
#######################################################
#                                                     #
#                        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   15 (  130),  selected   15 , name T0386TS103_5-D2
# Molecule2: number of CA atoms   81 (  636),  selected   15 , name T0386_D2.pdb
# PARAMETERS: T0386TS103_5-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:    15       219 - 233         3.42     3.42
  LCS_AVERAGE:     18.52

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       222 - 233         1.79     4.15
  LCS_AVERAGE:     13.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       225 - 233         0.94     4.04
  LCS_AVERAGE:      8.89

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   15     4    4    4    5    5    6    6   10   11   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     P     220     P     220      4    5   15     4    4    4    5    5    6    6    7    8    8   11   14   15   15   15   15   15   15   15   15 
LCS_GDT     E     221     E     221      4    5   15     4    4    4    5    5    6    6    7   11   12   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     K     222     K     222      5   12   15     4    5    7   10   11   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     I     223     I     223      5   12   15     4    5    5   10   11   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     R     224     R     224      5   12   15     4    5    6   10   11   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     L     225     L     225      9   12   15     4    7    8   10   11   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     L     226     L     226      9   12   15     6    7    8   10   11   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     K     227     K     227      9   12   15     6    7    8   10   11   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     E     228     E     228      9   12   15     6    7    8   10   11   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     F     229     F     229      9   12   15     6    7    8   10   11   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     M     230     M     230      9   12   15     6    7    8   10   11   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     H     231     H     231      9   12   15     6    7    8   10   11   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     T     232     T     232      9   12   15     3    7    8    9   11   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_GDT     M     233     M     233      9   12   15     3    3    8    9   10   12   12   12   12   13   13   14   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:  13.50  (   8.89   13.09   18.52 )

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     11     12     12     12     12     13     13     14     15     15     15     15     15     15     15     15 
GDT PERCENT_CA   7.41   8.64   9.88  12.35  13.58  14.81  14.81  14.81  14.81  16.05  16.05  17.28  18.52  18.52  18.52  18.52  18.52  18.52  18.52  18.52
GDT RMS_LOCAL    0.26   0.44   0.64   1.42   1.62   1.79   1.79   1.79   1.79   2.51   2.51   3.03   3.42   3.42   3.42   3.42   3.42   3.42   3.42   3.42
GDT RMS_ALL_CA   4.00   4.12   3.83   4.36   4.14   4.15   4.15   4.15   4.15   3.69   3.69   3.52   3.42   3.42   3.42   3.42   3.42   3.42   3.42   3.42

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          8.205
LGA    P     220      P     220          9.952
LGA    E     221      E     221          7.305
LGA    K     222      K     222          1.573
LGA    I     223      I     223          2.709
LGA    R     224      R     224          2.644
LGA    L     225      L     225          1.502
LGA    L     226      L     226          1.165
LGA    K     227      K     227          1.741
LGA    E     228      E     228          1.652
LGA    F     229      F     229          0.675
LGA    M     230      M     230          0.563
LGA    H     231      H     231          1.112
LGA    T     232      T     232          1.899
LGA    M     233      M     233          2.595

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   81    4.0     12    1.79    13.580    13.917     0.634

LGA_LOCAL      RMSD =  1.792  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.149  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  3.423  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.982603 * X  +  -0.145907 * Y  +   0.114906 * Z  +  15.704066
  Y_new =  -0.181264 * X  +   0.618721 * Y  +  -0.764413 * Z  +  24.108210
  Z_new =   0.040439 * X  +  -0.771943 * Y  +  -0.634405 * Z  + 119.734276 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.258707    0.882886  [ DEG:  -129.4144     50.5856 ]
  Theta =  -0.040450   -3.101143  [ DEG:    -2.3176   -177.6824 ]
  Phi   =  -2.959170    0.182423  [ DEG:  -169.5479     10.4521 ]
 
# 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: T0386TS103_5-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS103_5-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   81   4.0   12   1.79  13.917     3.42
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS103_5-D2
PFRMAT TS
TARGET T0386
MODEL 5
PARENT 2g03_A
ATOM   1761  N   ASN   219       9.132  56.297  81.318  1.00104.89       1SG1762
ATOM   1762  CA  ASN   219       9.031  55.983  79.925  1.00104.89       1SG1763
ATOM   1763  CB  ASN   219       7.603  55.688  79.449  1.00104.89       1SG1764
ATOM   1764  CG  ASN   219       7.716  55.127  78.041  1.00104.89       1SG1765
ATOM   1765  OD1 ASN   219       8.134  55.828  77.120  1.00104.89       1SG1766
ATOM   1766  ND2 ASN   219       7.354  53.828  77.870  1.00104.89       1SG1767
ATOM   1767  C   ASN   219       9.541  57.147  79.161  1.00104.89       1SG1768
ATOM   1768  O   ASN   219       9.112  58.292  79.314  1.00104.89       1SG1769
ATOM   1769  N   PRO   220      10.488  56.827  78.336  1.00164.63       1SG1770
ATOM   1770  CA  PRO   220      11.149  57.839  77.585  1.00164.63       1SG1771
ATOM   1771  CD  PRO   220      11.332  55.662  78.550  1.00164.63       1SG1772
ATOM   1772  CB  PRO   220      12.333  57.153  76.908  1.00164.63       1SG1773
ATOM   1773  CG  PRO   220      12.672  56.001  77.874  1.00164.63       1SG1774
ATOM   1774  C   PRO   220      10.294  58.637  76.677  1.00164.63       1SG1775
ATOM   1775  O   PRO   220      10.324  59.856  76.789  1.00164.63       1SG1776
ATOM   1776  N   GLU   221       9.471  57.990  75.840  1.00108.23       1SG1777
ATOM   1777  CA  GLU   221       8.768  58.718  74.826  1.00108.23       1SG1778
ATOM   1778  CB  GLU   221       7.929  57.807  73.913  1.00108.23       1SG1779
ATOM   1779  CG  GLU   221       7.162  58.574  72.833  1.00108.23       1SG1780
ATOM   1780  CD  GLU   221       6.378  57.567  72.002  1.00108.23       1SG1781
ATOM   1781  OE1 GLU   221       5.882  56.571  72.593  1.00108.23       1SG1782
ATOM   1782  OE2 GLU   221       6.264  57.780  70.766  1.00108.23       1SG1783
ATOM   1783  C   GLU   221       7.832  59.702  75.415  1.00108.23       1SG1784
ATOM   1784  O   GLU   221       7.808  60.843  74.948  1.00108.23       1SG1785
ATOM   1785  N   LYS   222       7.116  59.276  76.483  1.00186.29       1SG1786
ATOM   1786  CA  LYS   222       6.029  59.963  77.130  1.00186.29       1SG1787
ATOM   1787  CB  LYS   222       5.810  59.537  78.592  1.00186.29       1SG1788
ATOM   1788  CG  LYS   222       5.304  58.099  78.724  1.00186.29       1SG1789
ATOM   1789  CD  LYS   222       5.345  57.555  80.152  1.00186.29       1SG1790
ATOM   1790  CE  LYS   222       4.801  56.131  80.283  1.00186.29       1SG1791
ATOM   1791  NZ  LYS   222       4.876  55.694  81.695  1.00186.29       1SG1792
ATOM   1792  C   LYS   222       6.251  61.429  77.083  1.00186.29       1SG1793
ATOM   1793  O   LYS   222       7.380  61.901  77.189  1.00186.29       1SG1794
ATOM   1794  N   ILE   223       5.141  62.180  76.952  1.00 94.01       1SG1795
ATOM   1795  CA  ILE   223       5.189  63.578  76.660  1.00 94.01       1SG1796
ATOM   1796  CB  ILE   223       3.841  64.231  76.737  1.00 94.01       1SG1797
ATOM   1797  CG2 ILE   223       4.047  65.744  76.581  1.00 94.01       1SG1798
ATOM   1798  CG1 ILE   223       2.884  63.630  75.693  1.00 94.01       1SG1799
ATOM   1799  CD1 ILE   223       1.428  64.042  75.899  1.00 94.01       1SG1800
ATOM   1800  C   ILE   223       6.051  64.236  77.668  1.00 94.01       1SG1801
ATOM   1801  O   ILE   223       6.877  65.076  77.321  1.00 94.01       1SG1802
ATOM   1802  N   ARG   224       5.903  63.873  78.947  1.00120.05       1SG1803
ATOM   1803  CA  ARG   224       6.773  64.513  79.873  1.00120.05       1SG1804
ATOM   1804  CB  ARG   224       6.505  64.091  81.329  1.00120.05       1SG1805
ATOM   1805  CG  ARG   224       5.192  64.638  81.895  1.00120.05       1SG1806
ATOM   1806  CD  ARG   224       5.387  65.778  82.898  1.00120.05       1SG1807
ATOM   1807  NE  ARG   224       6.024  65.194  84.112  1.00120.05       1SG1808
ATOM   1808  CZ  ARG   224       6.543  65.999  85.085  1.00120.05       1SG1809
ATOM   1809  NH1 ARG   224       6.481  67.358  84.962  1.00120.05       1SG1810
ATOM   1810  NH2 ARG   224       7.129  65.441  86.184  1.00120.05       1SG1811
ATOM   1811  C   ARG   224       8.191  64.147  79.543  1.00120.05       1SG1812
ATOM   1812  O   ARG   224       9.052  65.018  79.456  1.00120.05       1SG1813
ATOM   1813  N   LEU   225       8.502  62.850  79.351  1.00127.57       1SG1814
ATOM   1814  CA  LEU   225       9.901  62.586  79.169  1.00127.57       1SG1815
ATOM   1815  CB  LEU   225      10.270  61.110  79.356  1.00127.57       1SG1816
ATOM   1816  CG  LEU   225      10.062  60.657  80.812  1.00127.57       1SG1817
ATOM   1817  CD1 LEU   225       8.572  60.549  81.168  1.00127.57       1SG1818
ATOM   1818  CD2 LEU   225      10.866  59.392  81.123  1.00127.57       1SG1819
ATOM   1819  C   LEU   225      10.496  63.055  77.870  1.00127.57       1SG1820
ATOM   1820  O   LEU   225      11.293  63.992  77.860  1.00127.57       1SG1821
ATOM   1821  N   LEU   226      10.112  62.446  76.728  1.00 91.59       1SG1822
ATOM   1822  CA  LEU   226      10.782  62.792  75.496  1.00 91.59       1SG1823
ATOM   1823  CB  LEU   226      10.513  61.851  74.295  1.00 91.59       1SG1824
ATOM   1824  CG  LEU   226      11.234  60.488  74.303  1.00 91.59       1SG1825
ATOM   1825  CD1 LEU   226      10.920  59.680  73.033  1.00 91.59       1SG1826
ATOM   1826  CD2 LEU   226      12.739  60.636  74.559  1.00 91.59       1SG1827
ATOM   1827  C   LEU   226      10.383  64.135  75.005  1.00 91.59       1SG1828
ATOM   1828  O   LEU   226      11.218  64.987  74.710  1.00 91.59       1SG1829
ATOM   1829  N   LYS   227       9.066  64.356  74.909  1.00138.83       1SG1830
ATOM   1830  CA  LYS   227       8.632  65.559  74.278  1.00138.83       1SG1831
ATOM   1831  CB  LYS   227       7.109  65.598  74.071  1.00138.83       1SG1832
ATOM   1832  CG  LYS   227       6.635  64.471  73.150  1.00138.83       1SG1833
ATOM   1833  CD  LYS   227       7.286  64.500  71.765  1.00138.83       1SG1834
ATOM   1834  CE  LYS   227       7.053  63.229  70.943  1.00138.83       1SG1835
ATOM   1835  NZ  LYS   227       7.804  62.097  71.532  1.00138.83       1SG1836
ATOM   1836  C   LYS   227       9.034  66.722  75.106  1.00138.83       1SG1837
ATOM   1837  O   LYS   227       9.612  67.684  74.605  1.00138.83       1SG1838
ATOM   1838  N   GLU   228       8.770  66.635  76.418  1.00 99.55       1SG1839
ATOM   1839  CA  GLU   228       9.054  67.740  77.276  1.00 99.55       1SG1840
ATOM   1840  CB  GLU   228       8.518  67.588  78.706  1.00 99.55       1SG1841
ATOM   1841  CG  GLU   228       7.030  67.902  78.854  1.00 99.55       1SG1842
ATOM   1842  CD  GLU   228       6.896  69.419  78.819  1.00 99.55       1SG1843
ATOM   1843  OE1 GLU   228       7.356  70.028  77.818  1.00 99.55       1SG1844
ATOM   1844  OE2 GLU   228       6.344  69.993  79.797  1.00 99.55       1SG1845
ATOM   1845  C   GLU   228      10.525  67.958  77.369  1.00 99.55       1SG1846
ATOM   1846  O   GLU   228      10.958  69.105  77.477  1.00 99.55       1SG1847
ATOM   1847  N   PHE   229      11.342  66.882  77.335  1.00 84.91       1SG1848
ATOM   1848  CA  PHE   229      12.738  67.150  77.551  1.00 84.91       1SG1849
ATOM   1849  CB  PHE   229      13.685  65.929  77.691  1.00 84.91       1SG1850
ATOM   1850  CG  PHE   229      13.979  65.244  76.398  1.00 84.91       1SG1851
ATOM   1851  CD1 PHE   229      14.899  65.770  75.516  1.00 84.91       1SG1852
ATOM   1852  CD2 PHE   229      13.385  64.046  76.087  1.00 84.91       1SG1853
ATOM   1853  CE1 PHE   229      15.185  65.141  74.327  1.00 84.91       1SG1854
ATOM   1854  CE2 PHE   229      13.668  63.413  74.899  1.00 84.91       1SG1855
ATOM   1855  CZ  PHE   229      14.565  63.959  74.013  1.00 84.91       1SG1856
ATOM   1856  C   PHE   229      13.246  68.014  76.449  1.00 84.91       1SG1857
ATOM   1857  O   PHE   229      14.007  68.950  76.686  1.00 84.91       1SG1858
ATOM   1858  N   MET   230      12.818  67.739  75.205  1.00 90.06       1SG1859
ATOM   1859  CA  MET   230      13.305  68.529  74.114  1.00 90.06       1SG1860
ATOM   1860  CB  MET   230      12.673  68.153  72.763  1.00 90.06       1SG1861
ATOM   1861  CG  MET   230      13.189  69.004  71.600  1.00 90.06       1SG1862
ATOM   1862  SD  MET   230      12.393  68.657  70.002  1.00 90.06       1SG1863
ATOM   1863  CE  MET   230      10.786  69.335  70.507  1.00 90.06       1SG1864
ATOM   1864  C   MET   230      12.929  69.955  74.367  1.00 90.06       1SG1865
ATOM   1865  O   MET   230      13.730  70.864  74.152  1.00 90.06       1SG1866
ATOM   1866  N   HIS   231      11.691  70.191  74.841  1.00 95.55       1SG1867
ATOM   1867  CA  HIS   231      11.243  71.534  75.058  1.00 95.55       1SG1868
ATOM   1868  ND1 HIS   231       8.316  69.977  74.250  1.00 95.55       1SG1869
ATOM   1869  CG  HIS   231       8.784  71.251  74.480  1.00 95.55       1SG1870
ATOM   1870  CB  HIS   231       9.783  71.610  75.538  1.00 95.55       1SG1871
ATOM   1871  NE2 HIS   231       7.297  71.299  72.782  1.00 95.55       1SG1872
ATOM   1872  CD2 HIS   231       8.150  72.046  73.574  1.00 95.55       1SG1873
ATOM   1873  CE1 HIS   231       7.429  70.063  73.225  1.00 95.55       1SG1874
ATOM   1874  C   HIS   231      12.082  72.223  76.092  1.00 95.55       1SG1875
ATOM   1875  O   HIS   231      12.563  73.327  75.853  1.00 95.55       1SG1876
ATOM   1876  N   THR   232      12.308  71.597  77.264  1.00226.80       1SG1877
ATOM   1877  CA  THR   232      13.024  72.309  78.292  1.00226.80       1SG1878
ATOM   1878  CB  THR   232      12.406  72.133  79.656  1.00226.80       1SG1879
ATOM   1879  OG1 THR   232      13.142  72.856  80.632  1.00226.80       1SG1880
ATOM   1880  CG2 THR   232      12.330  70.640  80.012  1.00226.80       1SG1881
ATOM   1881  C   THR   232      14.448  71.856  78.345  1.00226.80       1SG1882
ATOM   1882  O   THR   232      14.903  71.216  79.284  1.00226.80       1SG1883
ATOM   1883  N   MET   233      15.232  72.246  77.341  1.00243.11       1SG1884
ATOM   1884  CA  MET   233      16.592  71.823  77.252  1.00243.11       1SG1885
ATOM   1885  CB  MET   233      17.081  71.999  75.847  1.00243.11       1SG1886
ATOM   1886  CG  MET   233      16.587  70.876  74.934  1.00243.11       1SG1887
ATOM   1887  SD  MET   233      17.259  69.242  75.368  1.00243.11       1SG1888
ATOM   1888  CE  MET   233      16.498  68.383  73.962  1.00243.11       1SG1889
ATOM   1889  C   MET   233      17.505  72.419  78.304  1.00243.11       1SG1890
ATOM   1890  O   MET   233      18.492  71.791  78.683  1.00243.11       1SG1891
TER
END
