
#######################################################
#                                                     #
#                        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   16 (  125),  selected   16 , name T0383TS009_1_3
# Molecule2: number of CA atoms  125 ( 1020),  selected   16 , name T0383.pdb
# PARAMETERS: T0383TS009_1_3.T0383.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:    14       114 - 127         4.97     6.05
  LCS_AVERAGE:     11.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       112 - 116         1.99    15.31
  LONGEST_CONTINUOUS_SEGMENT:     5       113 - 117         1.54    18.62
  LONGEST_CONTINUOUS_SEGMENT:     5       118 - 122         1.52     9.62
  LONGEST_CONTINUOUS_SEGMENT:     5       122 - 126         1.83     6.62
  LCS_AVERAGE:      3.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       118 - 121         0.89    11.38
  LCS_AVERAGE:      2.60

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:  125
LCS_GDT     E     112     E     112      3    5   12     3    3    3    3    5    5    5    7    8    9    9   10   12   13   15   15   15   15   16   16 
LCS_GDT     V     113     V     113      3    5   12     3    4    4    4    5    5    6    7    8    9    9   10   12   13   15   15   15   15   16   16 
LCS_GDT     T     114     T     114      3    5   14     3    3    4    4    5    6    6    7    8    9    9   10   11   13   15   15   15   15   16   16 
LCS_GDT     E     115     E     115      3    5   14     3    3    4    4    5    5    6    6    6    7    9   11   12   13   15   15   15   15   16   16 
LCS_GDT     I     116     I     116      3    5   14     3    3    4    5    6    8    8    8    9   10   11   11   12   13   15   15   15   15   16   16 
LCS_GDT     A     117     A     117      3    5   14     3    4    4    4    5    8    8    8    9   10   11   11   12   13   15   15   15   15   16   16 
LCS_GDT     L     118     L     118      4    5   14     3    4    4    4    5    7    8    8    9   10   11   11   12   13   15   15   15   15   16   16 
LCS_GDT     D     119     D     119      4    5   14     3    4    4    4    5    6    8    8    9   10   11   11   12   13   13   15   15   15   16   16 
LCS_GDT     L     120     L     120      4    5   14     3    3    4    5    6    8    8    8    9   10   11   11   12   13   15   15   15   15   16   16 
LCS_GDT     P     121     P     121      4    5   14     3    3    4    4    5    7    8    8    9   10   11   11   12   13   15   15   15   15   16   16 
LCS_GDT     G     122     G     122      3    5   14     3    3    4    5    6    8    8    8    9   10   11   11   12   13   15   15   15   15   16   16 
LCS_GDT     I     123     I     123      3    5   14     3    3    4    4    6    8    8    8    9   10   11   11   12   13   15   15   15   15   16   16 
LCS_GDT     N     124     N     124      3    5   14     3    3    4    4    6    8    8    8    9   10   11   11   12   13   15   15   15   15   16   16 
LCS_GDT     L     125     L     125      3    5   14     3    3    4    5    6    8    8    8    9   10   11   11   12   13   15   15   15   15   16   16 
LCS_GDT     E     126     E     126      3    5   14     3    3    3    5    6    8    8    8    9   10   11   11   12   13   15   15   15   15   16   16 
LCS_GDT     F     127     F     127      3    4   14     0    3    3    4    4    4    4    5    7    9   10   11   12   13   15   15   15   15   16   16 
LCS_AVERAGE  LCS_A:   5.85  (   2.60    3.95   11.00 )

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      3      4      4      5      6      8      8      8      9     10     11     11     12     13     15     15     15     15     16     16 
GDT PERCENT_CA   2.40   3.20   3.20   4.00   4.80   6.40   6.40   6.40   7.20   8.00   8.80   8.80   9.60  10.40  12.00  12.00  12.00  12.00  12.80  12.80
GDT RMS_LOCAL    0.02   0.50   0.50   1.59   1.75   2.22   2.22   2.22   2.68   3.36   3.52   3.52   4.07   4.39   5.52   5.47   5.47   5.47   5.84   5.84
GDT RMS_ALL_CA  13.08  16.11  16.11   6.50   6.48   6.28   6.28   6.28   6.41   7.05   6.69   6.69   6.15   6.27   5.93   6.19   6.19   6.19   5.84   5.84

#      Molecule1      Molecule2       DISTANCE
LGA    E     112      E     112         10.967
LGA    V     113      V     113         11.924
LGA    T     114      T     114         10.555
LGA    E     115      E     115          7.416
LGA    I     116      I     116          2.190
LGA    A     117      A     117          3.592
LGA    L     118      L     118          7.125
LGA    D     119      D     119          6.813
LGA    L     120      L     120          1.577
LGA    P     121      P     121          4.421
LGA    G     122      G     122          1.542
LGA    I     123      I     123          2.912
LGA    N     124      N     124          2.550
LGA    L     125      L     125          1.621
LGA    E     126      E     126          2.216
LGA    F     127      F     127          8.116

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  125    4.0      8    2.22     6.400     5.886     0.345

LGA_LOCAL      RMSD =  2.221  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.406  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  5.845  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.204236 * X  +   0.137822 * Y  +  -0.969171 * Z  +  13.048238
  Y_new =  -0.968994 * X  +   0.169106 * Y  +  -0.180151 * Z  +   1.233466
  Z_new =   0.139064 * X  +   0.975914 * Y  +   0.168086 * Z  + -55.347088 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.400235   -1.741357  [ DEG:    80.2276    -99.7724 ]
  Theta =  -0.139517   -3.002076  [ DEG:    -7.9937   -172.0063 ]
  Phi   =  -1.363065    1.778527  [ DEG:   -78.0979    101.9021 ]
 
# 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: T0383TS009_1_3                                
REMARK     2: T0383.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0383TS009_1_3.T0383.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16  125   4.0    8   2.22   5.886     5.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0383TS009_1_3
REMARK PARENT number 3
PFRMAT TS                                                                       
TARGET T0383                                                                    
PARENT N/A                                                                      
ATOM    910  N   GLU   112      20.023  24.325 -13.086  1.00  0.00              
ATOM    911  CA  GLU   112      19.207  23.206 -12.629  1.00  0.00              
ATOM    912  C   GLU   112      19.915  21.875 -12.863  1.00  0.00              
ATOM    913  O   GLU   112      19.338  20.809 -12.653  1.00  0.00              
ATOM    914  CB  GLU   112      18.863  23.365 -11.146  1.00  0.00              
ATOM    915  CG  GLU   112      17.400  23.112 -10.819  1.00  0.00              
ATOM    916  CD  GLU   112      16.956  23.819  -9.554  1.00  0.00              
ATOM    917  OE1 GLU   112      16.060  24.685  -9.640  1.00  0.00              
ATOM    918  OE2 GLU   112      17.504  23.507  -8.475  1.00  0.00              
ATOM    919  N   VAL   113      21.169  21.947 -13.299  1.00  0.00              
ATOM    920  CA  VAL   113      21.975  20.722 -13.568  1.00  0.00              
ATOM    921  C   VAL   113      21.366  19.500 -12.888  1.00  0.00              
ATOM    922  O   VAL   113      21.928  18.964 -11.932  1.00  0.00              
ATOM    923  CB  VAL   113      22.099  20.448 -15.078  1.00  0.00              
ATOM    924  CG1 VAL   113      23.455  20.904 -15.593  1.00  0.00              
ATOM    925  CG2 VAL   113      20.973  21.133 -15.838  1.00  0.00              
ATOM    926  N   THR   114      20.214  19.064 -13.386  1.00  0.00              
ATOM    927  CA  THR   114      19.512  17.879 -12.815  1.00  0.00              
ATOM    928  C   THR   114      19.823  17.715 -11.332  1.00  0.00              
ATOM    929  O   THR   114      18.921  17.524 -10.516  1.00  0.00              
ATOM    930  CB  THR   114      17.987  17.983 -13.002  1.00  0.00              
ATOM    931  OG1 THR   114      17.593  19.361 -12.989  1.00  0.00              
ATOM    932  CG2 THR   114      17.566  17.353 -14.322  1.00  0.00              
ATOM    933  N   GLU   115      21.105  17.792 -10.989  1.00  0.00              
ATOM    934  CA  GLU   115      21.537  17.653  -9.604  1.00  0.00              
ATOM    935  C   GLU   115      20.751  18.581  -8.684  1.00  0.00              
ATOM    936  O   GLU   115      21.205  19.678  -8.361  1.00  0.00              
ATOM    937  CB  GLU   115      21.388  16.202  -9.140  1.00  0.00              
ATOM    938  CG  GLU   115      22.707  15.470  -8.953  1.00  0.00              
ATOM    939  CD  GLU   115      22.519  13.998  -8.645  1.00  0.00              
ATOM    940  OE1 GLU   115      22.167  13.238  -9.571  1.00  0.00              
ATOM    941  OE2 GLU   115      22.722  13.606  -7.478  1.00  0.00              
ATOM    942  N   ILE   116      19.571  18.134  -8.268  1.00  0.00              
ATOM    943  CA  ILE   116      18.701  18.940  -7.366  1.00  0.00              
ATOM    944  C   ILE   116      18.929  20.435  -7.571  1.00  0.00              
ATOM    945  O   ILE   116      18.758  21.231  -6.648  1.00  0.00              
ATOM    946  CB  ILE   116      17.210  18.624  -7.587  1.00  0.00              
ATOM    947  CG2 ILE   116      16.735  17.576  -6.593  1.00  0.00              
ATOM    948  CG1 ILE   116      16.972  18.154  -9.023  1.00  0.00              
ATOM    949  CD1 ILE   116      16.076  16.938  -9.128  1.00  0.00              
ATOM    950  N   ALA   117      19.316  20.807  -8.787  1.00  0.00              
ATOM    951  CA  ALA   117      19.569  22.206  -9.115  1.00  0.00              
ATOM    952  C   ALA   117      20.627  22.805  -8.195  1.00  0.00              
ATOM    953  O   ALA   117      20.698  24.023  -8.027  1.00  0.00              
ATOM    954  CB  ALA   117      20.000  22.339 -10.568  1.00  0.00              
ATOM    955  N   LEU   118      21.448  21.944  -7.604  1.00  0.00              
ATOM    956  CA  LEU   118      22.504  22.386  -6.701  1.00  0.00              
ATOM    957  C   LEU   118      22.512  23.906  -6.566  1.00  0.00              
ATOM    958  O   LEU   118      21.588  24.494  -6.003  1.00  0.00              
ATOM    959  CB  LEU   118      22.339  21.737  -5.325  1.00  0.00              
ATOM    960  CG  LEU   118      23.248  20.543  -5.026  1.00  0.00              
ATOM    961  CD1 LEU   118      23.228  20.209  -3.543  1.00  0.00              
ATOM    962  CD2 LEU   118      24.668  20.817  -5.500  1.00  0.00              
ATOM    963  N   ASP   119      23.561  24.535  -7.084  1.00  0.00              
ATOM    964  CA  ASP   119      23.692  25.986  -7.023  1.00  0.00              
ATOM    965  C   ASP   119      22.881  26.660  -8.125  1.00  0.00              
ATOM    966  O   ASP   119      22.590  27.854  -8.053  1.00  0.00              
ATOM    967  CB  ASP   119      23.251  26.505  -5.653  1.00  0.00              
ATOM    968  CG  ASP   119      24.263  27.450  -5.035  1.00  0.00              
ATOM    969  OD1 ASP   119      23.872  28.246  -4.154  1.00  0.00              
ATOM    970  OD2 ASP   119      25.446  27.395  -5.431  1.00  0.00              
ATOM    971  N   LEU   120      22.521  25.887  -9.144  1.00  0.00              
ATOM    972  CA  LEU   120      21.744  26.408 -10.263  1.00  0.00              
ATOM    973  C   LEU   120      20.976  27.663  -9.865  1.00  0.00              
ATOM    974  O   LEU   120      20.870  28.616 -10.638  1.00  0.00              
ATOM    975  CB  LEU   120      22.655  26.704 -11.456  1.00  0.00              
ATOM    976  CG  LEU   120      22.120  26.308 -12.834  1.00  0.00              
ATOM    977  CD1 LEU   120      22.765  27.150 -13.923  1.00  0.00              
ATOM    978  CD2 LEU   120      20.605  26.433 -12.877  1.00  0.00              
ATOM    979  N   PRO   121      20.429  27.677  -8.640  1.00  0.00              
ATOM    980  CA  PRO   121      19.665  28.819  -8.130  1.00  0.00              
ATOM    981  C   PRO   121      20.056  29.166  -6.697  1.00  0.00              
ATOM    982  O   PRO   121      19.827  30.285  -6.234  1.00  0.00              
ATOM    983  CB  PRO   121      20.069  29.954  -9.074  1.00  0.00              
ATOM    984  CG  PRO   121      21.270  29.433  -9.790  1.00  0.00              
ATOM    985  CD  PRO   121      20.515  26.577  -7.664  1.00  0.00              
ATOM    986  N   GLY   122      20.646  28.201  -5.999  1.00  0.00              
ATOM    987  CA  GLY   122      21.057  28.428  -4.626  1.00  0.00              
ATOM    988  C   GLY   122      21.247  29.899  -4.313  1.00  0.00              
ATOM    989  O   GLY   122      20.748  30.398  -3.304  1.00  0.00              
ATOM    990  N   ILE   123      21.972  30.599  -5.179  1.00  0.00              
ATOM    991  CA  ILE   123      22.233  32.054  -4.987  1.00  0.00              
ATOM    992  C   ILE   123      20.963  32.794  -4.579  1.00  0.00              
ATOM    993  O   ILE   123      20.975  34.010  -4.392  1.00  0.00              
ATOM    994  CB  ILE   123      23.320  32.297  -3.924  1.00  0.00              
ATOM    995  CG2 ILE   123      24.703  32.245  -4.556  1.00  0.00              
ATOM    996  CG1 ILE   123      23.202  31.268  -2.797  1.00  0.00              
ATOM    997  CD1 ILE   123      24.535  30.825  -2.234  1.00  0.00              
ATOM    998  N   ASN   124      19.869  32.050  -4.442  1.00  0.00              
ATOM    999  CA  ASN   124      18.591  32.633  -4.055  1.00  0.00              
ATOM   1000  C   ASN   124      18.713  34.138  -3.841  1.00  0.00              
ATOM   1001  O   ASN   124      19.159  34.867  -4.727  1.00  0.00              
ATOM   1002  CB  ASN   124      17.525  32.338  -5.114  1.00  0.00              
ATOM   1003  CG  ASN   124      16.176  32.012  -4.506  1.00  0.00              
ATOM   1004  OD1 ASN   124      15.166  31.954  -5.208  1.00  0.00              
ATOM   1005  ND2 ASN   124      16.154  31.797  -3.196  1.00  0.00              
ATOM   1006  N   LEU   125      18.313  34.596  -2.659  1.00  0.00              
ATOM   1007  CA  LEU   125      18.378  36.014  -2.325  1.00  0.00              
ATOM   1008  C   LEU   125      19.590  36.321  -1.452  1.00  0.00              
ATOM   1009  O   LEU   125      20.225  37.365  -1.601  1.00  0.00              
ATOM   1010  CB  LEU   125      18.418  36.862  -3.598  1.00  0.00              
ATOM   1011  CG  LEU   125      17.591  38.150  -3.580  1.00  0.00              
ATOM   1012  CD1 LEU   125      18.186  39.183  -4.525  1.00  0.00              
ATOM   1013  CD2 LEU   125      17.488  38.703  -2.167  1.00  0.00              
ATOM   1014  N   GLU   126      19.905  35.405  -0.542  1.00  0.00              
ATOM   1015  CA  GLU   126      21.041  35.576   0.356  1.00  0.00              
ATOM   1016  C   GLU   126      21.930  34.337   0.364  1.00  0.00              
ATOM   1017  O   GLU   126      22.395  33.889  -0.684  1.00  0.00              
ATOM   1018  CB  GLU   126      21.858  36.807  -0.042  1.00  0.00              
ATOM   1019  CG  GLU   126      22.482  37.543   1.132  1.00  0.00              
ATOM   1020  CD  GLU   126      22.748  39.006   0.828  1.00  0.00              
ATOM   1021  OE1 GLU   126      22.081  39.869   1.436  1.00  0.00              
ATOM   1022  OE2 GLU   126      23.622  39.287  -0.019  1.00  0.00              
ATOM   1023  N   PHE   127      22.160  33.787   1.551  1.00  0.00              
ATOM   1024  CA  PHE   127      22.993  32.600   1.698  1.00  0.00              
ATOM   1025  C   PHE   127      22.525  31.481   0.773  1.00  0.00              
ATOM   1026  O   PHE   127      23.214  30.440   0.749  1.00  0.00              
ATOM   1027  CB  PHE   127      24.459  32.935   1.418  1.00  0.00              
ATOM   1028  CG  PHE   127      25.341  32.862   2.632  1.00  0.00              
ATOM   1029  CD1 PHE   127      24.799  32.635   3.885  1.00  0.00              
ATOM   1030  CD2 PHE   127      26.711  33.018   2.521  1.00  0.00              
ATOM   1031  CE1 PHE   127      25.610  32.567   5.003  1.00  0.00              
ATOM   1032  CE2 PHE   127      27.522  32.950   3.637  1.00  0.00              
ATOM   1033  CZ  PHE   127      26.977  32.725   4.874  1.00  0.00              
ATOM   1034  OXT PHE   127      21.488  31.691   0.110  1.00  0.00              
TER
END
