
#######################################################
#                                                     #
#                        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_2_2
# Molecule2: number of CA atoms  125 ( 1020),  selected   16 , name T0383.pdb
# PARAMETERS: T0383TS009_2_2.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       113 - 126         4.70     6.16
  LONGEST_CONTINUOUS_SEGMENT:    14       114 - 127         4.83     6.36
  LCS_AVERAGE:     11.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       118 - 123         1.90     9.70
  LCS_AVERAGE:      3.65

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       114 - 117         0.77    16.08
  LONGEST_CONTINUOUS_SEGMENT:     4       117 - 120         0.50    12.22
  LONGEST_CONTINUOUS_SEGMENT:     4       118 - 121         0.97     9.61
  LONGEST_CONTINUOUS_SEGMENT:     4       122 - 125         0.79    10.53
  LCS_AVERAGE:      3.00

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    3   11     3    3    3    3    4    6    6    8    9    9    9   10   10   10   10   11   11   15   16   16 
LCS_GDT     V     113     V     113      3    3   14     3    3    4    4    4    6    7    8    9    9    9   12   14   14   14   15   15   15   16   16 
LCS_GDT     T     114     T     114      4    4   14     3    4    5    5    6    6    7    8    9   10   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     E     115     E     115      4    4   14     3    4    4    4    4    5    6    6    7    8    9   11   14   14   14   15   15   15   16   16 
LCS_GDT     I     116     I     116      4    4   14     3    4    4    4    4    7    8    9   10   11   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     A     117     A     117      4    5   14     4    4    5    5    6    7    8    9   10   11   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     L     118     L     118      4    6   14     3    4    5    5    6    6    8    9   10   11   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     D     119     D     119      4    6   14     3    4    5    5    6    6    7    9   10   11   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     L     120     L     120      4    6   14     4    4    5    5    6    7    8    9   10   11   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     P     121     P     121      4    6   14     3    3    4    5    6    6    8    9   10   11   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     G     122     G     122      4    6   14     4    4    4    4    5    7    8    9   10   11   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     I     123     I     123      4    6   14     4    4    4    4    5    7    8    9   10   11   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     N     124     N     124      4    4   14     3    4    4    4    4    7    8    9   10   11   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     L     125     L     125      4    4   14     3    4    4    4    5    7    8    9   10   11   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     E     126     E     126      3    3   14     3    3    3    3    4    4    7    9   10   11   12   12   14   14   14   15   15   15   16   16 
LCS_GDT     F     127     F     127      3    3   14     0    3    3    3    4    4    4    4    7    8    9   10   11   11   12   15   15   15   16   16 
LCS_AVERAGE  LCS_A:   5.90  (   3.00    3.65   11.05 )

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      5      6      7      8      9     10     11     12     12     14     14     14     15     15     15     16     16 
GDT PERCENT_CA   3.20   3.20   4.00   4.00   4.80   5.60   6.40   7.20   8.00   8.80   9.60   9.60  11.20  11.20  11.20  12.00  12.00  12.00  12.80  12.80
GDT RMS_LOCAL    0.27   0.27   0.99   0.99   1.71   2.46   2.61   2.83   3.08   3.37   3.76   3.76   4.70   4.70   4.70   5.15   5.15   5.15   5.84   5.84
GDT RMS_ALL_CA   8.13   8.13  13.13  13.13  11.10   7.02   7.16   7.99   7.46   7.21   6.81   6.81   6.16   6.16   6.16   6.00   6.00   6.00   5.84   5.84

#      Molecule1      Molecule2       DISTANCE
LGA    E     112      E     112         18.478
LGA    V     113      V     113         14.003
LGA    T     114      T     114          8.440
LGA    E     115      E     115         10.269
LGA    I     116      I     116          5.983
LGA    A     117      A     117          3.161
LGA    L     118      L     118          2.235
LGA    D     119      D     119          3.991
LGA    L     120      L     120          0.281
LGA    P     121      P     121          3.075
LGA    G     122      G     122          1.490
LGA    I     123      I     123          2.648
LGA    N     124      N     124          3.932
LGA    L     125      L     125          2.607
LGA    E     126      E     126          6.101
LGA    F     127      F     127         12.755

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  125    4.0      9    2.83     6.600     6.049     0.307

LGA_LOCAL      RMSD =  2.827  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.992  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 =  -0.295892 * X  +  -0.427481 * Y  +  -0.854230 * Z  +   6.179437
  Y_new =  -0.945735 * X  +   0.256822 * Y  +   0.199066 * Z  +  34.459560
  Z_new =   0.134288 * X  +   0.866777 * Y  +  -0.480275 * Z  +  -8.087305 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.076777   -1.064816  [ DEG:   118.9905    -61.0094 ]
  Theta =  -0.134695   -3.006898  [ DEG:    -7.7174   -172.2826 ]
  Phi   =  -1.874018    1.267575  [ DEG:  -107.3733     72.6267 ]
 
# 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_2_2                                
REMARK     2: T0383.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0383TS009_2_2.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    9   2.83   6.049     5.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0383TS009_2_2
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0383                                                                    
PARENT N/A                                                                      
ATOM    910  N   GLU   112      13.459  21.198 -18.359  1.00  0.00              
ATOM    911  CA  GLU   112      12.664  22.415 -18.478  1.00  0.00              
ATOM    912  C   GLU   112      11.907  22.708 -17.187  1.00  0.00              
ATOM    913  O   GLU   112      11.935  23.830 -16.681  1.00  0.00              
ATOM    914  CB  GLU   112      13.557  23.603 -18.845  1.00  0.00              
ATOM    915  CG  GLU   112      13.007  24.469 -19.965  1.00  0.00              
ATOM    916  CD  GLU   112      14.094  25.229 -20.702  1.00  0.00              
ATOM    917  OE1 GLU   112      14.264  24.993 -21.916  1.00  0.00              
ATOM    918  OE2 GLU   112      14.774  26.059 -20.064  1.00  0.00              
ATOM    919  N   VAL   113      11.231  21.692 -16.661  1.00  0.00              
ATOM    920  CA  VAL   113      10.446  21.842 -15.401  1.00  0.00              
ATOM    921  C   VAL   113      11.364  22.066 -14.204  1.00  0.00              
ATOM    922  O   VAL   113      11.333  21.307 -13.235  1.00  0.00              
ATOM    923  CB  VAL   113       9.447  23.009 -15.495  1.00  0.00              
ATOM    924  CG1 VAL   113       8.045  22.488 -15.771  1.00  0.00              
ATOM    925  CG2 VAL   113       9.877  23.996 -16.569  1.00  0.00              
ATOM    926  N   THR   114      12.181  23.112 -14.278  1.00  0.00              
ATOM    927  CA  THR   114      13.129  23.445 -13.177  1.00  0.00              
ATOM    928  C   THR   114      13.369  22.240 -12.272  1.00  0.00              
ATOM    929  O   THR   114      14.021  22.352 -11.234  1.00  0.00              
ATOM    930  CB  THR   114      14.480  23.939 -13.726  1.00  0.00              
ATOM    931  OG1 THR   114      14.743  23.316 -14.989  1.00  0.00              
ATOM    932  CG2 THR   114      14.461  25.450 -13.905  1.00  0.00              
ATOM    933  N   GLU   115      12.839  21.090 -12.675  1.00  0.00              
ATOM    934  CA  GLU   115      12.995  19.864 -11.903  1.00  0.00              
ATOM    935  C   GLU   115      13.815  20.107 -10.640  1.00  0.00              
ATOM    936  O   GLU   115      15.028  20.311 -10.706  1.00  0.00              
ATOM    937  CB  GLU   115      11.627  19.283 -11.536  1.00  0.00              
ATOM    938  CG  GLU   115      11.273  18.009 -12.286  1.00  0.00              
ATOM    939  CD  GLU   115       9.854  17.549 -12.016  1.00  0.00              
ATOM    940  OE1 GLU   115       8.915  18.182 -12.543  1.00  0.00              
ATOM    941  OE2 GLU   115       9.681  16.557 -11.278  1.00  0.00              
ATOM    942  N   ILE   116      13.146  20.083  -9.492  1.00  0.00              
ATOM    943  CA  ILE   116      13.827  20.307  -8.185  1.00  0.00              
ATOM    944  C   ILE   116      14.622  21.608  -8.191  1.00  0.00              
ATOM    945  O   ILE   116      15.663  21.714  -7.545  1.00  0.00              
ATOM    946  CB  ILE   116      12.818  20.337  -7.022  1.00  0.00              
ATOM    947  CG2 ILE   116      12.708  18.965  -6.375  1.00  0.00              
ATOM    948  CG1 ILE   116      11.450  20.813  -7.514  1.00  0.00              
ATOM    949  CD1 ILE   116      10.293  19.987  -6.997  1.00  0.00              
ATOM    950  N   ALA   117      14.121  22.597  -8.924  1.00  0.00              
ATOM    951  CA  ALA   117      14.782  23.893  -9.016  1.00  0.00              
ATOM    952  C   ALA   117      16.298  23.736  -9.067  1.00  0.00              
ATOM    953  O   ALA   117      17.038  24.620  -8.636  1.00  0.00              
ATOM    954  CB  ALA   117      14.292  24.653 -10.239  1.00  0.00              
ATOM    955  N   LEU   118      16.754  22.607  -9.598  1.00  0.00              
ATOM    956  CA  LEU   118      18.181  22.332  -9.707  1.00  0.00              
ATOM    957  C   LEU   118      18.997  23.321  -8.881  1.00  0.00              
ATOM    958  O   LEU   118      18.507  23.879  -7.900  1.00  0.00              
ATOM    959  CB  LEU   118      18.487  20.899  -9.263  1.00  0.00              
ATOM    960  CG  LEU   118      18.695  19.874 -10.379  1.00  0.00              
ATOM    961  CD1 LEU   118      19.311  18.597  -9.829  1.00  0.00              
ATOM    962  CD2 LEU   118      19.558  20.455 -11.489  1.00  0.00              
ATOM    963  N   ASP   119      20.245  23.534  -9.286  1.00  0.00              
ATOM    964  CA  ASP   119      21.131  24.457  -8.586  1.00  0.00              
ATOM    965  C   ASP   119      21.713  25.494  -9.540  1.00  0.00              
ATOM    966  O   ASP   119      22.186  26.547  -9.114  1.00  0.00              
ATOM    967  CB  ASP   119      20.388  25.150  -7.443  1.00  0.00              
ATOM    968  CG  ASP   119      21.150  25.094  -6.133  1.00  0.00              
ATOM    969  OD1 ASP   119      20.881  25.939  -5.254  1.00  0.00              
ATOM    970  OD2 ASP   119      22.015  24.205  -5.988  1.00  0.00              
ATOM    971  N   LEU   120      21.674  25.190 -10.833  1.00  0.00              
ATOM    972  CA  LEU   120      22.195  26.095 -11.850  1.00  0.00              
ATOM    973  C   LEU   120      22.145  27.545 -11.376  1.00  0.00              
ATOM    974  O   LEU   120      22.831  28.414 -11.913  1.00  0.00              
ATOM    975  CB  LEU   120      23.630  25.713 -12.221  1.00  0.00              
ATOM    976  CG  LEU   120      23.982  25.774 -13.709  1.00  0.00              
ATOM    977  CD1 LEU   120      25.478  25.976 -13.899  1.00  0.00              
ATOM    978  CD2 LEU   120      23.195  26.873 -14.405  1.00  0.00              
ATOM    979  N   PRO   121      21.322  27.820 -10.354  1.00  0.00              
ATOM    980  CA  PRO   121      21.175  29.170  -9.800  1.00  0.00              
ATOM    981  C   PRO   121      21.797  29.282  -8.412  1.00  0.00              
ATOM    982  O   PRO   121      21.715  30.328  -7.767  1.00  0.00              
ATOM    983  CB  PRO   121      21.948  30.036 -10.795  1.00  0.00              
ATOM    984  CG  PRO   121      22.739  29.063 -11.603  1.00  0.00              
ATOM    985  CD  PRO   121      20.472  26.834  -9.663  1.00  0.00              
ATOM    986  N   GLY   122      22.421  28.199  -7.958  1.00  0.00              
ATOM    987  CA  GLY   122      23.047  28.201  -6.650  1.00  0.00              
ATOM    988  C   GLY   122      22.631  29.392  -5.810  1.00  0.00              
ATOM    989  O   GLY   122      22.439  29.273  -4.599  1.00  0.00              
ATOM    990  N   ILE   123      22.490  30.548  -6.450  1.00  0.00              
ATOM    991  CA  ILE   123      22.085  31.793  -5.738  1.00  0.00              
ATOM    992  C   ILE   123      20.840  31.563  -4.888  1.00  0.00              
ATOM    993  O   ILE   123      20.308  32.494  -4.284  1.00  0.00              
ATOM    994  CB  ILE   123      23.217  32.323  -4.840  1.00  0.00              
ATOM    995  CG2 ILE   123      24.156  33.217  -5.636  1.00  0.00              
ATOM    996  CG1 ILE   123      23.984  31.162  -4.206  1.00  0.00              
ATOM    997  CD1 ILE   123      25.469  31.413  -4.067  1.00  0.00              
ATOM    998  N   ASN   124      20.380  30.317  -4.847  1.00  0.00              
ATOM    999  CA  ASN   124      19.197  29.962  -4.072  1.00  0.00              
ATOM   1000  C   ASN   124      18.267  31.159  -3.906  1.00  0.00              
ATOM   1001  O   ASN   124      17.501  31.492  -4.810  1.00  0.00              
ATOM   1002  CB  ASN   124      18.449  28.803  -4.736  1.00  0.00              
ATOM   1003  CG  ASN   124      17.911  27.806  -3.729  1.00  0.00              
ATOM   1004  OD1 ASN   124      17.114  26.933  -4.072  1.00  0.00              
ATOM   1005  ND2 ASN   124      18.345  27.932  -2.482  1.00  0.00              
ATOM   1006  N   LEU   125      18.341  31.802  -2.746  1.00  0.00              
ATOM   1007  CA  LEU   125      17.506  32.963  -2.458  1.00  0.00              
ATOM   1008  C   LEU   125      17.870  34.139  -3.357  1.00  0.00              
ATOM   1009  O   LEU   125      17.027  34.981  -3.667  1.00  0.00              
ATOM   1010  CB  LEU   125      16.025  32.613  -2.624  1.00  0.00              
ATOM   1011  CG  LEU   125      15.069  33.200  -1.584  1.00  0.00              
ATOM   1012  CD1 LEU   125      13.675  33.366  -2.169  1.00  0.00              
ATOM   1013  CD2 LEU   125      15.597  34.526  -1.057  1.00  0.00              
ATOM   1014  N   GLU   126      19.132  34.192  -3.772  1.00  0.00              
ATOM   1015  CA  GLU   126      19.610  35.266  -4.635  1.00  0.00              
ATOM   1016  C   GLU   126      19.893  34.755  -6.044  1.00  0.00              
ATOM   1017  O   GLU   126      19.024  34.168  -6.688  1.00  0.00              
ATOM   1018  CB  GLU   126      18.593  36.408  -4.684  1.00  0.00              
ATOM   1019  CG  GLU   126      19.216  37.789  -4.811  1.00  0.00              
ATOM   1020  CD  GLU   126      18.320  38.884  -4.267  1.00  0.00              
ATOM   1021  OE1 GLU   126      18.682  39.492  -3.238  1.00  0.00              
ATOM   1022  OE2 GLU   126      17.256  39.135  -4.871  1.00  0.00              
ATOM   1023  N   PHE   127      21.113  34.983  -6.517  1.00  0.00              
ATOM   1024  CA  PHE   127      21.513  34.547  -7.849  1.00  0.00              
ATOM   1025  C   PHE   127      21.751  33.042  -7.889  1.00  0.00              
ATOM   1026  O   PHE   127      21.981  32.533  -9.006  1.00  0.00              
ATOM   1027  CB  PHE   127      20.454  34.940  -8.881  1.00  0.00              
ATOM   1028  CG  PHE   127      20.907  36.002  -9.842  1.00  0.00              
ATOM   1029  CD1 PHE   127      22.133  36.625  -9.680  1.00  0.00              
ATOM   1030  CD2 PHE   127      20.110  36.377 -10.909  1.00  0.00              
ATOM   1031  CE1 PHE   127      22.551  37.601 -10.564  1.00  0.00              
ATOM   1032  CE2 PHE   127      20.527  37.353 -11.794  1.00  0.00              
ATOM   1033  CZ  PHE   127      21.742  37.965 -11.624  1.00  0.00              
ATOM   1034  OXT PHE   127      21.699  32.431  -6.801  1.00  0.00              
TER
END
