
#######################################################
#                                                     #
#                        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   31 (  124),  selected   27 , name T0316TS383_2-D2
# Molecule2: number of CA atoms   60 (  457),  selected   27 , name T0316_D2.pdb
# PARAMETERS: T0316TS383_2-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       234 - 257         4.82    14.83
  LCS_AVERAGE:     23.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       234 - 239         1.88    16.08
  LONGEST_CONTINUOUS_SEGMENT:     6       235 - 240         1.00    16.47
  LCS_AVERAGE:      8.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       235 - 240         1.00    16.47
  LCS_AVERAGE:      6.73

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     V     225     V     225      4    5   14     3    4    4    4    5    5    6    8    8    9   10   14   15   16   17   17   17   19   20   20 
LCS_GDT     D     226     D     226      4    5   14     3    4    4    4    5    5    6    8    8    9   10   14   15   16   17   17   17   19   20   20 
LCS_GDT     G     227     G     227      4    5   14     3    4    4    4    5    5    6    8    8    9   10   14   15   16   17   17   17   19   20   22 
LCS_GDT     R     228     R     228      4    5   14     3    4    4    4    5    5    6    8    8   10   11   14   15   16   17   17   17   19   20   22 
LCS_GDT     D     229     D     229      3    5   14     3    3    3    3    5    5    6    8    9   10   11   14   15   16   17   17   17   19   20   22 
LCS_GDT     M     230     M     230      3    4   14     3    3    3    3    4    4    6    7    8   10   11   14   15   16   17   17   17   19   20   22 
LCS_GDT     G     231     G     231      3    4   14     3    3    3    4    5    6    7    9    9   11   12   14   15   16   17   17   18   19   20   22 
LCS_GDT     E     232     E     232      3    4   14     2    3    3    4    5    6    7    9   10   12   12   14   15   16   17   18   18   19   20   22 
LCS_GDT     H     233     H     233      3    4   14     3    3    3    4    5    6    7    9   10   12   12   14   15   16   18   18   18   19   20   22 
LCS_GDT     A     234     A     234      3    6   15     3    3    3    6    7    8    8    9   11   13   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     G     235     G     235      6    6   15     4    4    5    6    6    8    8    9   11   13   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     L     236     L     236      6    6   15     4    4    5    6    7    8    8    9   11   13   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     M     237     M     237      6    6   15     4    4    5    6    6    7    8    8   11   13   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     Y     238     Y     238      6    6   15     4    4    5    6    6    7    8    8   11   12   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     Y     239     Y     239      6    6   15     3    4    5    6    6    7    8    8   11   13   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     T     240     T     240      6    6   15     3    4    5    6    7    8    8    9   11   13   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     I     241     I     241      4    5   15     3    4    4    4    5    6    8    8   10   12   12   12   16   17   18   18   18   19   20   22 
LCS_GDT     G     242     G     242      4    5   15     3    4    4    6    7    8    8    9   11   13   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     Q     243     Q     243      4    5   15     3    4    4    4    6    7    8    9   11   13   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     R     244     R     244      4    5   15     3    3    4    4    6    6    8    9   11   13   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     G     245     G     245      4    4   15     3    3    4    4    5    5    6    8   11   13   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     G     246     G     246      4    4   15     3    3    4    4    4    5    6    7    8    8   11   12   12   12   13   13   14   17   17   21 
LCS_GDT     D     256     D     256      3    4   15     3    3    4    4    5    5    6    8   11   13   14   16   16   17   18   18   18   19   20   20 
LCS_GDT     N     257     N     257      3    4   15     3    3    4    4    5    5    6    7   11   13   14   16   16   17   18   18   18   19   20   21 
LCS_GDT     A     258     A     258      3    4   12     3    3    4    6    7    8    8    9   10   12   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     P     259     P     259      3    4   12     3    3    4    6    7    8    8    9   10   12   14   16   16   17   18   18   18   19   20   22 
LCS_GDT     W     260     W     260      3    4   12     1    3    3    6    7    8    8    9   10   13   14   16   16   17   18   18   18   19   20   22 
LCS_AVERAGE  LCS_A:  12.90  (   6.73    8.09   23.89 )

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      6      7      8      8      9     11     13     14     16     16     17     18     18     18     19     20     22 
GDT PERCENT_CA   6.67   6.67   8.33  10.00  11.67  13.33  13.33  15.00  18.33  21.67  23.33  26.67  26.67  28.33  30.00  30.00  30.00  31.67  33.33  36.67
GDT RMS_LOCAL    0.31   0.31   0.70   1.00   1.89   2.14   2.14   2.38   3.41   3.75   3.91   4.27   4.27   4.49   4.88   4.88   4.88   5.34   5.74   7.24
GDT RMS_ALL_CA  16.43  16.43  16.58  16.47  12.68  13.14  13.14  12.98  15.62  14.09  14.46  13.91  13.91  14.02  13.35  13.35  13.35  12.89  12.30   9.82

#      Molecule1      Molecule2       DISTANCE
LGA    V     225      V     225         30.126
LGA    D     226      D     226         30.750
LGA    G     227      G     227         24.421
LGA    R     228      R     228         21.916
LGA    D     229      D     229         20.127
LGA    M     230      M     230         17.316
LGA    G     231      G     231         10.976
LGA    E     232      E     232          9.379
LGA    H     233      H     233          7.504
LGA    A     234      A     234          1.512
LGA    G     235      G     235          3.199
LGA    L     236      L     236          1.843
LGA    M     237      M     237          5.927
LGA    Y     238      Y     238          6.634
LGA    Y     239      Y     239          4.668
LGA    T     240      T     240          2.632
LGA    I     241      I     241          6.452
LGA    G     242      G     242          2.046
LGA    Q     243      Q     243          3.524
LGA    R     244      R     244          6.066
LGA    G     245      G     245          8.099
LGA    G     246      G     246         13.527
LGA    D     256      D     256         10.583
LGA    N     257      N     257          7.801
LGA    A     258      A     258          2.156
LGA    P     259      P     259          2.355
LGA    W     260      W     260          1.210

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31   60    4.0      9    2.38    15.417    14.266     0.362

LGA_LOCAL      RMSD =  2.383  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.983  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  9.276  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.206036 * X  +  -0.015289 * Y  +   0.978425 * Z  +  12.564546
  Y_new =   0.628808 * X  +  -0.764044 * Y  +  -0.144353 * Z  +  25.558996
  Z_new =   0.749766 * X  +   0.644983 * Y  +  -0.147807 * Z  + -69.017822 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.796070   -1.345523  [ DEG:   102.9072    -77.0928 ]
  Theta =  -0.847709   -2.293884  [ DEG:   -48.5702   -131.4298 ]
  Phi   =   1.254159   -1.887433  [ DEG:    71.8580   -108.1420 ]
 
# 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: T0316TS383_2-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS383_2-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31   60   4.0    9   2.38  14.266     9.28
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS383_2-D2
PFRMAT TS
TARGET T0316
MODEL 2
PARENT 1wxeA
ATOM    693  N   VAL   225      50.627  35.044 -14.200  1.00  0.00
ATOM    694  CA  VAL   225      51.116  33.793 -13.637  1.00  0.00
ATOM    695  C   VAL   225      51.712  32.953 -14.759  1.00  0.00
ATOM    696  O   VAL   225      51.490  33.236 -15.938  1.00  0.00
ATOM    697  N   ASP   226      52.502  31.926 -14.412  1.00  0.00
ATOM    698  CA  ASP   226      53.093  31.084 -15.459  1.00  0.00
ATOM    699  C   ASP   226      51.972  30.575 -16.373  1.00  0.00
ATOM    700  O   ASP   226      50.883  30.248 -15.904  1.00  0.00
ATOM    701  N   GLY   227      52.231  30.514 -17.674  1.00  0.00
ATOM    702  CA  GLY   227      51.209  30.074 -18.616  1.00  0.00
ATOM    703  C   GLY   227      50.675  28.672 -18.340  1.00  0.00
ATOM    704  O   GLY   227      49.482  28.418 -18.509  1.00  0.00
ATOM    705  N   ARG   228      51.546  27.762 -17.917  1.00  0.00
ATOM    706  CA  ARG   228      51.115  26.395 -17.626  1.00  0.00
ATOM    707  C   ARG   228      50.124  26.406 -16.463  1.00  0.00
ATOM    708  O   ARG   228      49.195  25.601 -16.415  1.00  0.00
ATOM    709  N   ASP   229      50.331  27.331 -15.530  1.00  0.00
ATOM    710  CA  ASP   229      49.457  27.472 -14.368  1.00  0.00
ATOM    711  C   ASP   229      48.103  28.023 -14.808  1.00  0.00
ATOM    712  O   ASP   229      47.051  27.554 -14.362  1.00  0.00
ATOM    713  N   MET   230      48.133  29.021 -15.687  1.00  0.00
ATOM    714  CA  MET   230      46.907  29.616 -16.205  1.00  0.00
ATOM    715  C   MET   230      46.084  28.566 -16.955  1.00  0.00
ATOM    716  O   MET   230      44.865  28.508 -16.804  1.00  0.00
ATOM    717  N   GLY   231      46.751  27.736 -17.756  1.00  0.00
ATOM    718  CA  GLY   231      46.055  26.701 -18.518  1.00  0.00
ATOM    719  C   GLY   231      45.373  25.684 -17.607  1.00  0.00
ATOM    720  O   GLY   231      44.267  25.232 -17.893  1.00  0.00
ATOM    721  N   GLU   232      46.036  25.320 -16.516  1.00  0.00
ATOM    722  CA  GLU   232      45.477  24.350 -15.578  1.00  0.00
ATOM    723  C   GLU   232      44.208  24.902 -14.941  1.00  0.00
ATOM    724  O   GLU   232      43.172  24.237 -14.909  1.00  0.00
ATOM    725  N   HIS   233      44.296  26.130 -14.446  1.00  0.00
ATOM    726  CA  HIS   233      43.157  26.779 -13.805  1.00  0.00
ATOM    727  C   HIS   233      41.989  26.914 -14.770  1.00  0.00
ATOM    728  O   HIS   233      40.843  26.642 -14.415  1.00  0.00
ATOM    729  N   ALA   234      42.289  27.325 -15.995  1.00  0.00
ATOM    730  CA  ALA   234      41.259  27.497 -17.002  1.00  0.00
ATOM    731  C   ALA   234      40.641  26.164 -17.408  1.00  0.00
ATOM    732  O   ALA   234      39.445  26.091 -17.682  1.00  0.00
ATOM    733  N   GLY   235      41.446  25.106 -17.425  1.00  0.00
ATOM    734  CA  GLY   235      40.943  23.783 -17.784  1.00  0.00
ATOM    735  C   GLY   235      39.889  23.359 -16.764  1.00  0.00
ATOM    736  O   GLY   235      38.821  22.858 -17.129  1.00  0.00
ATOM    737  N   LEU   236      40.197  23.562 -15.486  1.00  0.00
ATOM    738  CA  LEU   236      39.273  23.224 -14.410  1.00  0.00
ATOM    739  C   LEU   236      37.995  24.044 -14.531  1.00  0.00
ATOM    740  O   LEU   236      36.894  23.528 -14.349  1.00  0.00
ATOM    741  N   MET   237      38.150  25.329 -14.825  1.00  0.00
ATOM    742  CA  MET   237      37.005  26.216 -14.959  1.00  0.00
ATOM    743  C   MET   237      36.056  25.729 -16.048  1.00  0.00
ATOM    744  O   MET   237      34.855  25.600 -15.821  1.00  0.00
ATOM    745  N   TYR   238      36.608  25.460 -17.226  1.00  0.00
ATOM    746  CA  TYR   238      35.820  24.995 -18.360  1.00  0.00
ATOM    747  C   TYR   238      35.177  23.639 -18.088  1.00  0.00
ATOM    748  O   TYR   238      34.015  23.405 -18.424  1.00  0.00
ATOM    749  N   TYR   239      35.941  22.751 -17.467  1.00  0.00
ATOM    750  CA  TYR   239      35.467  21.412 -17.151  1.00  0.00
ATOM    751  C   TYR   239      34.307  21.384 -16.159  1.00  0.00
ATOM    752  O   TYR   239      33.476  20.476 -16.198  1.00  0.00
ATOM    753  N   THR   240      34.232  22.381 -15.285  1.00  0.00
ATOM    754  CA  THR   240      33.189  22.397 -14.266  1.00  0.00
ATOM    755  C   THR   240      32.072  23.430 -14.397  1.00  0.00
ATOM    756  O   THR   240      31.416  23.759 -13.412  1.00  0.00
ATOM    757  N   ILE   241      31.835  23.928 -15.605  1.00  0.00
ATOM    758  CA  ILE   241      30.771  24.907 -15.800  1.00  0.00
ATOM    759  C   ILE   241      29.407  24.318 -15.409  1.00  0.00
ATOM    760  O   ILE   241      28.533  25.034 -14.911  1.00  0.00
ATOM    761  N   GLY   242      29.228  23.015 -15.613  1.00  0.00
ATOM    762  CA  GLY   242      27.960  22.374 -15.264  1.00  0.00
ATOM    763  C   GLY   242      27.622  22.502 -13.770  1.00  0.00
ATOM    764  O   GLY   242      26.456  22.429 -13.383  1.00  0.00
ATOM    765  N   GLN   243      28.636  22.691 -12.928  1.00  0.00
ATOM    766  CA  GLN   243      28.409  22.826 -11.487  1.00  0.00
ATOM    767  C   GLN   243      27.929  24.219 -11.083  1.00  0.00
ATOM    768  O   GLN   243      27.360  24.400 -10.004  1.00  0.00
ATOM    769  N   ARG   244      28.167  25.203 -11.943  1.00  0.00
ATOM    770  CA  ARG   244      27.788  26.577 -11.639  1.00  0.00
ATOM    771  C   ARG   244      26.530  27.046 -12.372  1.00  0.00
ATOM    772  O   ARG   244      26.204  28.232 -12.343  1.00  0.00
ATOM    773  N   GLY   245      25.831  26.112 -13.014  1.00  0.00
ATOM    774  CA  GLY   245      24.609  26.409 -13.762  1.00  0.00
ATOM    775  C   GLY   245      23.514  25.396 -13.429  1.00  0.00
ATOM    776  O   GLY   245      23.800  24.302 -12.953  1.00  0.00
ATOM    777  N   GLY   246      22.239  25.759 -13.661  1.00  0.00
ATOM    778  CA  GLY   246      21.125  24.844 -13.382  1.00  0.00
ATOM    779  C   GLY   246      21.235  23.667 -14.355  1.00  0.00
ATOM    780  O   GLY   246      22.022  23.716 -15.302  1.00  0.00
ATOM    781  N   GLN   252      20.445  22.599 -14.143  1.00  0.00
ATOM    782  CA  GLN   252      20.481  21.426 -15.027  1.00  0.00
ATOM    783  C   GLN   252      20.391  21.804 -16.508  1.00  0.00
ATOM    784  O   GLN   252      19.637  22.700 -16.885  1.00  0.00
ATOM    785  N   HIS   253      21.154  21.101 -17.340  1.00  0.00
ATOM    786  CA  HIS   253      21.199  21.366 -18.773  1.00  0.00
ATOM    787  C   HIS   253      19.928  20.966 -19.523  1.00  0.00
ATOM    788  O   HIS   253      19.393  19.880 -19.320  1.00  0.00
ATOM    789  N   GLY   254      19.465  21.850 -20.403  1.00  0.00
ATOM    790  CA  GLY   254      18.260  21.602 -21.192  1.00  0.00
ATOM    791  C   GLY   254      18.553  21.770 -22.680  1.00  0.00
ATOM    792  O   GLY   254      19.641  22.203 -23.057  1.00  0.00
ATOM    793  N   GLY   255      17.571  21.451 -23.521  1.00  0.00
ATOM    794  CA  GLY   255      17.745  21.561 -24.968  1.00  0.00
ATOM    795  C   GLY   255      18.023  22.991 -25.420  1.00  0.00
ATOM    796  O   GLY   255      18.470  23.211 -26.539  1.00  0.00
ATOM    797  N   ASP   256      17.776  23.961 -24.545  1.00  0.00
ATOM    798  CA  ASP   256      17.990  25.365 -24.890  1.00  0.00
ATOM    799  C   ASP   256      19.412  25.863 -24.649  1.00  0.00
ATOM    800  O   ASP   256      19.803  26.907 -25.179  1.00  0.00
ATOM    801  N   ASN   257      20.185  25.123 -23.857  1.00  0.00
ATOM    802  CA  ASN   257      21.559  25.524 -23.560  1.00  0.00
ATOM    803  C   ASN   257      22.521  25.260 -24.707  1.00  0.00
ATOM    804  O   ASN   257      22.355  24.308 -25.465  1.00  0.00
ATOM    805  N   ALA   258      23.538  26.107 -24.826  1.00  0.00
ATOM    806  CA  ALA   258      24.521  25.933 -25.884  1.00  0.00
ATOM    807  C   ALA   258      25.937  26.175 -25.377  1.00  0.00
ATOM    808  O   ALA   258      26.902  26.028 -26.130  1.00  0.00
ATOM    809  N   PRO   259      26.069  26.526 -24.099  1.00  0.00
ATOM    810  CA  PRO   259      27.392  26.787 -23.539  1.00  0.00
ATOM    811  C   PRO   259      28.302  25.563 -23.640  1.00  0.00
ATOM    812  O   PRO   259      29.521  25.693 -23.778  1.00  0.00
ATOM    813  N   TRP   260      27.710  24.374 -23.573  1.00  0.00
ATOM    814  CA  TRP   260      28.493  23.146 -23.647  1.00  0.00
ATOM    815  C   TRP   260      28.935  22.801 -25.064  1.00  0.00
ATOM    816  O   TRP   260      29.731  21.884 -25.267  1.00  0.00
TER
END
