
#######################################################
#                                                     #
#                        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 (  158),  selected   19 , name T0386TS028_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   19 , name T0386_D2.pdb
# PARAMETERS: T0386TS028_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:    19       219 - 237         3.34     3.34
  LCS_AVERAGE:     23.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       222 - 237         1.41     4.15
  LCS_AVERAGE:     18.19

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       222 - 234         0.83     4.22
  LCS_AVERAGE:     12.54

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      4    5   19     4    4    4    5    5    6    7    9   11   14   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     P     220     P     220      4    5   19     4    4    4    5    5    6    7    9   11   13   13   17   19   19   19   19   19   19   19   19 
LCS_GDT     E     221     E     221      4   14   19     4    4    4    5    5    6    7   12   15   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     K     222     K     222     13   16   19     9   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     I     223     I     223     13   16   19     9   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     R     224     R     224     13   16   19     9   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     L     225     L     225     13   16   19     9   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     L     226     L     226     13   16   19     9   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     K     227     K     227     13   16   19     9   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     E     228     E     228     13   16   19     8   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     F     229     F     229     13   16   19     9   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     M     230     M     230     13   16   19     9   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     H     231     H     231     13   16   19     9   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     T     232     T     232     13   16   19     4   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     M     233     M     233     13   16   19     4    9   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     K     234     K     234     13   16   19     4   11   13   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     N     235     N     235      4   16   19     3    3    4   11   12   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     T     236     T     236      4   16   19     3    8   12   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_GDT     G     237     G     237      4   16   19     3    3    6   15   15   16   16   16   16   17   18   18   19   19   19   19   19   19   19   19 
LCS_AVERAGE  LCS_A:  18.06  (  12.54   18.19   23.46 )

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      9     11     13     15     15     16     16     16     16     17     18     18     19     19     19     19     19     19     19     19 
GDT PERCENT_CA  11.11  13.58  16.05  18.52  18.52  19.75  19.75  19.75  19.75  20.99  22.22  22.22  23.46  23.46  23.46  23.46  23.46  23.46  23.46  23.46
GDT RMS_LOCAL    0.34   0.56   0.83   1.18   1.18   1.41   1.41   1.41   1.41   2.07   2.90   2.90   3.34   3.34   3.34   3.34   3.34   3.34   3.34   3.34
GDT RMS_ALL_CA   4.33   4.19   4.22   4.09   4.09   4.15   4.15   4.15   4.15   3.91   3.44   3.44   3.34   3.34   3.34   3.34   3.34   3.34   3.34   3.34

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         10.649
LGA    P     220      P     220         11.408
LGA    E     221      E     221          7.169
LGA    K     222      K     222          1.014
LGA    I     223      I     223          1.155
LGA    R     224      R     224          1.387
LGA    L     225      L     225          1.221
LGA    L     226      L     226          0.572
LGA    K     227      K     227          0.729
LGA    E     228      E     228          1.299
LGA    F     229      F     229          1.109
LGA    M     230      M     230          1.056
LGA    H     231      H     231          1.170
LGA    T     232      T     232          0.577
LGA    M     233      M     233          1.193
LGA    K     234      K     234          1.661
LGA    N     235      N     235          3.104
LGA    T     236      T     236          1.519
LGA    G     237      G     237          1.832

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   81    4.0     16    1.41    18.827    19.125     1.059

LGA_LOCAL      RMSD =  1.411  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.147  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  3.337  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.978797 * X  +  -0.109534 * Y  +   0.173084 * Z  +  11.682364
  Y_new =  -0.200188 * X  +   0.690459 * Y  +  -0.695120 * Z  +  19.579029
  Z_new =  -0.043368 * X  +  -0.715031 * Y  +  -0.697746 * Z  + 116.099808 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.343961    0.797632  [ DEG:  -134.2991     45.7009 ]
  Theta =   0.043382    3.098211  [ DEG:     2.4856    177.5144 ]
  Phi   =  -2.939851    0.201742  [ DEG:  -168.4411     11.5589 ]
 
# 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: T0386TS028_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS028_2-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   16   1.41  19.125     3.34
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS028_2-D2
PFRMAT TS
TARGET T0386
MODEL 2
PARENT 2g03-A
ATOM   1470  N   ASN   219      12.164  55.937  82.277  1.00  9.00
ATOM   1471  CA  ASN   219      10.944  55.930  81.452  1.00  9.00
ATOM   1472  C   ASN   219      11.216  56.609  80.105  1.00  9.00
ATOM   1473  O   ASN   219      10.820  57.767  79.922  1.00  9.00
ATOM   1474  CB  ASN   219       9.850  56.728  82.165  1.00  9.00
ATOM   1475  CG  ASN   219       9.624  56.283  83.612  1.00  9.00
ATOM   1476  OD1 ASN   219       9.830  55.122  83.982  1.00  9.00
ATOM   1477  ND2 ASN   219       9.204  57.240  84.422  1.00  9.00
ATOM   1478  N   PRO   220      11.692  55.856  79.122  1.00  9.00
ATOM   1479  CA  PRO   220      12.341  56.476  77.959  1.00  9.00
ATOM   1480  C   PRO   220      11.364  56.966  76.887  1.00  9.00
ATOM   1481  O   PRO   220      11.705  57.817  76.063  1.00  9.00
ATOM   1482  CB  PRO   220      13.202  55.394  77.387  1.00  9.00
ATOM   1483  CG  PRO   220      12.775  54.062  77.982  1.00  9.00
ATOM   1484  CD  PRO   220      11.815  54.394  79.110  1.00  9.00
ATOM   1485  N   GLU   221      10.131  56.499  76.957  1.00  9.00
ATOM   1486  CA  GLU   221       9.148  56.821  75.926  1.00  9.00
ATOM   1487  C   GLU   221       7.990  57.663  76.450  1.00  9.00
ATOM   1488  O   GLU   221       6.960  57.773  75.775  1.00  9.00
ATOM   1489  CB  GLU   221       8.636  55.514  75.335  1.00  9.00
ATOM   1490  CG  GLU   221       9.743  54.796  74.569  1.00  9.00
ATOM   1491  CD  GLU   221       9.257  53.431  74.099  1.00  9.00
ATOM   1492  OE1 GLU   221       8.646  52.749  74.910  1.00  9.00
ATOM   1493  OE2 GLU   221       9.627  53.040  73.002  1.00  9.00
ATOM   1494  N   LYS   222       8.128  58.202  77.650  1.00  9.00
ATOM   1495  CA  LYS   222       7.046  59.016  78.214  1.00  9.00
ATOM   1496  C   LYS   222       6.938  60.343  77.461  1.00  9.00
ATOM   1497  O   LYS   222       7.906  61.108  77.395  1.00  9.00
ATOM   1498  CB  LYS   222       7.337  59.250  79.692  1.00  9.00
ATOM   1499  CG  LYS   222       6.219  60.023  80.384  1.00  9.00
ATOM   1500  CD  LYS   222       6.539  60.279  81.851  1.00  9.00
ATOM   1501  CE  LYS   222       5.468  61.137  82.508  1.00  9.00
ATOM   1502  NZ  LYS   222       5.830  61.454  83.898  1.00  9.00
ATOM   1503  N   ILE   223       5.723  60.670  77.046  1.00  9.00
ATOM   1504  CA  ILE   223       5.469  61.853  76.210  1.00  9.00
ATOM   1505  C   ILE   223       5.759  63.182  76.906  1.00  9.00
ATOM   1506  O   ILE   223       6.436  64.029  76.308  1.00  9.00
ATOM   1507  CB  ILE   223       3.999  61.819  75.808  1.00  9.00
ATOM   1508  CG1 ILE   223       3.690  60.568  74.995  1.00  9.00
ATOM   1509  CG2 ILE   223       3.612  63.071  75.031  1.00  9.00
ATOM   1510  CD1 ILE   223       2.218  60.520  74.603  1.00  9.00
ATOM   1511  N   ARG   224       5.520  63.247  78.209  1.00  9.00
ATOM   1512  CA  ARG   224       5.812  64.479  78.950  1.00  9.00
ATOM   1513  C   ARG   224       7.307  64.682  79.083  1.00  9.00
ATOM   1514  O   ARG   224       7.796  65.792  78.838  1.00  9.00
ATOM   1515  CB  ARG   224       5.243  64.392  80.357  1.00  9.00
ATOM   1516  CG  ARG   224       3.725  64.379  80.375  1.00  9.00
ATOM   1517  CD  ARG   224       3.234  64.341  81.815  1.00  9.00
ATOM   1518  NE  ARG   224       1.769  64.398  81.882  1.00  9.00
ATOM   1519  CZ  ARG   224       1.099  64.262  83.027  1.00  9.00
ATOM   1520  NH1 ARG   224      -0.231  64.373  83.039  1.00  9.00
ATOM   1521  NH2 ARG   224       1.764  64.056  84.167  1.00  9.00
ATOM   1522  N   LEU   225       8.021  63.574  79.173  1.00  9.00
ATOM   1523  CA  LEU   225       9.465  63.641  79.268  1.00  9.00
ATOM   1524  C   LEU   225      10.027  64.104  77.934  1.00  9.00
ATOM   1525  O   LEU   225      10.466  65.256  77.867  1.00  9.00
ATOM   1526  CB  LEU   225      10.022  62.272  79.645  1.00  9.00
ATOM   1527  CG  LEU   225       9.628  61.856  81.060  1.00  9.00
ATOM   1528  CD1 LEU   225      10.330  60.560  81.448  1.00  9.00
ATOM   1529  CD2 LEU   225       9.945  62.939  82.086  1.00  9.00
ATOM   1530  N   LEU   226       9.649  63.424  76.866  1.00  9.00
ATOM   1531  CA  LEU   226      10.211  63.715  75.538  1.00  9.00
ATOM   1532  C   LEU   226       9.930  65.140  75.050  1.00  9.00
ATOM   1533  O   LEU   226      10.880  65.857  74.709  1.00  9.00
ATOM   1534  CB  LEU   226       9.611  62.722  74.548  1.00  9.00
ATOM   1535  CG  LEU   226      10.008  61.284  74.870  1.00  9.00
ATOM   1536  CD1 LEU   226       9.195  60.295  74.046  1.00  9.00
ATOM   1537  CD2 LEU   226      11.503  61.062  74.667  1.00  9.00
ATOM   1538  N   LYS   227       8.716  65.627  75.254  1.00  9.00
ATOM   1539  CA  LYS   227       8.380  66.966  74.757  1.00  9.00
ATOM   1540  C   LYS   227       8.904  68.098  75.641  1.00  9.00
ATOM   1541  O   LYS   227       9.385  69.103  75.101  1.00  9.00
ATOM   1542  CB  LYS   227       6.869  67.077  74.623  1.00  9.00
ATOM   1543  CG  LYS   227       6.350  66.133  73.546  1.00  9.00
ATOM   1544  CD  LYS   227       4.854  66.318  73.325  1.00  9.00
ATOM   1545  CE  LYS   227       4.351  65.431  72.192  1.00  9.00
ATOM   1546  NZ  LYS   227       2.908  65.624  71.975  1.00  9.00
ATOM   1547  N   GLU   228       9.058  67.851  76.932  1.00  9.00
ATOM   1548  CA  GLU   228       9.610  68.895  77.802  1.00  9.00
ATOM   1549  C   GLU   228      11.133  68.900  77.742  1.00  9.00
ATOM   1550  O   GLU   228      11.754  69.961  77.876  1.00  9.00
ATOM   1551  CB  GLU   228       9.159  68.649  79.236  1.00  9.00
ATOM   1552  CG  GLU   228       7.654  68.816  79.397  1.00  9.00
ATOM   1553  CD  GLU   228       7.240  68.363  80.794  1.00  9.00
ATOM   1554  OE1 GLU   228       8.101  67.875  81.515  1.00  9.00
ATOM   1555  OE2 GLU   228       6.068  68.502  81.114  1.00  9.00
ATOM   1556  N   PHE   229      11.699  67.785  77.309  1.00  9.00
ATOM   1557  CA  PHE   229      13.153  67.693  77.150  1.00  9.00
ATOM   1558  C   PHE   229      13.572  68.379  75.871  1.00  9.00
ATOM   1559  O   PHE   229      14.575  69.098  75.866  1.00  9.00
ATOM   1560  CB  PHE   229      13.602  66.241  77.037  1.00  9.00
ATOM   1561  CG  PHE   229      13.364  65.351  78.248  1.00  9.00
ATOM   1562  CD1 PHE   229      12.898  65.880  79.446  1.00  9.00
ATOM   1563  CD2 PHE   229      13.601  63.991  78.137  1.00  9.00
ATOM   1564  CE1 PHE   229      12.665  65.050  80.530  1.00  9.00
ATOM   1565  CE2 PHE   229      13.373  63.161  79.224  1.00  9.00
ATOM   1566  CZ  PHE   229      12.907  63.690  80.418  1.00  9.00
ATOM   1567  N   MET   230      12.696  68.336  74.883  1.00  9.00
ATOM   1568  CA  MET   230      12.961  69.017  73.619  1.00  9.00
ATOM   1569  C   MET   230      12.815  70.523  73.781  1.00  9.00
ATOM   1570  O   MET   230      13.681  71.278  73.316  1.00  9.00
ATOM   1571  CB  MET   230      11.946  68.530  72.597  1.00  9.00
ATOM   1572  CG  MET   230      12.142  69.237  71.263  1.00  9.00
ATOM   1573  SD  MET   230      10.859  68.920  70.035  1.00  9.00
ATOM   1574  CE  MET   230       9.441  69.595  70.930  1.00  9.00
ATOM   1575  N   HIS   231      11.897  70.924  74.645  1.00  9.00
ATOM   1576  CA  HIS   231      11.719  72.346  74.924  1.00  9.00
ATOM   1577  C   HIS   231      12.904  72.898  75.710  1.00  9.00
ATOM   1578  O   HIS   231      13.529  73.854  75.238  1.00  9.00
ATOM   1579  CB  HIS   231      10.434  72.520  75.724  1.00  9.00
ATOM   1580  CG  HIS   231      10.079  73.962  76.017  1.00  9.00
ATOM   1581  ND1 HIS   231       9.958  74.960  75.120  1.00  9.00
ATOM   1582  CD2 HIS   231       9.811  74.503  77.253  1.00  9.00
ATOM   1583  CE1 HIS   231       9.626  76.099  75.760  1.00  9.00
ATOM   1584  NE2 HIS   231       9.536  75.815  77.079  1.00  9.00
ATOM   1585  N   THR   232      13.400  72.135  76.673  1.00  9.00
ATOM   1586  CA  THR   232      14.536  72.606  77.478  1.00  9.00
ATOM   1587  C   THR   232      15.853  72.546  76.704  1.00  9.00
ATOM   1588  O   THR   232      16.660  73.477  76.805  1.00  9.00
ATOM   1589  CB  THR   232      14.656  71.743  78.729  1.00  9.00
ATOM   1590  OG1 THR   232      13.420  71.786  79.430  1.00  9.00
ATOM   1591  CG2 THR   232      15.747  72.277  79.650  1.00  9.00
ATOM   1592  N   MET   233      15.926  71.622  75.759  1.00  9.00
ATOM   1593  CA  MET   233      17.081  71.494  74.869  1.00  9.00
ATOM   1594  C   MET   233      17.190  72.689  73.931  1.00  9.00
ATOM   1595  O   MET   233      18.235  73.352  73.898  1.00  9.00
ATOM   1596  CB  MET   233      16.854  70.226  74.053  1.00  9.00
ATOM   1597  CG  MET   233      17.901  70.013  72.974  1.00  9.00
ATOM   1598  SD  MET   233      17.680  68.534  71.969  1.00  9.00
ATOM   1599  CE  MET   233      16.199  69.055  71.079  1.00  9.00
ATOM   1600  N   LYS   234      16.047  73.133  73.433  1.00  9.00
ATOM   1601  CA  LYS   234      16.019  74.287  72.536  1.00  9.00
ATOM   1602  C   LYS   234      16.253  75.595  73.296  1.00  9.00
ATOM   1603  O   LYS   234      17.045  76.426  72.829  1.00  9.00
ATOM   1604  CB  LYS   234      14.653  74.315  71.865  1.00  9.00
ATOM   1605  CG  LYS   234      14.534  75.472  70.884  1.00  9.00
ATOM   1606  CD  LYS   234      13.129  75.549  70.306  1.00  9.00
ATOM   1607  CE  LYS   234      12.983  76.739  69.369  1.00  9.00
ATOM   1608  NZ  LYS   234      11.584  76.897  68.940  1.00  9.00
ATOM   1609  N   ASN   235      15.877  75.600  74.567  1.00  9.00
ATOM   1610  CA  ASN   235      16.106  76.763  75.436  1.00  9.00
ATOM   1611  C   ASN   235      17.554  76.906  75.898  1.00  9.00
ATOM   1612  O   ASN   235      17.906  77.959  76.440  1.00  9.00
ATOM   1613  CB  ASN   235      15.287  76.618  76.713  1.00  9.00
ATOM   1614  CG  ASN   235      13.784  76.622  76.476  1.00  9.00
ATOM   1615  OD1 ASN   235      13.277  77.077  75.443  1.00  9.00
ATOM   1616  ND2 ASN   235      13.081  76.180  77.504  1.00  9.00
ATOM   1617  N   THR   236      18.394  75.915  75.648  1.00  9.00
ATOM   1618  CA  THR   236      19.789  76.006  76.081  1.00  9.00
ATOM   1619  C   THR   236      20.651  76.761  75.066  1.00  9.00
ATOM   1620  O   THR   236      21.702  77.302  75.433  1.00  9.00
ATOM   1621  CB  THR   236      20.324  74.590  76.260  1.00  9.00
ATOM   1622  OG1 THR   236      19.447  73.882  77.126  1.00  9.00
ATOM   1623  CG2 THR   236      21.721  74.577  76.870  1.00  9.00
ATOM   1624  N   GLY   237      20.146  76.926  73.854  1.00  9.00
ATOM   1625  CA  GLY   237      20.915  77.631  72.823  1.00  9.00
ATOM   1626  C   GLY   237      20.111  78.753  72.173  1.00  9.00
ATOM   1627  O   GLY   237      20.183  78.855  70.956  1.00  9.00
TER
END
