
#######################################################
#                                                     #
#                        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   10 (   84),  selected   10 , name T0386TS074_4_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected   10 , name T0386_D1.pdb
# PARAMETERS: T0386TS074_4_2-D1.T0386_D1.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:     9       210 - 218         0.91    10.42
  LCS_AVERAGE:      3.93

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       210 - 218         0.91    10.42
  LCS_AVERAGE:      3.93

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       210 - 218         0.91    10.42
  LCS_AVERAGE:      3.93

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:  206
LCS_GDT     P     209     P     209      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
LCS_GDT     M     210     M     210      9    9    9     0    6    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Q     211     Q     211      9    9    9     6    7    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     H     212     H     212      9    9    9     6    7    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L     213     L     213      9    9    9     6    7    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     F     214     F     214      9    9    9     6    7    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     E     215     E     215      9    9    9     6    7    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     D     216     D     216      9    9    9     5    7    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     I     217     I     217      9    9    9     6    7    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     S     218     S     218      9    9    9     3    3    3    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   3.93  (   3.93    3.93    3.93 )

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      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   2.91   3.40   3.88   4.37   4.37   4.37   4.37   4.37   4.37   4.37   4.37   4.37   4.37   4.37   4.37   4.37   4.37   4.37   4.37   4.37
GDT RMS_LOCAL    0.40   0.44   0.67   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91   0.91
GDT RMS_ALL_CA  10.27  10.27  10.36  10.42  10.42  10.42  10.42  10.42  10.42  10.42  10.42  10.42  10.42  10.42  10.42  10.42  10.42  10.42  10.42  10.42

#      Molecule1      Molecule2       DISTANCE
LGA    P     209      P     209         32.845
LGA    M     210      M     210          1.269
LGA    Q     211      Q     211          0.771
LGA    H     212      H     212          0.735
LGA    L     213      L     213          0.507
LGA    F     214      F     214          0.524
LGA    E     215      E     215          0.647
LGA    D     216      D     216          0.815
LGA    I     217      I     217          0.423
LGA    S     218      S     218          1.720

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  206    4.0      9    0.91     4.126     4.147     0.889

LGA_LOCAL      RMSD =  0.913  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.423  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  8.481  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.434371 * X  +  -0.844347 * Y  +  -0.313689 * Z  +  60.032608
  Y_new =  -0.868120 * X  +  -0.299570 * Y  +  -0.395760 * Z  +  67.288628
  Z_new =   0.240187 * X  +   0.444226 * Y  +  -0.863118 * Z  +  40.976192 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.666274   -0.475319  [ DEG:   152.7662    -27.2338 ]
  Theta =  -0.242558   -2.899035  [ DEG:   -13.8976   -166.1024 ]
  Phi   =  -1.106862    2.034731  [ DEG:   -63.4185    116.5815 ]
 
# 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: T0386TS074_4_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_4_2-D1.T0386_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  206   4.0    9   0.91   4.147     8.48
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209      14.504  79.238  52.362  1.00  0.22
ATOM   1387  CA  PRO   209      15.259  77.983  52.325  1.00  0.22
ATOM   1388  C   PRO   209      16.767  78.190  52.480  1.00  0.22
ATOM   1389  O   PRO   209      17.392  77.634  53.379  1.00  0.22
ATOM   1390  CB  PRO   209      14.886  77.406  50.962  1.00  0.22
ATOM   1391  CG  PRO   209      13.956  78.440  50.418  1.00  0.32
ATOM   1392  CD  PRO   209      14.342  79.764  50.954  1.00  0.32
ATOM   1393  N   MET   210      14.329  49.750  66.325  1.00  0.20
ATOM   1394  CA  MET   210      12.999  49.433  65.877  1.00  0.20
ATOM   1395  C   MET   210      11.918  49.565  66.915  1.00  0.20
ATOM   1396  O   MET   210      10.991  50.328  66.689  1.00  0.20
ATOM   1397  CB  MET   210      12.999  48.021  65.291  1.00  0.20
ATOM   1398  CG  MET   210      11.661  47.564  64.702  1.00  0.30
ATOM   1399  SD  MET   210      11.166  48.557  63.238  1.00  0.30
ATOM   1400  CE  MET   210      12.253  47.915  62.009  1.00  0.50
ATOM   1401  N   GLN   211      12.062  49.220  68.013  1.00  0.20
ATOM   1402  CA  GLN   211      10.961  49.055  68.962  1.00  0.20
ATOM   1403  C   GLN   211      10.874  50.187  70.009  1.00  0.20
ATOM   1404  O   GLN   211       9.784  50.656  70.317  1.00  0.20
ATOM   1405  CB  GLN   211      11.016  47.672  69.637  1.00  0.20
ATOM   1406  CG  GLN   211       9.884  47.380  70.581  1.00  0.30
ATOM   1407  CD  GLN   211       8.557  47.292  69.980  1.00  0.30
ATOM   1408  OE1 GLN   211       8.342  46.435  69.104  1.00  0.50
ATOM   1409  NE2 GLN   211       7.602  48.109  70.418  1.00  0.50
ATOM   1410  N   HIS   212      12.012  50.638  70.526  1.00  0.20
ATOM   1411  CA  HIS   212      12.019  51.661  71.558  1.00  0.20
ATOM   1412  C   HIS   212      11.573  53.029  71.021  1.00  0.20
ATOM   1413  O   HIS   212      10.786  53.743  71.666  1.00  0.20
ATOM   1414  CB  HIS   212      13.397  51.759  72.196  1.00  0.20
ATOM   1415  CG  HIS   212      13.498  52.762  73.351  1.00  0.30
ATOM   1416  ND1 HIS   212      13.638  54.138  73.099  1.00  0.30
ATOM   1417  CD2 HIS   212      13.371  52.543  74.647  1.00  0.50
ATOM   1418  CE1 HIS   212      13.621  54.790  74.308  1.00  0.50
ATOM   1419  NE2 HIS   212      13.461  53.807  75.278  1.00  0.80
ATOM   1420  N   LEU   213      12.064  53.390  69.835  1.00  0.20
ATOM   1421  CA  LEU   213      11.655  54.619  69.167  1.00  0.20
ATOM   1422  C   LEU   213      10.171  54.566  68.835  1.00  0.20
ATOM   1423  O   LEU   213       9.453  55.540  69.071  1.00  0.20
ATOM   1424  CB  LEU   213      12.521  54.895  67.903  1.00  0.20
ATOM   1425  CG  LEU   213      13.966  55.153  68.332  1.00  0.30
ATOM   1426  CD1 LEU   213      14.843  55.301  67.170  1.00  0.30
ATOM   1427  CD2 LEU   213      13.943  56.680  68.965  1.00  0.50
ATOM   1428  N   PHE   214       9.697  53.444  68.295  1.00  0.20
ATOM   1429  CA  PHE   214       8.271  53.324  67.980  1.00  0.20
ATOM   1430  C   PHE   214       7.409  53.448  69.267  1.00  0.20
ATOM   1431  O   PHE   214       6.561  54.329  69.377  1.00  0.20
ATOM   1432  CB  PHE   214       7.949  52.007  67.224  1.00  0.20
ATOM   1433  CG  PHE   214       8.627  52.001  65.843  1.00  0.30
ATOM   1434  CD1 PHE   214       8.823  53.240  65.217  1.00  0.30
ATOM   1435  CD2 PHE   214       8.590  50.869  65.065  1.00  0.50
ATOM   1436  CE1 PHE   214       9.197  53.264  63.889  1.00  0.50
ATOM   1437  CE2 PHE   214       8.976  50.859  63.751  1.00  0.80
ATOM   1438  CZ  PHE   214       9.310  52.101  63.150  1.00  0.80
ATOM   1439  N   GLU   215       7.659  52.608  70.255  1.00  0.20
ATOM   1440  CA  GLU   215       6.788  52.567  71.422  1.00  0.20
ATOM   1441  C   GLU   215       6.892  53.748  72.405  1.00  0.20
ATOM   1442  O   GLU   215       5.868  54.198  72.896  1.00  0.20
ATOM   1443  CB  GLU   215       6.842  51.186  72.095  1.00  0.20
ATOM   1444  CG  GLU   215       6.291  50.103  71.208  1.00  0.30
ATOM   1445  CD  GLU   215       4.764  50.284  70.925  1.00  0.30
ATOM   1446  OE1 GLU   215       3.980  50.656  71.812  1.00  0.50
ATOM   1447  OE2 GLU   215       4.367  49.992  69.764  1.00  0.50
ATOM   1448  N   ASP   216       8.100  54.242  72.677  1.00  0.20
ATOM   1449  CA  ASP   216       8.258  55.456  73.478  1.00  0.20
ATOM   1450  C   ASP   216       7.698  56.661  72.734  1.00  0.20
ATOM   1451  O   ASP   216       7.220  57.610  73.361  1.00  0.20
ATOM   1452  CB  ASP   216       9.716  55.703  73.868  1.00  0.20
ATOM   1453  CG  ASP   216      10.257  54.719  74.879  1.00  0.30
ATOM   1454  OD1 ASP   216       9.490  53.975  75.541  1.00  0.30
ATOM   1455  OD2 ASP   216      11.459  54.672  75.150  1.00  0.50
ATOM   1456  N   ILE   217       7.222  56.815  71.570  1.00  0.20
ATOM   1457  CA  ILE   217       6.632  57.842  70.733  1.00  0.20
ATOM   1458  C   ILE   217       5.127  57.941  70.869  1.00  0.20
ATOM   1459  O   ILE   217       4.585  59.035  70.975  1.00  0.20
ATOM   1460  CB  ILE   217       6.575  58.722  71.984  1.00  0.20
ATOM   1461  CG1 ILE   217       7.932  59.047  72.609  1.00  0.30
ATOM   1462  CG2 ILE   217       5.595  58.063  72.963  1.00  0.30
ATOM   1463  CD1 ILE   217       8.472  60.400  72.269  1.00  0.50
ATOM   1464  N   SER   218       4.007  58.295  71.000  1.00  0.20
ATOM   1465  CA  SER   218       2.578  58.082  71.221  1.00  0.20
ATOM   1466  C   SER   218       2.195  58.446  72.662  1.00  0.20
ATOM   1467  O   SER   218       1.198  59.120  72.882  1.00  0.20
ATOM   1468  CB  SER   218       2.171  56.606  70.931  1.00  0.20
ATOM   1469  OG  SER   218       0.663  56.409  71.093  1.00  0.30
TER
END
