
#######################################################
#                                                     #
#                        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 (  145),  selected   19 , name T0316TS021_1_1-D2
# Molecule2: number of CA atoms   60 (  457),  selected   19 , name T0316_D2.pdb
# PARAMETERS: T0316TS021_1_1-D2.T0316_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:    15       223 - 237         4.73     7.13
  LCS_AVERAGE:     23.68

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       230 - 236         1.99     7.76
  LONGEST_CONTINUOUS_SEGMENT:     7       231 - 237         1.81     7.48
  LCS_AVERAGE:      9.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       220 - 223         0.37    13.76
  LONGEST_CONTINUOUS_SEGMENT:     4       224 - 227         0.14    14.63
  LONGEST_CONTINUOUS_SEGMENT:     4       232 - 235         0.55     9.41
  LONGEST_CONTINUOUS_SEGMENT:     4       234 - 237         0.79    16.08
  LCS_AVERAGE:      6.23

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:   60
LCS_GDT     G     220     G     220      4    5   11     4    4    5    7    7    7    7    7    8    8    9   10   10   10   11   13   13   15   19   19 
LCS_GDT     R     221     R     221      4    5   11     4    4    5    7    7    7    7    7    8    8    9   10   10   13   15   15   17   18   19   19 
LCS_GDT     M     222     M     222      4    5   11     4    4    5    7    7    7    7    7    8    8    9   10   10   13   15   15   17   18   19   19 
LCS_GDT     M     223     M     223      4    5   15     4    4    4    7    7    7    8    9   10   10   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     T     224     T     224      4    5   15     4    4    4    7    7    7    8    9   10   10   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     V     225     V     225      4    5   15     4    4    4    4    4    5    6    7    8    9   11   13   14   15   15   16   17   18   19   19 
LCS_GDT     D     226     D     226      4    5   15     4    4    4    4    4    5    6    6    8    9   11   12   14   15   15   16   16   18   19   19 
LCS_GDT     G     227     G     227      4    5   15     4    4    5    7    7    7    7    7    8    9   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     R     228     R     228      3    4   15     3    3    5    7    7    7    7    7    8    9   10   12   13   15   15   16   17   18   19   19 
LCS_GDT     D     229     D     229      3    4   15     3    3    3    3    5    5    6    8    8   10   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     M     230     M     230      3    7   15     3    3    3    4    6    8    8    9   10   10   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     G     231     G     231      3    7   15     3    3    5    5    7    8    8    9   10   10   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     E     232     E     232      4    7   15     3    4    5    5    7    8    8    9   10   10   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     H     233     H     233      4    7   15     3    4    5    5    7    8    8    9   10   10   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     A     234     A     234      4    7   15     3    4    5    5    7    8    8    9   10   10   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     G     235     G     235      4    7   15     3    4    4    5    7    8    8    9   10   10   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     L     236     L     236      4    7   15     3    3    5    5    7    8    8    9   10   10   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     M     237     M     237      4    7   15     3    3    4    4    7    8    8    9   10   10   12   13   14   15   15   16   17   18   19   19 
LCS_GDT     Y     238     Y     238      3    4   12     3    3    3    3    3    4    6    9    9    9    9   10   13   14   15   16   17   18   19   19 
LCS_AVERAGE  LCS_A:  13.13  (   6.23    9.47   23.68 )

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      4      4      5      7      7      8      8      9     10     10     12     13     14     15     15     16     17     18     19     19 
GDT PERCENT_CA   6.67   6.67   8.33  11.67  11.67  13.33  13.33  15.00  16.67  16.67  20.00  21.67  23.33  25.00  25.00  26.67  28.33  30.00  31.67  31.67
GDT RMS_LOCAL    0.14   0.14   0.81   1.38   1.38   2.18   2.18   2.53   2.96   2.96   3.84   4.16   4.47   4.73   4.73   5.09   5.66   5.87   6.43   6.43
GDT RMS_ALL_CA  14.63  14.63  13.91  13.94  13.94   8.37   8.37   7.00   6.87   6.87   6.81   6.91   7.07   7.13   7.13   6.95   6.51   6.57   6.43   6.43

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220         14.386
LGA    R     221      R     221         10.162
LGA    M     222      M     222          8.222
LGA    M     223      M     223          3.022
LGA    T     224      T     224          3.747
LGA    V     225      V     225          8.517
LGA    D     226      D     226         10.088
LGA    G     227      G     227          7.471
LGA    R     228      R     228          9.742
LGA    D     229      D     229          7.810
LGA    M     230      M     230          6.206
LGA    G     231      G     231          1.410
LGA    E     232      E     232          2.017
LGA    H     233      H     233          2.524
LGA    A     234      A     234          0.576
LGA    G     235      G     235          2.804
LGA    L     236      L     236          1.695
LGA    M     237      M     237          3.293
LGA    Y     238      Y     238          8.417

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   60    4.0      9    2.53    15.000    13.721     0.342

LGA_LOCAL      RMSD =  2.528  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.999  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  6.432  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.480987 * X  +   0.282789 * Y  +  -0.829869 * Z  +  74.098709
  Y_new =   0.719743 * X  +  -0.667855 * Y  +   0.189578 * Z  +  27.626196
  Z_new =  -0.500621 * X  +  -0.688477 * Y  +  -0.524765 * Z  +  42.128460 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.222067    0.919525  [ DEG:  -127.3151     52.6849 ]
  Theta =   0.524316    2.617277  [ DEG:    30.0411    149.9589 ]
  Phi   =   0.981681   -2.159912  [ DEG:    56.2462   -123.7538 ]
 
# 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: T0316TS021_1_1-D2                             
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS021_1_1-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19   60   4.0    9   2.53  13.721     6.43
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS021_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0316
PARENT N/A
ATOM   1736  N   GLY   220      40.661   8.186 -19.521  1.00115.68       1SG1737
ATOM   1737  CA  GLY   220      39.906   8.440 -18.337  1.00115.68       1SG1738
ATOM   1738  C   GLY   220      39.591   9.893 -18.373  1.00115.68       1SG1739
ATOM   1739  O   GLY   220      39.700  10.594 -17.369  1.00115.68       1SG1740
ATOM   1740  N   ARG   221      39.175  10.374 -19.557  1.00 66.13       1SG1741
ATOM   1741  CA  ARG   221      38.861  11.761 -19.689  1.00 66.13       1SG1742
ATOM   1742  CB  ARG   221      40.053  12.614 -20.142  1.00 66.13       1SG1743
ATOM   1743  CG  ARG   221      41.220  12.536 -19.157  1.00 66.13       1SG1744
ATOM   1744  CD  ARG   221      42.340  13.545 -19.410  1.00 66.13       1SG1745
ATOM   1745  NE  ARG   221      43.468  13.161 -18.514  1.00 66.13       1SG1746
ATOM   1746  CZ  ARG   221      43.456  13.521 -17.198  1.00 66.13       1SG1747
ATOM   1747  NH1 ARG   221      42.420  14.256 -16.699  1.00 66.13       1SG1748
ATOM   1748  NH2 ARG   221      44.474  13.132 -16.377  1.00 66.13       1SG1749
ATOM   1749  C   ARG   221      37.788  11.870 -20.716  1.00 66.13       1SG1750
ATOM   1750  O   ARG   221      37.536  10.932 -21.469  1.00 66.13       1SG1751
ATOM   1751  N   MET   222      37.115  13.031 -20.770  1.00101.42       1SG1752
ATOM   1752  CA  MET   222      36.037  13.161 -21.699  1.00101.42       1SG1753
ATOM   1753  CB  MET   222      34.728  13.646 -21.057  1.00101.42       1SG1754
ATOM   1754  CG  MET   222      34.097  12.580 -20.159  1.00101.42       1SG1755
ATOM   1755  SD  MET   222      32.681  13.143 -19.170  1.00101.42       1SG1756
ATOM   1756  CE  MET   222      33.699  13.866 -17.852  1.00101.42       1SG1757
ATOM   1757  C   MET   222      36.427  14.113 -22.776  1.00101.42       1SG1758
ATOM   1758  O   MET   222      37.465  14.770 -22.716  1.00101.42       1SG1759
ATOM   1759  N   MET   223      35.578  14.176 -23.815  1.00129.30       1SG1760
ATOM   1760  CA  MET   223      35.791  15.005 -24.960  1.00129.30       1SG1761
ATOM   1761  CB  MET   223      34.622  14.913 -25.953  1.00129.30       1SG1762
ATOM   1762  CG  MET   223      33.291  15.336 -25.337  1.00129.30       1SG1763
ATOM   1763  SD  MET   223      31.866  15.278 -26.461  1.00129.30       1SG1764
ATOM   1764  CE  MET   223      30.706  15.854 -25.190  1.00129.30       1SG1765
ATOM   1765  C   MET   223      35.826  16.415 -24.496  1.00129.30       1SG1766
ATOM   1766  O   MET   223      36.627  17.215 -24.973  1.00129.30       1SG1767
ATOM   1767  N   THR   224      34.948  16.749 -23.537  1.00 94.72       1SG1768
ATOM   1768  CA  THR   224      34.849  18.099 -23.083  1.00 94.72       1SG1769
ATOM   1769  CB  THR   224      33.834  18.255 -21.994  1.00 94.72       1SG1770
ATOM   1770  OG1 THR   224      32.561  17.815 -22.443  1.00 94.72       1SG1771
ATOM   1771  CG2 THR   224      33.773  19.739 -21.596  1.00 94.72       1SG1772
ATOM   1772  C   THR   224      36.165  18.531 -22.517  1.00 94.72       1SG1773
ATOM   1773  O   THR   224      36.657  19.610 -22.843  1.00 94.72       1SG1774
ATOM   1774  N   VAL   225      36.776  17.701 -21.650  1.00 96.93       1SG1775
ATOM   1775  CA  VAL   225      38.009  18.104 -21.035  1.00 96.93       1SG1776
ATOM   1776  CB  VAL   225      38.487  17.176 -19.955  1.00 96.93       1SG1777
ATOM   1777  CG1 VAL   225      37.427  17.146 -18.841  1.00 96.93       1SG1778
ATOM   1778  CG2 VAL   225      38.814  15.806 -20.566  1.00 96.93       1SG1779
ATOM   1779  C   VAL   225      39.088  18.202 -22.065  1.00 96.93       1SG1780
ATOM   1780  O   VAL   225      39.878  19.144 -22.055  1.00 96.93       1SG1781
ATOM   1781  N   ASP   226      39.151  17.225 -22.990  1.00 46.39       1SG1782
ATOM   1782  CA  ASP   226      40.193  17.230 -23.977  1.00 46.39       1SG1783
ATOM   1783  CB  ASP   226      40.129  16.016 -24.920  1.00 46.39       1SG1784
ATOM   1784  CG  ASP   226      40.530  14.778 -24.130  1.00 46.39       1SG1785
ATOM   1785  OD1 ASP   226      41.500  14.874 -23.331  1.00 46.39       1SG1786
ATOM   1786  OD2 ASP   226      39.866  13.722 -24.307  1.00 46.39       1SG1787
ATOM   1787  C   ASP   226      40.059  18.460 -24.816  1.00 46.39       1SG1788
ATOM   1788  O   ASP   226      41.044  19.139 -25.100  1.00 46.39       1SG1789
ATOM   1789  N   GLY   227      38.821  18.784 -25.228  1.00 30.22       1SG1790
ATOM   1790  CA  GLY   227      38.583  19.921 -26.069  1.00 30.22       1SG1791
ATOM   1791  C   GLY   227      38.938  21.169 -25.330  1.00 30.22       1SG1792
ATOM   1792  O   GLY   227      39.499  22.103 -25.898  1.00 30.22       1SG1793
ATOM   1793  N   ARG   228      38.599  21.218 -24.031  1.00139.77       1SG1794
ATOM   1794  CA  ARG   228      38.842  22.391 -23.248  1.00139.77       1SG1795
ATOM   1795  CB  ARG   228      38.348  22.221 -21.804  1.00139.77       1SG1796
ATOM   1796  CG  ARG   228      36.825  22.136 -21.702  1.00139.77       1SG1797
ATOM   1797  CD  ARG   228      36.191  23.387 -21.100  1.00139.77       1SG1798
ATOM   1798  NE  ARG   228      36.638  23.452 -19.682  1.00139.77       1SG1799
ATOM   1799  CZ  ARG   228      35.832  24.020 -18.740  1.00139.77       1SG1800
ATOM   1800  NH1 ARG   228      34.628  24.550 -19.105  1.00139.77       1SG1801
ATOM   1801  NH2 ARG   228      36.224  24.048 -17.432  1.00139.77       1SG1802
ATOM   1802  C   ARG   228      40.315  22.634 -23.208  1.00139.77       1SG1803
ATOM   1803  O   ARG   228      40.770  23.766 -23.364  1.00139.77       1SG1804
ATOM   1804  N   ASP   229      41.103  21.565 -22.998  1.00 39.86       1SG1805
ATOM   1805  CA  ASP   229      42.525  21.714 -22.912  1.00 39.86       1SG1806
ATOM   1806  CB  ASP   229      43.230  20.395 -22.546  1.00 39.86       1SG1807
ATOM   1807  CG  ASP   229      44.663  20.706 -22.134  1.00 39.86       1SG1808
ATOM   1808  OD1 ASP   229      45.300  21.579 -22.782  1.00 39.86       1SG1809
ATOM   1809  OD2 ASP   229      45.141  20.065 -21.159  1.00 39.86       1SG1810
ATOM   1810  C   ASP   229      43.054  22.168 -24.240  1.00 39.86       1SG1811
ATOM   1811  O   ASP   229      43.890  23.067 -24.309  1.00 39.86       1SG1812
ATOM   1812  N   MET   230      42.556  21.565 -25.336  1.00150.53       1SG1813
ATOM   1813  CA  MET   230      43.030  21.846 -26.664  1.00150.53       1SG1814
ATOM   1814  CB  MET   230      42.384  20.930 -27.719  1.00150.53       1SG1815
ATOM   1815  CG  MET   230      43.169  20.852 -29.030  1.00150.53       1SG1816
ATOM   1816  SD  MET   230      43.162  22.370 -30.026  1.00150.53       1SG1817
ATOM   1817  CE  MET   230      41.561  22.020 -30.809  1.00150.53       1SG1818
ATOM   1818  C   MET   230      42.706  23.269 -27.000  1.00150.53       1SG1819
ATOM   1819  O   MET   230      43.483  23.959 -27.660  1.00150.53       1SG1820
ATOM   1820  N   GLY   231      41.535  23.734 -26.537  1.00 64.10       1SG1821
ATOM   1821  CA  GLY   231      41.045  25.066 -26.742  1.00 64.10       1SG1822
ATOM   1822  C   GLY   231      42.007  25.998 -26.086  1.00 64.10       1SG1823
ATOM   1823  O   GLY   231      42.113  27.164 -26.466  1.00 64.10       1SG1824
ATOM   1824  N   GLU   232      42.730  25.490 -25.071  1.00240.53       1SG1825
ATOM   1825  CA  GLU   232      43.641  26.284 -24.305  1.00240.53       1SG1826
ATOM   1826  CB  GLU   232      44.539  27.172 -25.184  1.00240.53       1SG1827
ATOM   1827  CG  GLU   232      45.640  27.904 -24.419  1.00240.53       1SG1828
ATOM   1828  CD  GLU   232      46.423  28.726 -25.431  1.00240.53       1SG1829
ATOM   1829  OE1 GLU   232      45.974  28.795 -26.606  1.00240.53       1SG1830
ATOM   1830  OE2 GLU   232      47.478  29.296 -25.046  1.00240.53       1SG1831
ATOM   1831  C   GLU   232      42.853  27.156 -23.389  1.00240.53       1SG1832
ATOM   1832  O   GLU   232      43.296  28.235 -22.997  1.00240.53       1SG1833
ATOM   1833  N   HIS   233      41.641  26.694 -23.024  1.00383.42       1SG1834
ATOM   1834  CA  HIS   233      40.873  27.384 -22.032  1.00383.42       1SG1835
ATOM   1835  ND1 HIS   233      38.567  26.678 -24.408  1.00383.42       1SG1836
ATOM   1836  CG  HIS   233      38.648  27.437 -23.262  1.00383.42       1SG1837
ATOM   1837  CB  HIS   233      39.380  27.012 -22.022  1.00383.42       1SG1838
ATOM   1838  NE2 HIS   233      37.430  28.548 -24.802  1.00383.42       1SG1839
ATOM   1839  CD2 HIS   233      37.948  28.576 -23.519  1.00383.42       1SG1840
ATOM   1840  CE1 HIS   233      37.827  27.390 -25.296  1.00383.42       1SG1841
ATOM   1841  C   HIS   233      41.451  26.945 -20.728  1.00383.42       1SG1842
ATOM   1842  O   HIS   233      42.030  25.864 -20.637  1.00383.42       1SG1843
ATOM   1843  N   ALA   234      41.352  27.778 -19.679  1.00879.62       1SG1844
ATOM   1844  CA  ALA   234      41.916  27.329 -18.444  1.00879.62       1SG1845
ATOM   1845  CB  ALA   234      41.881  28.384 -17.325  1.00879.62       1SG1846
ATOM   1846  C   ALA   234      41.100  26.166 -17.999  1.00879.62       1SG1847
ATOM   1847  O   ALA   234      39.882  26.265 -17.867  1.00879.62       1SG1848
ATOM   1848  N   GLY   235      41.765  25.023 -17.750  1.00403.43       1SG1849
ATOM   1849  CA  GLY   235      41.046  23.861 -17.333  1.00403.43       1SG1850
ATOM   1850  C   GLY   235      40.826  23.981 -15.867  1.00403.43       1SG1851
ATOM   1851  O   GLY   235      41.548  24.698 -15.176  1.00403.43       1SG1852
ATOM   1852  N   LEU   236      39.813  23.265 -15.355  1.00771.71       1SG1853
ATOM   1853  CA  LEU   236      39.564  23.291 -13.949  1.00771.71       1SG1854
ATOM   1854  CB  LEU   236      38.098  23.569 -13.576  1.00771.71       1SG1855
ATOM   1855  CG  LEU   236      37.843  23.593 -12.058  1.00771.71       1SG1856
ATOM   1856  CD1 LEU   236      38.624  24.730 -11.375  1.00771.71       1SG1857
ATOM   1857  CD2 LEU   236      36.339  23.632 -11.745  1.00771.71       1SG1858
ATOM   1858  C   LEU   236      39.898  21.932 -13.451  1.00771.71       1SG1859
ATOM   1859  O   LEU   236      39.733  20.947 -14.167  1.00771.71       1SG1860
ATOM   1860  N   MET   237      40.409  21.836 -12.210  1.00393.20       1SG1861
ATOM   1861  CA  MET   237      40.698  20.517 -11.746  1.00393.20       1SG1862
ATOM   1862  CB  MET   237      41.529  20.468 -10.451  1.00393.20       1SG1863
ATOM   1863  CG  MET   237      42.012  19.057 -10.106  1.00393.20       1SG1864
ATOM   1864  SD  MET   237      43.108  18.957  -8.658  1.00393.20       1SG1865
ATOM   1865  CE  MET   237      41.808  19.310  -7.441  1.00393.20       1SG1866
ATOM   1866  C   MET   237      39.372  19.894 -11.481  1.00393.20       1SG1867
ATOM   1867  O   MET   237      38.571  20.412 -10.707  1.00393.20       1SG1868
ATOM   1868  N   TYR   238      39.099  18.760 -12.152  1.00287.12       1SG1869
ATOM   1869  CA  TYR   238      37.831  18.119 -11.994  1.00287.12       1SG1870
ATOM   1870  CB  TYR   238      36.875  18.433 -13.162  1.00287.12       1SG1871
ATOM   1871  CG  TYR   238      35.624  17.638 -13.012  1.00287.12       1SG1872
ATOM   1872  CD1 TYR   238      34.637  18.024 -12.136  1.00287.12       1SG1873
ATOM   1873  CD2 TYR   238      35.439  16.503 -13.769  1.00287.12       1SG1874
ATOM   1874  CE1 TYR   238      33.484  17.282 -12.013  1.00287.12       1SG1875
ATOM   1875  CE2 TYR   238      34.290  15.759 -13.650  1.00287.12       1SG1876
ATOM   1876  CZ  TYR   238      33.311  16.148 -12.769  1.00287.12       1SG1877
ATOM   1877  OH  TYR   238      32.128  15.386 -12.646  1.00287.12       1SG1878
ATOM   1878  C   TYR   238      38.085  16.618 -11.982  1.00287.12       1SG1879
ATOM   1879  O   TYR   238      39.212  16.209 -12.368  1.00287.12       1SG1880
ATOM   1880  OXT TYR   238      37.157  15.863 -11.589  1.00287.12       1SG1881
TER
END
