
#######################################################
#                                                     #
#                        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   12 (  105),  selected   12 , name T0386TS468_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   12 , name T0386_D2.pdb
# PARAMETERS: T0386TS468_1-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:    12       219 - 230         1.74     1.74
  LCS_AVERAGE:     14.81

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       219 - 230         1.74     1.74
  LCS_AVERAGE:     14.81

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       219 - 226         0.94     2.00
  LCS_AVERAGE:      8.64

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      8   12   12     6    7    8   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     P     220     P     220      8   12   12     6    7    8   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     E     221     E     221      8   12   12     6    7    8   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     K     222     K     222      8   12   12     6    7    8   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     I     223     I     223      8   12   12     6    7    8   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     R     224     R     224      8   12   12     6    7    8   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     L     225     L     225      8   12   12     5    7    8   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     L     226     L     226      8   12   12     3    5    8   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     K     227     K     227      5   12   12     3    5    6   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     E     228     E     228      5   12   12     3    5    6   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     F     229     F     229      5   12   12     3    5    5   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     M     230     M     230      5   12   12     3    5    5   10   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_AVERAGE  LCS_A:  12.76  (   8.64   14.81   14.81 )

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      6      7      8     10     12     12     12     12     12     12     12     12     12     12     12     12     12     12     12     12 
GDT PERCENT_CA   7.41   8.64   9.88  12.35  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81
GDT RMS_LOCAL    0.30   0.45   0.94   1.40   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74
GDT RMS_ALL_CA   2.73   2.48   2.00   2.00   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74   1.74

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          1.131
LGA    P     220      P     220          1.373
LGA    E     221      E     221          1.960
LGA    K     222      K     222          1.866
LGA    I     223      I     223          1.617
LGA    R     224      R     224          1.150
LGA    L     225      L     225          0.576
LGA    L     226      L     226          1.110
LGA    K     227      K     227          1.911
LGA    E     228      E     228          2.432
LGA    F     229      F     229          2.237
LGA    M     230      M     230          2.360

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12   81    4.0     12    1.74    12.654    13.786     0.654

LGA_LOCAL      RMSD =  1.735  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.735  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  1.735  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.081177 * X  +   0.963410 * Y  +  -0.255444 * Z  +  21.059137
  Y_new =  -0.951166 * X  +  -0.001698 * Y  +  -0.308674 * Z  +  77.528831
  Z_new =  -0.297814 * X  +   0.268027 * Y  +   0.916225 * Z  +  62.298374 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.284593   -2.857000  [ DEG:    16.3060   -163.6940 ]
  Theta =   0.302402    2.839191  [ DEG:    17.3263    162.6737 ]
  Phi   =  -1.485658    1.655935  [ DEG:   -85.1219     94.8781 ]
 
# 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: T0386TS468_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS468_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12   81   4.0   12   1.74  13.786     1.74
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS468_1-D2
PFRMAT TS
TARGET T0386    
MODEL  1
PARENT n/a
ATOM   1449  N   ASN   219       3.094  55.707  75.008  1.00  0.00
ATOM   1450  CA  ASN   219       2.785  56.938  74.341  1.00  0.00
ATOM   1451  C   ASN   219       2.666  58.141  75.286  1.00  0.00
ATOM   1452  O   ASN   219       3.239  59.211  75.011  1.00  0.00
ATOM   1453  CB  ASN   219       1.450  56.827  73.602  1.00  0.00
ATOM   1454  CG  ASN   219       1.541  55.959  72.363  1.00  0.00
ATOM   1455  OD1 ASN   219       2.626  55.743  71.823  1.00  0.00
ATOM   1456  ND2 ASN   219       0.398  55.458  71.907  1.00  0.00
ATOM   1457  N   PRO   220       1.939  57.969  76.397  1.00  0.00
ATOM   1458  CA  PRO   220       1.729  59.042  77.380  1.00  0.00
ATOM   1459  C   PRO   220       2.988  59.382  78.185  1.00  0.00
ATOM   1460  O   PRO   220       3.261  60.560  78.473  1.00  0.00
ATOM   1461  CB  PRO   220       0.638  58.492  78.300  1.00  0.00
ATOM   1462  CG  PRO   220      -0.070  57.472  77.473  1.00  0.00
ATOM   1463  CD  PRO   220       0.977  56.848  76.595  1.00  0.00
ATOM   1464  N   GLU   221       3.763  58.375  78.576  1.00  0.00
ATOM   1465  CA  GLU   221       5.001  58.684  79.287  1.00  0.00
ATOM   1466  C   GLU   221       5.954  59.298  78.250  1.00  0.00
ATOM   1467  O   GLU   221       6.733  60.187  78.559  1.00  0.00
ATOM   1468  CB  GLU   221       5.607  57.413  79.885  1.00  0.00
ATOM   1469  CG  GLU   221       4.816  56.836  81.048  1.00  0.00
ATOM   1470  CD  GLU   221       5.394  55.530  81.555  1.00  0.00
ATOM   1471  OE1 GLU   221       6.377  55.043  80.957  1.00  0.00
ATOM   1472  OE2 GLU   221       4.865  54.992  82.551  1.00  0.00
ATOM   1473  N   LYS   222       5.858  58.832  77.012  1.00  0.00
ATOM   1474  CA  LYS   222       6.684  59.359  75.931  1.00  0.00
ATOM   1475  C   LYS   222       6.392  60.841  75.740  1.00  0.00
ATOM   1476  O   LYS   222       7.327  61.638  75.570  1.00  0.00
ATOM   1477  CB  LYS   222       6.388  58.623  74.623  1.00  0.00
ATOM   1478  CG  LYS   222       7.240  59.077  73.448  1.00  0.00
ATOM   1479  CD  LYS   222       6.949  58.254  72.204  1.00  0.00
ATOM   1480  CE  LYS   222       7.780  58.728  71.023  1.00  0.00
ATOM   1481  NZ  LYS   222       7.495  57.940  69.792  1.00  0.00
ATOM   1482  N   ILE   223       5.111  61.228  75.792  1.00  0.00
ATOM   1483  CA  ILE   223       4.728  62.639  75.625  1.00  0.00
ATOM   1484  C   ILE   223       5.312  63.496  76.745  1.00  0.00
ATOM   1485  O   ILE   223       5.802  64.597  76.512  1.00  0.00
ATOM   1486  CB  ILE   223       3.199  62.816  75.648  1.00  0.00
ATOM   1487  CG1 ILE   223       2.567  62.155  74.421  1.00  0.00
ATOM   1488  CG2 ILE   223       2.832  64.292  75.642  1.00  0.00
ATOM   1489  CD1 ILE   223       1.062  62.023  74.505  1.00  0.00
ATOM   1490  N   ARG   224       4.956  63.141  77.989  1.00  0.00
ATOM   1491  CA  ARG   224       5.335  64.015  79.113  1.00  0.00
ATOM   1492  C   ARG   224       6.838  64.122  79.300  1.00  0.00
ATOM   1493  O   ARG   224       7.367  65.199  79.585  1.00  0.00
ATOM   1494  CB  ARG   224       4.754  63.483  80.424  1.00  0.00
ATOM   1495  CG  ARG   224       5.107  64.320  81.644  1.00  0.00
ATOM   1496  CD  ARG   224       4.527  65.720  81.538  1.00  0.00
ATOM   1497  NE  ARG   224       4.809  66.521  82.728  1.00  0.00
ATOM   1498  CZ  ARG   224       4.590  67.828  82.819  1.00  0.00
ATOM   1499  NH1 ARG   224       4.877  68.473  83.940  1.00  0.00
ATOM   1500  NH2 ARG   224       4.083  68.488  81.786  1.00  0.00
ATOM   1501  N   LEU   225       7.576  63.012  79.147  1.00  0.00
ATOM   1502  CA  LEU   225       9.021  63.069  79.309  1.00  0.00
ATOM   1503  C   LEU   225       9.788  63.330  78.021  1.00  0.00
ATOM   1504  O   LEU   225      10.521  64.315  77.902  1.00  0.00
ATOM   1505  CB  LEU   225       9.550  61.747  79.867  1.00  0.00
ATOM   1506  CG  LEU   225       9.061  61.355  81.262  1.00  0.00
ATOM   1507  CD1 LEU   225       9.557  59.966  81.635  1.00  0.00
ATOM   1508  CD2 LEU   225       9.569  62.337  82.306  1.00  0.00
ATOM   1509  N   LEU   226       9.637  62.448  77.016  1.00  0.00
ATOM   1510  CA  LEU   226      10.425  62.577  75.782  1.00  0.00
ATOM   1511  C   LEU   226      10.182  63.895  75.084  1.00  0.00
ATOM   1512  O   LEU   226      11.101  64.676  74.819  1.00  0.00
ATOM   1513  CB  LEU   226      10.065  61.461  74.799  1.00  0.00
ATOM   1514  CG  LEU   226      10.772  61.500  73.442  1.00  0.00
ATOM   1515  CD1 LEU   226      12.275  61.339  73.613  1.00  0.00
ATOM   1516  CD2 LEU   226      10.272  60.380  72.543  1.00  0.00
ATOM   1517  N   LYS   227       8.898  64.167  74.767  1.00  0.00
ATOM   1518  CA  LYS   227       8.600  65.469  74.112  1.00  0.00
ATOM   1519  C   LYS   227       8.629  66.656  75.059  1.00  0.00
ATOM   1520  O   LYS   227       9.249  67.679  74.759  1.00  0.00
ATOM   1521  CB  LYS   227       7.207  65.446  73.481  1.00  0.00
ATOM   1522  CG  LYS   227       6.838  66.724  72.744  1.00  0.00
ATOM   1523  CD  LYS   227       5.514  66.575  72.011  1.00  0.00
ATOM   1524  CE  LYS   227       5.176  67.830  71.223  1.00  0.00
ATOM   1525  NZ  LYS   227       3.899  67.687  70.473  1.00  0.00
ATOM   1526  N   GLU   228       7.968  66.574  76.229  1.00  0.00
ATOM   1527  CA  GLU   228       7.879  67.873  76.966  1.00  0.00
ATOM   1528  C   GLU   228       9.077  68.177  77.866  1.00  0.00
ATOM   1529  O   GLU   228       9.293  69.343  78.207  1.00  0.00
ATOM   1530  CB  GLU   228       6.646  67.892  77.872  1.00  0.00
ATOM   1531  CG  GLU   228       5.324  67.837  77.123  1.00  0.00
ATOM   1532  CD  GLU   228       4.128  67.851  78.053  1.00  0.00
ATOM   1533  OE1 GLU   228       4.331  67.928  79.284  1.00  0.00
ATOM   1534  OE2 GLU   228       2.986  67.784  77.553  1.00  0.00
ATOM   1535  N   PHE   229       9.937  67.226  78.228  1.00  0.00
ATOM   1536  CA  PHE   229      11.025  67.568  79.130  1.00  0.00
ATOM   1537  C   PHE   229      12.300  67.736  78.321  1.00  0.00
ATOM   1538  O   PHE   229      13.197  68.484  78.714  1.00  0.00
ATOM   1539  CB  PHE   229      11.227  66.463  80.168  1.00  0.00
ATOM   1540  CG  PHE   229      10.076  66.308  81.120  1.00  0.00
ATOM   1541  CD1 PHE   229       9.121  67.303  81.242  1.00  0.00
ATOM   1542  CD2 PHE   229       9.947  65.167  81.894  1.00  0.00
ATOM   1543  CE1 PHE   229       8.062  67.160  82.119  1.00  0.00
ATOM   1544  CE2 PHE   229       8.889  65.025  82.770  1.00  0.00
ATOM   1545  CZ  PHE   229       7.947  66.015  82.883  1.00  0.00
ATOM   1546  N   MET   230      12.373  67.045  77.187  1.00  0.00
ATOM   1547  CA  MET   230      13.546  67.113  76.328  1.00  0.00
ATOM   1548  C   MET   230      13.531  68.382  75.476  1.00  0.00
ATOM   1549  O   MET   230      12.466  68.733  74.914  1.00  0.00
ATOM   1550  CB  MET   230      13.592  65.908  75.387  1.00  0.00
ATOM   1551  CG  MET   230      13.787  64.576  76.093  1.00  0.00
ATOM   1552  SD  MET   230      15.357  64.479  76.975  1.00  0.00
ATOM   1553  CE  MET   230      16.505  64.333  75.608  1.00  0.00
TER
END
