
#######################################################
#                                                     #
#                        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 T0386TS046_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   19 , name T0386_D2.pdb
# PARAMETERS: T0386TS046_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:    19       219 - 237         2.80     2.80
  LCS_AVERAGE:     23.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18       220 - 237         1.79     2.98
  LCS_AVERAGE:     21.25

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       221 - 234         0.94     3.13
  LCS_AVERAGE:     14.42

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    3   19     3    3    3    3    3    3    6    7    8   10   13   13   16   16   19   19   19   19   19   19 
LCS_GDT     P     220     P     220     12   18   19     4    6    9   13   15   15   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     E     221     E     221     14   18   19     4   10   12   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     K     222     K     222     14   18   19     9   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     I     223     I     223     14   18   19     9   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     R     224     R     224     14   18   19     9   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     L     225     L     225     14   18   19     9   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     L     226     L     226     14   18   19     9   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     K     227     K     227     14   18   19     9   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     E     228     E     228     14   18   19     9   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     F     229     F     229     14   18   19     9   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     M     230     M     230     14   18   19     9   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     H     231     H     231     14   18   19     9   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     T     232     T     232     14   18   19     5   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     M     233     M     233     14   18   19     5   11   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     K     234     K     234     14   18   19     5   12   13   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     N     235     N     235      4   18   19     3    4    4    8   13   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     T     236     T     236      4   18   19     3    8   11   14   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_GDT     G     237     G     237      3   18   19     3    3    3   10   15   16   18   18   18   18   18   18   18   18   19   19   19   19   19   19 
LCS_AVERAGE  LCS_A:  19.71  (  14.42   21.25   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     12     13     14     15     16     18     18     18     18     18     18     18     18     19     19     19     19     19     19 
GDT PERCENT_CA  11.11  14.81  16.05  17.28  18.52  19.75  22.22  22.22  22.22  22.22  22.22  22.22  22.22  22.22  23.46  23.46  23.46  23.46  23.46  23.46
GDT RMS_LOCAL    0.26   0.64   0.73   0.94   1.20   1.38   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   2.80   2.80   2.80   2.80   2.80   2.80
GDT RMS_ALL_CA   3.34   3.20   3.20   3.13   3.31   3.17   2.98   2.98   2.98   2.98   2.98   2.98   2.98   2.98   2.80   2.80   2.80   2.80   2.80   2.80

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         10.536
LGA    P     220      P     220          3.411
LGA    E     221      E     221          2.324
LGA    K     222      K     222          0.447
LGA    I     223      I     223          0.342
LGA    R     224      R     224          0.780
LGA    L     225      L     225          1.083
LGA    L     226      L     226          0.990
LGA    K     227      K     227          1.473
LGA    E     228      E     228          1.696
LGA    F     229      F     229          1.250
LGA    M     230      M     230          1.250
LGA    H     231      H     231          1.707
LGA    T     232      T     232          0.801
LGA    M     233      M     233          0.912
LGA    K     234      K     234          1.628
LGA    N     235      N     235          3.199
LGA    T     236      T     236          2.350
LGA    G     237      G     237          2.529

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   81    4.0     18    1.79    19.444    20.273     0.954

LGA_LOCAL      RMSD =  1.787  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.978  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  2.803  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.296794 * X  +   0.806384 * Y  +   0.511525 * Z  + -32.685566
  Y_new =  -0.938628 * X  +   0.147752 * Y  +   0.311684 * Z  +  51.554760
  Z_new =   0.175758 * X  +  -0.572637 * Y  +   0.800747 * Z  + 122.661598 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.620808    2.520785  [ DEG:   -35.5697    144.4303 ]
  Theta =  -0.176676   -2.964917  [ DEG:   -10.1228   -169.8772 ]
  Phi   =  -1.264544    1.877048  [ DEG:   -72.4531    107.5469 ]
 
# 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: T0386TS046_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS046_4-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   18   1.79  20.273     2.80
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS046_4-D2
PFRMAT TS
TARGET T0386
MODEL 4
PARENT 2G03_A
ATOM   1462  N   ASN   219      -0.302  63.511  81.574  1.00  5.27
ATOM   1463  CA  ASN   219       0.651  62.674  82.236  1.00  5.27
ATOM   1464  C   ASN   219       1.285  61.653  81.301  1.00  5.27
ATOM   1465  O   ASN   219       2.396  61.304  81.710  1.00  5.27
ATOM   1466  CB  ASN   219      -0.017  61.897  83.373  1.00  5.27
ATOM   1467  CG  ASN   219      -0.362  62.779  84.556  1.00  5.27
ATOM   1468  OD1 ASN   219       0.202  63.861  84.723  1.00  5.27
ATOM   1469  ND2 ASN   219      -1.292  62.317  85.385  1.00  5.27
ATOM   1470  N   PRO   220       0.771  61.198  80.101  1.00  6.15
ATOM   1471  CA  PRO   220       1.332  60.109  79.289  1.00  6.15
ATOM   1472  C   PRO   220       2.670  60.378  79.110  1.00  6.15
ATOM   1473  O   PRO   220       3.078  61.144  78.247  1.00  6.15
ATOM   1474  CB  PRO   220       0.531  60.167  77.987  1.00  6.15
ATOM   1475  CG  PRO   220      -0.800  60.707  78.392  1.00  6.15
ATOM   1476  CD  PRO   220      -0.523  61.782  79.405  1.00  6.15
ATOM   1477  N   GLU   221       3.290  59.597  79.965  1.00  6.01
ATOM   1478  CA  GLU   221       4.549  59.837  80.433  1.00  6.01
ATOM   1479  C   GLU   221       5.504  59.912  79.351  1.00  6.01
ATOM   1480  O   GLU   221       6.190  60.915  79.297  1.00  6.01
ATOM   1481  CB  GLU   221       4.992  58.719  81.379  1.00  6.01
ATOM   1482  CG  GLU   221       6.370  58.928  81.986  1.00  6.01
ATOM   1483  CD  GLU   221       6.759  57.818  82.942  1.00  6.01
ATOM   1484  OE1 GLU   221       5.945  56.891  83.141  1.00  6.01
ATOM   1485  OE2 GLU   221       7.878  57.874  83.493  1.00  6.01
ATOM   1486  N   LYS   222       5.525  58.941  78.434  1.00  5.95
ATOM   1487  CA  LYS   222       6.590  58.923  77.485  1.00  5.95
ATOM   1488  C   LYS   222       6.586  60.096  76.592  1.00  5.95
ATOM   1489  O   LYS   222       7.624  60.720  76.345  1.00  5.95
ATOM   1490  CB  LYS   222       6.495  57.680  76.597  1.00  5.95
ATOM   1491  CG  LYS   222       6.816  56.379  77.314  1.00  5.95
ATOM   1492  CD  LYS   222       6.705  55.189  76.376  1.00  5.95
ATOM   1493  CE  LYS   222       7.001  53.886  77.099  1.00  5.95
ATOM   1494  NZ  LYS   222       6.863  52.707  76.199  1.00  5.95
ATOM   1495  N   ILE   223       5.385  60.421  76.106  1.00  5.85
ATOM   1496  CA  ILE   223       5.265  61.438  75.130  1.00  5.85
ATOM   1497  C   ILE   223       5.678  62.739  75.653  1.00  5.85
ATOM   1498  O   ILE   223       6.456  63.483  75.038  1.00  5.85
ATOM   1499  CB  ILE   223       3.812  61.581  74.641  1.00  5.85
ATOM   1500  CG1 ILE   223       3.388  60.339  73.856  1.00  5.85
ATOM   1501  CG2 ILE   223       3.672  62.795  73.735  1.00  5.85
ATOM   1502  CD1 ILE   223       1.904  60.274  73.570  1.00  5.85
ATOM   1503  N   ARG   224       5.164  62.991  76.854  1.00  6.08
ATOM   1504  CA  ARG   224       5.359  64.239  77.466  1.00  6.08
ATOM   1505  C   ARG   224       6.792  64.431  77.730  1.00  6.08
ATOM   1506  O   ARG   224       7.269  65.535  77.521  1.00  6.08
ATOM   1507  CB  ARG   224       4.593  64.314  78.788  1.00  6.08
ATOM   1508  CG  ARG   224       4.719  65.650  79.503  1.00  6.08
ATOM   1509  CD  ARG   224       4.115  66.775  78.679  1.00  6.08
ATOM   1510  NE  ARG   224       2.710  66.530  78.363  1.00  6.08
ATOM   1511  CZ  ARG   224       1.705  66.752  79.204  1.00  6.08
ATOM   1512  NH1 ARG   224       0.459  66.500  78.830  1.00  6.08
ATOM   1513  NH2 ARG   224       1.949  67.228  80.418  1.00  6.08
ATOM   1514  N   LEU   225       7.496  63.381  78.198  1.00  6.19
ATOM   1515  CA  LEU   225       8.884  63.497  78.565  1.00  6.19
ATOM   1516  C   LEU   225       9.715  63.833  77.393  1.00  6.19
ATOM   1517  O   LEU   225      10.597  64.683  77.500  1.00  6.19
ATOM   1518  CB  LEU   225       9.396  62.179  79.150  1.00  6.19
ATOM   1519  CG  LEU   225       8.842  61.785  80.522  1.00  6.19
ATOM   1520  CD1 LEU   225       9.288  60.382  80.899  1.00  6.19
ATOM   1521  CD2 LEU   225       9.335  62.745  81.594  1.00  6.19
ATOM   1522  N   LEU   226       9.465  63.179  76.247  1.00  6.32
ATOM   1523  CA  LEU   226      10.317  63.448  75.131  1.00  6.32
ATOM   1524  C   LEU   226      10.218  64.858  74.686  1.00  6.32
ATOM   1525  O   LEU   226      11.221  65.542  74.434  1.00  6.32
ATOM   1526  CB  LEU   226       9.942  62.558  73.944  1.00  6.32
ATOM   1527  CG  LEU   226      10.764  62.750  72.667  1.00  6.32
ATOM   1528  CD1 LEU   226      12.230  62.429  72.917  1.00  6.32
ATOM   1529  CD2 LEU   226      10.259  61.836  71.561  1.00  6.32
ATOM   1530  N   LYS   227       8.964  65.311  74.601  1.00  6.14
ATOM   1531  CA  LYS   227       8.739  66.610  74.075  1.00  6.14
ATOM   1532  C   LYS   227       9.366  67.632  74.943  1.00  6.14
ATOM   1533  O   LYS   227       9.965  68.593  74.455  1.00  6.14
ATOM   1534  CB  LYS   227       7.239  66.899  73.988  1.00  6.14
ATOM   1535  CG  LYS   227       6.513  66.099  72.919  1.00  6.14
ATOM   1536  CD  LYS   227       5.031  66.437  72.887  1.00  6.14
ATOM   1537  CE  LYS   227       4.301  65.619  71.835  1.00  6.14
ATOM   1538  NZ  LYS   227       2.842  65.916  71.815  1.00  6.14
ATOM   1539  N   GLU   228       9.226  67.442  76.263  1.00  5.97
ATOM   1540  CA  GLU   228       9.697  68.423  77.193  1.00  5.97
ATOM   1541  C   GLU   228      11.181  68.508  77.144  1.00  5.97
ATOM   1542  O   GLU   228      11.713  69.603  77.302  1.00  5.97
ATOM   1543  CB  GLU   228       9.276  68.056  78.617  1.00  5.97
ATOM   1544  CG  GLU   228       7.785  68.190  78.878  1.00  5.97
ATOM   1545  CD  GLU   228       7.388  67.703  80.258  1.00  5.97
ATOM   1546  OE1 GLU   228       8.268  67.193  80.983  1.00  5.97
ATOM   1547  OE2 GLU   228       6.198  67.830  80.614  1.00  5.97
ATOM   1548  N   PHE   229      11.885  67.362  76.972  1.00  6.74
ATOM   1549  CA  PHE   229      13.327  67.406  76.958  1.00  6.74
ATOM   1550  C   PHE   229      13.794  68.189  75.785  1.00  6.74
ATOM   1551  O   PHE   229      14.739  68.979  75.880  1.00  6.74
ATOM   1552  CB  PHE   229      13.906  65.992  76.868  1.00  6.74
ATOM   1553  CG  PHE   229      15.407  65.952  76.841  1.00  6.74
ATOM   1554  CD1 PHE   229      16.139  66.097  78.007  1.00  6.74
ATOM   1555  CD2 PHE   229      16.087  65.771  75.650  1.00  6.74
ATOM   1556  CE1 PHE   229      17.520  66.060  77.981  1.00  6.74
ATOM   1557  CE2 PHE   229      17.469  65.734  75.625  1.00  6.74
ATOM   1558  CZ  PHE   229      18.185  65.878  76.783  1.00  6.74
ATOM   1559  N   MET   230      13.138  67.973  74.632  1.00  6.86
ATOM   1560  CA  MET   230      13.591  68.682  73.476  1.00  6.86
ATOM   1561  C   MET   230      13.439  70.159  73.672  1.00  6.86
ATOM   1562  O   MET   230      14.330  70.941  73.325  1.00  6.86
ATOM   1563  CB  MET   230      12.782  68.272  72.245  1.00  6.86
ATOM   1564  CG  MET   230      13.045  66.851  71.773  1.00  6.86
ATOM   1565  SD  MET   230      14.760  66.586  71.286  1.00  6.86
ATOM   1566  CE  MET   230      14.848  67.583  69.800  1.00  6.86
ATOM   1567  N   HIS   231      12.288  70.573  74.235  1.00  6.24
ATOM   1568  CA  HIS   231      12.022  71.979  74.362  1.00  6.24
ATOM   1569  C   HIS   231      12.994  72.623  75.309  1.00  6.24
ATOM   1570  O   HIS   231      13.417  73.755  75.076  1.00  6.24
ATOM   1571  CB  HIS   231      10.607  72.210  74.897  1.00  6.24
ATOM   1572  CG  HIS   231      10.239  73.655  75.028  1.00  6.24
ATOM   1573  ND1 HIS   231      10.036  74.473  73.938  1.00  6.24
ATOM   1574  CD2 HIS   231      10.002  74.570  76.136  1.00  6.24
ATOM   1575  CE1 HIS   231       9.720  75.707  74.369  1.00  6.24
ATOM   1576  NE2 HIS   231       9.698  75.773  75.686  1.00  6.24
ATOM   1577  N   THR   232      13.348  71.937  76.418  1.00  6.79
ATOM   1578  CA  THR   232      14.252  72.494  77.398  1.00  6.79
ATOM   1579  C   THR   232      15.599  72.714  76.796  1.00  6.79
ATOM   1580  O   THR   232      16.258  73.724  77.060  1.00  6.79
ATOM   1581  CB  THR   232      14.419  71.557  78.608  1.00  6.79
ATOM   1582  OG1 THR   232      13.154  71.377  79.257  1.00  6.79
ATOM   1583  CG2 THR   232      15.404  72.146  79.607  1.00  6.79
ATOM   1584  N   MET   233      16.058  71.745  75.985  1.00  6.95
ATOM   1585  CA  MET   233      17.359  71.902  75.403  1.00  6.95
ATOM   1586  C   MET   233      17.373  73.092  74.475  1.00  6.95
ATOM   1587  O   MET   233      18.355  73.835  74.415  1.00  6.95
ATOM   1588  CB  MET   233      17.743  70.655  74.604  1.00  6.95
ATOM   1589  CG  MET   233      19.122  70.726  73.970  1.00  6.95
ATOM   1590  SD  MET   233      19.531  69.244  73.026  1.00  6.95
ATOM   1591  CE  MET   233      18.483  69.459  71.590  1.00  6.95
ATOM   1592  N   LYS   234      16.286  73.299  73.704  1.00  6.93
ATOM   1593  CA  LYS   234      16.246  74.405  72.773  1.00  6.93
ATOM   1594  C   LYS   234      16.296  75.714  73.520  1.00  6.93
ATOM   1595  O   LYS   234      16.939  76.665  73.069  1.00  6.93
ATOM   1596  CB  LYS   234      14.960  74.363  71.947  1.00  6.93
ATOM   1597  CG  LYS   234      14.906  73.225  70.939  1.00  6.93
ATOM   1598  CD  LYS   234      13.606  73.245  70.152  1.00  6.93
ATOM   1599  CE  LYS   234      13.541  72.093  69.163  1.00  6.93
ATOM   1600  NZ  LYS   234      12.257  72.080  68.409  1.00  6.93
ATOM   1601  N   ASN   235      15.592  75.808  74.673  1.00  7.42
ATOM   1602  CA  ASN   235      15.542  77.037  75.429  1.00  7.42
ATOM   1603  C   ASN   235      16.909  77.372  75.919  1.00  7.42
ATOM   1604  O   ASN   235      17.306  78.536  75.891  1.00  7.42
ATOM   1605  CB  ASN   235      14.604  76.889  76.628  1.00  7.42
ATOM   1606  CG  ASN   235      13.142  76.863  76.226  1.00  7.42
ATOM   1607  OD1 ASN   235      12.781  77.307  75.136  1.00  7.42
ATOM   1608  ND2 ASN   235      12.297  76.342  77.106  1.00  7.42
ATOM   1609  N   THR   236      17.655  76.361  76.407  1.00  7.57
ATOM   1610  CA  THR   236      18.971  76.607  76.930  1.00  7.57
ATOM   1611  C   THR   236      19.901  77.061  75.849  1.00  7.57
ATOM   1612  O   THR   236      20.727  77.950  76.063  1.00  7.57
ATOM   1613  CB  THR   236      19.573  75.338  77.561  1.00  7.57
ATOM   1614  OG1 THR   236      18.756  74.913  78.659  1.00  7.57
ATOM   1615  CG2 THR   236      20.979  75.613  78.072  1.00  7.57
ATOM   1616  N   GLY   237      19.802  76.444  74.656  1.00  7.22
ATOM   1617  CA  GLY   237      20.683  76.811  73.589  1.00  7.22
ATOM   1618  C   GLY   237      19.893  77.648  72.594  1.00  7.22
ATOM   1619  O   GLY   237      19.451  78.765  72.975  1.00  7.22
TER
END
