069  66.564  1.00  0.00
ATOM   1637  NH1 ARG   238      20.857  81.244  66.446  1.00  0.00
ATOM   1638  NH2 ARG   238      19.520  79.607  65.544  1.00  0.00
ATOM   1639  OXT ARG   238      18.031  77.991  71.836  1.00  0.00
TER
END
