
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   20 , name T0386_D2.pdb
# PARAMETERS: T0386TS351_3-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         3.82     3.82
  LCS_AVERAGE:     24.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       222 - 237         1.44     4.91
  LCS_AVERAGE:     17.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       222 - 234         0.88     5.03
  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    5    5    5    7   10   11   11   16   17   20   20   20   20   20   20   20   20 
LCS_GDT     P     220     P     220      3    4   20     0    3    4    5    5    5    7   10   11   13   16   19   20   20   20   20   20   20   20   20 
LCS_GDT     E     221     E     221      3   14   20     3    3    4    5    5    5    7   12   17   17   18   19   20   20   20   20   20   20   20   20 
LCS_GDT     K     222     K     222     13   16   20     8   10   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     8   10   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     8   10   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     8   10   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     8   10   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     8   10   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     8   10   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     8   10   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     8   10   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     8   10   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   10   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      5   16   20     3    4    4   10   12   16   16   16   17   17   18   19   20   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   20   20   20   20   20   20   20   20 
LCS_GDT     G     237     G     237      5   16   20     3    4    9   15   15   16   16   16   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    5    9   12   12   14   16   18   19   20   20   20   20   20   20   20   20 
LCS_AVERAGE  LCS_A:  17.98  (  11.91   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      8     10     13     15     15     16     16     16     17     17     18     19     20     20     20     20     20     20     20     20 
GDT PERCENT_CA   9.88  12.35  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   0.41   0.88   1.22   1.22   1.44   1.44   1.44   2.07   2.07   2.58   3.33   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82
GDT RMS_ALL_CA   5.14   5.13   5.03   4.87   4.87   4.91   4.91   4.91   4.61   4.61   4.52   4.06   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         13.715
LGA    P     220      P     220         11.872
LGA    E     221      E     221          7.061
LGA    K     222      K     222          1.207
LGA    I     223      I     223          1.092
LGA    R     224      R     224          1.488
LGA    L     225      L     225          1.349
LGA    L     226      L     226          0.535
LGA    K     227      K     227          0.804
LGA    E     228      E     228          1.287
LGA    F     229      F     229          1.254
LGA    M     230      M     230          1.322
LGA    H     231      H     231          1.135
LGA    T     232      T     232          0.468
LGA    M     233      M     233          1.234
LGA    K     234      K     234          1.532
LGA    N     235      N     235          3.079
LGA    T     236      T     236          1.632
LGA    G     237      G     237          1.786
LGA    R     238      R     238          8.335

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20   81    4.0     16    1.44    18.827    19.070     1.037

LGA_LOCAL      RMSD =  1.443  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.908  Number of atoms =   20 
Std_ALL_ATOMS  RMSD =  3.825  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.983054 * X  +  -0.118935 * Y  +   0.139497 * Z  +  11.945069
  Y_new =  -0.182263 * X  +   0.715599 * Y  +  -0.674313 * Z  +  18.412609
  Z_new =  -0.019625 * X  +  -0.688311 * Y  +  -0.725150 * Z  + 114.325737 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.382252    0.759341  [ DEG:  -136.4930     43.5070 ]
  Theta =   0.019626    3.121967  [ DEG:     1.1245    178.8755 ]
  Phi   =  -2.958270    0.183323  [ DEG:  -169.4964     10.5036 ]
 
# 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_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS351_3-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   1.44  19.070     3.82
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS351_3-D2
PFRMAT TS
TARGET T0386
MODEL  3  REFINED
PARENT 2G03_A
ATOM   1470  N   ASN   219      15.171  57.748  82.750  1.00  0.00
ATOM   1471  CA  ASN   219      14.356  56.705  81.942  1.00  0.00
ATOM   1472  C   ASN   219      13.636  57.134  80.550  1.00  0.00
ATOM   1473  O   ASN   219      13.340  58.329  80.448  1.00  0.00
ATOM   1474  CB  ASN   219      13.302  56.188  82.927  1.00  0.00
ATOM   1475  CG  ASN   219      13.839  55.173  83.954  1.00  0.00
ATOM   1476  OD1 ASN   219      14.094  53.996  83.657  1.00  0.00
ATOM   1477  ND2 ASN   219      14.076  55.672  85.158  1.00  0.00
ATOM   1478  N   PRO   220      13.331  56.274  79.464  1.00  0.00
ATOM   1479  CA  PRO   220      12.857  56.745  78.097  1.00  0.00
ATOM   1480  C   PRO   220      11.382  57.176  77.591  1.00  0.00
ATOM   1481  O   PRO   220      11.125  58.374  77.585  1.00  0.00
ATOM   1482  CB  PRO   220      13.366  55.667  77.109  1.00  0.00
ATOM   1483  CG  PRO   220      13.127  54.368  78.020  1.00  0.00
ATOM   1484  CD  PRO   220      13.122  54.834  79.444  1.00  0.00
ATOM   1485  N   GLU   221      10.466  56.287  77.006  1.00  0.00
ATOM   1486  CA  GLU   221       9.133  56.515  76.296  1.00  0.00
ATOM   1487  C   GLU   221       8.198  57.660  76.774  1.00  0.00
ATOM   1488  O   GLU   221       7.467  58.148  75.908  1.00  0.00
ATOM   1489  CB  GLU   221       8.346  55.194  76.423  1.00  0.00
ATOM   1490  CG  GLU   221       9.228  53.941  76.345  1.00  0.00
ATOM   1491  CD  GLU   221       8.773  52.532  76.177  1.00  0.00
ATOM   1492  OE1 GLU   221       9.567  51.588  76.223  1.00  0.00
ATOM   1493  OE2 GLU   221       7.539  52.397  75.985  1.00  0.00
ATOM   1494  N   LYS   222       8.097  58.040  78.038  1.00  0.00
ATOM   1495  CA  LYS   222       7.105  59.067  78.416  1.00  0.00
ATOM   1496  C   LYS   222       7.115  60.337  77.490  1.00  0.00
ATOM   1497  O   LYS   222       8.153  60.951  77.206  1.00  0.00
ATOM   1498  CB  LYS   222       7.373  59.499  79.864  1.00  0.00
ATOM   1499  CG  LYS   222       6.321  60.495  80.403  1.00  0.00
ATOM   1500  CD  LYS   222       4.956  59.850  80.660  1.00  0.00
ATOM   1501  CE  LYS   222       3.939  60.831  81.247  1.00  0.00
ATOM   1502  NZ  LYS   222       2.588  60.264  81.355  1.00  0.00
ATOM   1503  N   ILE   223       5.876  60.653  77.039  1.00  0.00
ATOM   1504  CA  ILE   223       5.517  61.786  76.177  1.00  0.00
ATOM   1505  C   ILE   223       5.945  63.126  76.857  1.00  0.00
ATOM   1506  O   ILE   223       6.462  63.968  76.114  1.00  0.00
ATOM   1507  CB  ILE   223       3.997  61.738  75.875  1.00  0.00
ATOM   1508  CG1 ILE   223       3.514  60.388  75.359  1.00  0.00
ATOM   1509  CG2 ILE   223       3.616  62.880  74.911  1.00  0.00
ATOM   1510  CD1 ILE   223       4.379  59.740  74.273  1.00  0.00
ATOM   1511  N   ARG   224       5.480  63.483  78.086  1.00  0.00
ATOM   1512  CA  ARG   224       5.929  64.693  78.811  1.00  0.00
ATOM   1513  C   ARG   224       7.494  64.729  78.873  1.00  0.00
ATOM   1514  O   ARG   224       8.026  65.784  78.597  1.00  0.00
ATOM   1515  CB  ARG   224       5.252  64.675  80.184  1.00  0.00
ATOM   1516  CG  ARG   224       5.000  66.073  80.687  1.00  0.00
ATOM   1517  CD  ARG   224       4.146  66.039  81.897  1.00  0.00
ATOM   1518  NE  ARG   224       2.703  65.981  81.622  1.00  0.00
ATOM   1519  CZ  ARG   224       1.882  66.050  82.704  1.00  0.00
ATOM   1520  NH1 ARG   224       2.325  66.184  83.957  1.00  0.00
ATOM   1521  NH2 ARG   224       0.563  65.971  82.521  1.00  0.00
ATOM   1522  N   LEU   225       8.182  63.736  79.459  1.00  0.00
ATOM   1523  CA  LEU   225       9.633  63.626  79.482  1.00  0.00
ATOM   1524  C   LEU   225      10.271  64.023  78.094  1.00  0.00
ATOM   1525  O   LEU   225      11.387  64.512  78.149  1.00  0.00
ATOM   1526  CB  LEU   225       9.952  62.173  79.832  1.00  0.00
ATOM   1527  CG  LEU   225       9.760  61.653  81.248  1.00  0.00
ATOM   1528  CD1 LEU   225      10.371  60.253  81.382  1.00  0.00
ATOM   1529  CD2 LEU   225      10.417  62.573  82.281  1.00  0.00
ATOM   1530  N   LEU   226       9.820  63.477  76.941  1.00  0.00
ATOM   1531  CA  LEU   226      10.328  63.746  75.590  1.00  0.00
ATOM   1532  C   LEU   226       9.972  65.186  75.110  1.00  0.00
ATOM   1533  O   LEU   226      10.843  65.765  74.481  1.00  0.00
ATOM   1534  CB  LEU   226       9.773  62.717  74.613  1.00  0.00
ATOM   1535  CG  LEU   226      10.243  61.302  74.677  1.00  0.00
ATOM   1536  CD1 LEU   226       9.498  60.471  73.639  1.00  0.00
ATOM   1537  CD2 LEU   226      11.690  61.245  74.286  1.00  0.00
ATOM   1538  N   LYS   227       8.670  65.596  75.026  1.00  0.00
ATOM   1539  CA  LYS   227       8.235  66.954  74.663  1.00  0.00
ATOM   1540  C   LYS   227       8.912  68.016  75.574  1.00  0.00
ATOM   1541  O   LYS   227       9.343  69.007  75.001  1.00  0.00
ATOM   1542  CB  LYS   227       6.710  67.059  74.746  1.00  0.00
ATOM   1543  CG  LYS   227       5.910  66.231  73.791  1.00  0.00
ATOM   1544  CD  LYS   227       4.411  66.490  73.930  1.00  0.00
ATOM   1545  CE  LYS   227       3.986  67.872  73.505  1.00  0.00
ATOM   1546  NZ  LYS   227       4.238  68.077  72.040  1.00  0.00
ATOM   1547  N   GLU   228       8.735  68.012  76.933  1.00  0.00
ATOM   1548  CA  GLU   228       9.451  68.943  77.835  1.00  0.00
ATOM   1549  C   GLU   228      10.985  68.944  77.463  1.00  0.00
ATOM   1550  O   GLU   228      11.537  70.019  77.455  1.00  0.00
ATOM   1551  CB  GLU   228       9.320  68.618  79.300  1.00  0.00
ATOM   1552  CG  GLU   228       7.999  68.612  79.966  1.00  0.00
ATOM   1553  CD  GLU   228       7.315  69.852  79.648  1.00  0.00
ATOM   1554  OE1 GLU   228       6.362  69.968  78.862  1.00  0.00
ATOM   1555  OE2 GLU   228       7.949  70.876  80.289  1.00  0.00
ATOM   1556  N   PHE   229      11.652  67.778  77.360  1.00  0.00
ATOM   1557  CA  PHE   229      13.059  67.507  76.931  1.00  0.00
ATOM   1558  C   PHE   229      13.482  68.351  75.693  1.00  0.00
ATOM   1559  O   PHE   229      14.584  68.872  75.674  1.00  0.00
ATOM   1560  CB  PHE   229      13.119  65.956  76.672  1.00  0.00
ATOM   1561  CG  PHE   229      14.317  65.530  75.827  1.00  0.00
ATOM   1562  CD1 PHE   229      15.616  65.618  76.319  1.00  0.00
ATOM   1563  CD2 PHE   229      14.115  65.126  74.522  1.00  0.00
ATOM   1564  CE1 PHE   229      16.693  65.316  75.507  1.00  0.00
ATOM   1565  CE2 PHE   229      15.199  64.832  73.723  1.00  0.00
ATOM   1566  CZ  PHE   229      16.483  64.926  74.206  1.00  0.00
ATOM   1567  N   MET   230      12.680  68.239  74.588  1.00  0.00
ATOM   1568  CA  MET   230      12.816  69.002  73.353  1.00  0.00
ATOM   1569  C   MET   230      12.692  70.528  73.731  1.00  0.00
ATOM   1570  O   MET   230      13.400  71.303  73.082  1.00  0.00
ATOM   1571  CB  MET   230      11.762  68.479  72.366  1.00  0.00
ATOM   1572  CG  MET   230      12.200  67.113  71.795  1.00  0.00
ATOM   1573  SD  MET   230      11.094  66.625  70.492  1.00  0.00
ATOM   1574  CE  MET   230       9.501  66.593  71.338  1.00  0.00
ATOM   1575  N   HIS   231      11.668  70.985  74.505  1.00  0.00
ATOM   1576  CA  HIS   231      11.565  72.366  74.966  1.00  0.00
ATOM   1577  C   HIS   231      12.863  72.825  75.741  1.00  0.00
ATOM   1578  O   HIS   231      13.341  73.900  75.390  1.00  0.00
ATOM   1579  CB  HIS   231      10.281  72.470  75.798  1.00  0.00
ATOM   1580  CG  HIS   231       9.914  73.870  76.182  1.00  0.00
ATOM   1581  ND1 HIS   231      10.465  74.622  77.155  1.00  0.00
ATOM   1582  CD2 HIS   231       8.902  74.595  75.577  1.00  0.00
ATOM   1583  CE1 HIS   231       9.819  75.765  77.158  1.00  0.00
ATOM   1584  NE2 HIS   231       8.885  75.739  76.210  1.00  0.00
ATOM   1585  N   THR   232      13.295  72.179  76.854  1.00  0.00
ATOM   1586  CA  THR   232      14.556  72.515  77.574  1.00  0.00
ATOM   1587  C   THR   232      15.789  72.551  76.633  1.00  0.00
ATOM   1588  O   THR   232      16.585  73.446  76.815  1.00  0.00
ATOM   1589  CB  THR   232      14.759  71.752  78.915  1.00  0.00
ATOM   1590  OG1 THR   232      16.074  71.413  79.390  1.00  0.00
ATOM   1591  CG2 THR   232      13.697  70.731  79.231  1.00  0.00
ATOM   1592  N   MET   233      16.101  71.453  75.877  1.00  0.00
ATOM   1593  CA  MET   233      17.132  71.445  74.825  1.00  0.00
ATOM   1594  C   MET   233      17.112  72.689  73.976  1.00  0.00
ATOM   1595  O   MET   233      18.203  73.103  73.579  1.00  0.00
ATOM   1596  CB  MET   233      16.802  70.268  73.916  1.00  0.00
ATOM   1597  CG  MET   233      17.389  68.912  74.451  1.00  0.00
ATOM   1598  SD  MET   233      16.988  67.618  73.248  1.00  0.00
ATOM   1599  CE  MET   233      18.328  67.629  72.023  1.00  0.00
ATOM   1600  N   LYS   234      15.985  73.092  73.332  1.00  0.00
ATOM   1601  CA  LYS   234      15.867  74.327  72.578  1.00  0.00
ATOM   1602  C   LYS   234      16.398  75.542  73.374  1.00  0.00
ATOM   1603  O   LYS   234      17.046  76.387  72.751  1.00  0.00
ATOM   1604  CB  LYS   234      14.440  74.562  72.185  1.00  0.00
ATOM   1605  CG  LYS   234      13.943  74.079  70.880  1.00  0.00
ATOM   1606  CD  LYS   234      14.637  72.899  70.271  1.00  0.00
ATOM   1607  CE  LYS   234      14.132  72.651  68.831  1.00  0.00
ATOM   1608  NZ  LYS   234      15.171  71.873  68.101  1.00  0.00
ATOM   1609  N   ASN   235      15.764  75.767  74.553  1.00  0.00
ATOM   1610  CA  ASN   235      16.147  76.802  75.452  1.00  0.00
ATOM   1611  C   ASN   235      17.697  76.910  75.722  1.00  0.00
ATOM   1612  O   ASN   235      18.137  78.041  75.976  1.00  0.00
ATOM   1613  CB  ASN   235      15.386  76.548  76.775  1.00  0.00
ATOM   1614  CG  ASN   235      15.763  77.464  77.967  1.00  0.00
ATOM   1615  OD1 ASN   235      16.962  77.602  78.327  1.00  0.00
ATOM   1616  ND2 ASN   235      14.766  78.021  78.646  1.00  0.00
ATOM   1617  N   THR   236      18.461  75.786  75.870  1.00  0.00
ATOM   1618  CA  THR   236      19.900  75.833  76.116  1.00  0.00
ATOM   1619  C   THR   236      20.612  76.917  75.221  1.00  0.00
ATOM   1620  O   THR   236      21.169  77.858  75.808  1.00  0.00
ATOM   1621  CB  THR   236      20.566  74.444  76.070  1.00  0.00
ATOM   1622  OG1 THR   236      21.331  74.130  74.853  1.00  0.00
ATOM   1623  CG2 THR   236      19.600  73.217  76.165  1.00  0.00
ATOM   1624  N   GLY   237      20.477  76.854  73.873  1.00  0.00
ATOM   1625  CA  GLY   237      21.029  77.796  72.889  1.00  0.00
ATOM   1626  C   GLY   237      20.379  79.197  72.981  1.00  0.00
ATOM   1627  O   GLY   237      21.102  80.177  72.778  1.00  0.00
ATOM   1628  N   ARG   238      19.046  79.281  72.844  1.00  0.00
ATOM   1629  CA  ARG   238      18.235  80.479  72.960  1.00  0.00
ATOM   1630  C   ARG   238      17.344  80.398  74.217  1.00  0.00
ATOM   1631  O   ARG   238      17.580  81.072  75.203  1.00  0.00
ATOM   1632  CB  ARG   238      17.384  80.517  71.741  1.00  0.00
ATOM   1633  CG  ARG   238      17.883  81.000  70.430  1.00  0.00
ATOM   1634  CD  ARG   238      18.064  82.446  70.070  1.00  0.00
ATOM   1635  NE  ARG   238      18.981  82.456  68.868  1.00  0.00
ATOM   1636  CZ  ARG   238      19.310  83.587  68.205  1.00  0.00
ATOM   1637  NH1 ARG   238      18.763  84.722  68.668  1.00  0.00
ATOM   1638  NH2 ARG   238      20.123  83.619  67.138  1.00  0.00
ATOM   1639  OXT ARG   238      16.311  79.656  74.149  1.00  0.00
TER
END
