
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0316TS383_3-D3
# Molecule2: number of CA atoms   90 (  711),  selected   23 , name T0316_D3.pdb
# PARAMETERS: T0316TS383_3-D3.T0316_D3.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:    13       286 - 298         4.46    14.18
  LONGEST_CONTINUOUS_SEGMENT:    13       287 - 299         5.00    12.21
  LONGEST_CONTINUOUS_SEGMENT:    13       294 - 306         4.77    14.32
  LCS_AVERAGE:     13.96

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       288 - 295         1.85    16.67
  LONGEST_CONTINUOUS_SEGMENT:     8       289 - 296         1.57    15.55
  LCS_AVERAGE:      6.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       290 - 295         0.92    15.92
  LCS_AVERAGE:      4.40

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:   90
LCS_GDT     M     284     M     284      0    0    8     0    0    0    1    1    1    3    5    6    6    7    7    8    8    8    8    9    9   11   11 
LCS_GDT     S     285     S     285      0    0    8     0    0    0    0    0    0    2    2    2    6    7    7    8    8    9    9   10   11   15   15 
LCS_GDT     T     286     T     286      4    4   13     0    4    4    4    4    4    5    5    7    8    9   11   12   12   13   13   15   16   17   19 
LCS_GDT     S     287     S     287      4    4   13     0    4    4    4    4    5    8    8   10   10   11   11   12   14   15   15   17   18   18   19 
LCS_GDT     L     288     L     288      4    8   13     3    4    4    6    6    8    9    9   10   10   11   12   13   14   15   16   17   18   18   19 
LCS_GDT     E     289     E     289      5    8   13     3    4    7    7    7    8    9    9   11   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     A     290     A     290      6    8   13     3    4    7    7    7    8    9    9   11   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     S     291     S     291      6    8   13     3    4    7    7    7    8    9    9   11   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     Q     292     Q     292      6    8   13     3    4    7    7    7    8    9    9   11   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     V     293     V     293      6    8   13     3    4    7    7    7    8    9    9   11   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     H     294     H     294      6    8   13     3    4    7    7    7    8    9    9   11   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     F     295     F     295      6    8   13     3    4    7    7    7    8    9    9   11   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     T     296     T     296      3    8   13     3    3    3    5    7    8    9    9   11   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     R     297     R     297      3    5   13     3    3    3    4    6    7    8    9   11   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     E     298     E     298      3    5   13     3    3    3    4    6    7    8    9    9   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     M     299     M     299      3    6   13     3    3    3    4    6    7    8    9    9   10   11   12   12   14   15   16   17   18   18   19 
LCS_GDT     P     300     P     300      4    6   13     1    4    4    5    5    7    8    9    9   10   11   12   12   14   14   16   17   18   18   19 
LCS_GDT     E     301     E     301      4    6   13     3    4    4    5    5    7    7    7    8   10   11   12   12   12   12   13   14   14   16   18 
LCS_GDT     E     302     E     302      4    6   13     3    4    4    5    5    7    7    7    8    8   11   12   12   12   13   14   16   16   17   18 
LCS_GDT     F     303     F     303      4    6   13     3    4    4    5    5    7    8    9    9   10   11   12   12   14   14   16   17   18   18   19 
LCS_GDT     T     304     T     304      4    6   13     0    4    4    5    5    7    8    9   10   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     L     305     L     305      3    6   13     1    4    4    5    7    7    9    9   11   11   13   13   13   14   15   16   17   18   18   19 
LCS_GDT     E     306     E     306      3    6   13     0    4    4    5    7    7    9    9   11   11   13   13   13   14   15   16   17   18   18   19 
LCS_AVERAGE  LCS_A:   8.34  (   4.40    6.67   13.96 )

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      7      7      7      8      9      9     11     11     13     13     13     14     15     16     17     18     18     19 
GDT PERCENT_CA   3.33   4.44   7.78   7.78   7.78   8.89  10.00  10.00  12.22  12.22  14.44  14.44  14.44  15.56  16.67  17.78  18.89  20.00  20.00  21.11
GDT RMS_LOCAL    0.06   0.38   1.16   1.16   1.16   1.57   2.16   2.16   3.09   3.09   3.82   3.82   3.82   4.40   4.84   5.28   5.75   6.15   6.15   6.84
GDT RMS_ALL_CA  15.98  15.77  15.91  15.91  15.91  15.55  16.16  16.16  13.56  13.56  12.89  12.89  12.89  12.32  11.99  11.80  11.49  10.91  10.91  10.32

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284         29.895
LGA    S     285      S     285         25.016
LGA    T     286      T     286         12.309
LGA    S     287      S     287          5.927
LGA    L     288      L     288          3.414
LGA    E     289      E     289          2.967
LGA    A     290      A     290          0.942
LGA    S     291      S     291          1.429
LGA    Q     292      Q     292          2.144
LGA    V     293      V     293          0.979
LGA    H     294      H     294          0.527
LGA    F     295      F     295          0.954
LGA    T     296      T     296          3.466
LGA    R     297      R     297          7.899
LGA    E     298      E     298         12.880
LGA    M     299      M     299         18.413
LGA    P     300      P     300         24.341
LGA    E     301      E     301         27.528
LGA    E     302      E     302         26.448
LGA    F     303      F     303         24.123
LGA    T     304      T     304         19.752
LGA    L     305      L     305         17.629
LGA    E     306      E     306         18.958

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23   90    4.0      9    2.16    10.000     9.542     0.398

LGA_LOCAL      RMSD =  2.164  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.162  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  9.426  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.554917 * X  +  -0.824156 * Y  +  -0.113288 * Z  + 144.794632
  Y_new =  -0.362833 * X  +   0.117226 * Y  +   0.924451 * Z  +  -9.993587
  Z_new =  -0.748612 * X  +   0.554098 * Y  +  -0.364082 * Z  +  97.001358 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.152126   -0.989467  [ DEG:   123.3077    -56.6923 ]
  Theta =   0.845966    2.295627  [ DEG:    48.4703    131.5297 ]
  Phi   =  -2.562515    0.579077  [ DEG:  -146.8213     33.1787 ]
 
# 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_3-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS383_3-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23   90   4.0    9   2.16   9.542     9.43
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS383_3-D3
PFRMAT TS
TARGET T0316
MODEL 3
PARENT 1gpmA
ATOM    897  N   MET   284      29.404   1.707  13.161  1.00  0.00
ATOM    898  CA  MET   284      30.565   1.390  12.355  1.00  0.00
ATOM    899  C   MET   284      30.180   0.515  11.174  1.00  0.00
ATOM    900  O   MET   284      30.810   0.578  10.113  1.00  0.00
ATOM    901  N   SER   285      29.152  -0.309  11.360  1.00  0.00
ATOM    902  CA  SER   285      28.658  -1.209  10.318  1.00  0.00
ATOM    903  C   SER   285      28.027  -0.411   9.183  1.00  0.00
ATOM    904  O   SER   285      28.238  -0.724   8.010  1.00  0.00
ATOM    905  N   THR   286      29.977   0.784  -0.337  1.00  0.00
ATOM    906  CA  THR   286      28.942   0.513  -1.329  1.00  0.00
ATOM    907  C   THR   286      28.488   1.658  -2.215  1.00  0.00
ATOM    908  O   THR   286      28.104   1.434  -3.375  1.00  0.00
ATOM    909  N   SER   287      28.496   2.874  -1.685  1.00  0.00
ATOM    910  CA  SER   287      28.055   4.025  -2.465  1.00  0.00
ATOM    911  C   SER   287      29.245   4.749  -3.066  1.00  0.00
ATOM    912  O   SER   287      29.941   5.491  -2.380  1.00  0.00
ATOM    913  N   LEU   288      29.472   4.531  -4.356  1.00  0.00
ATOM    914  CA  LEU   288      30.579   5.169  -5.063  1.00  0.00
ATOM    915  C   LEU   288      30.322   6.666  -5.111  1.00  0.00
ATOM    916  O   LEU   288      29.343   7.102  -5.712  1.00  0.00
ATOM    917  N   GLU   289      31.178   7.442  -4.459  1.00  0.00
ATOM    918  CA  GLU   289      31.002   8.884  -4.441  1.00  0.00
ATOM    919  C   GLU   289      30.996   9.440  -3.027  1.00  0.00
ATOM    920  O   GLU   289      31.003  10.659  -2.828  1.00  0.00
ATOM    921  N   ALA   290      30.933   8.544  -2.041  1.00  0.00
ATOM    922  CA  ALA   290      30.929   8.929  -0.628  1.00  0.00
ATOM    923  C   ALA   290      32.130   8.268   0.058  1.00  0.00
ATOM    924  O   ALA   290      32.280   7.043   0.018  1.00  0.00
ATOM    925  N   SER   291      32.992   9.084   0.658  1.00  0.00
ATOM    926  CA  SER   291      34.186   8.575   1.326  1.00  0.00
ATOM    927  C   SER   291      34.196   8.750   2.846  1.00  0.00
ATOM    928  O   SER   291      35.090   8.231   3.528  1.00  0.00
ATOM    929  N   GLN   292      33.209   9.463   3.385  1.00  0.00
ATOM    930  CA  GLN   292      33.149   9.679   4.825  1.00  0.00
ATOM    931  C   GLN   292      31.726   9.789   5.342  1.00  0.00
ATOM    932  O   GLN   292      30.854  10.353   4.678  1.00  0.00
ATOM    933  N   VAL   293      31.500   9.246   6.532  1.00  0.00
ATOM    934  CA  VAL   293      30.193   9.290   7.161  1.00  0.00
ATOM    935  C   VAL   293      30.388   9.849   8.558  1.00  0.00
ATOM    936  O   VAL   293      31.345   9.476   9.245  1.00  0.00
ATOM    937  N   HIS   294      29.511  10.776   8.948  1.00  0.00
ATOM    938  CA  HIS   294      29.562  11.400  10.273  1.00  0.00
ATOM    939  C   HIS   294      28.210  11.221  10.965  1.00  0.00
ATOM    940  O   HIS   294      27.215  10.893  10.321  1.00  0.00
ATOM    941  N   PHE   295      28.174  11.451  12.270  1.00  0.00
ATOM    942  CA  PHE   295      26.937  11.295  13.013  1.00  0.00
ATOM    943  C   PHE   295      26.572  12.579  13.747  1.00  0.00
ATOM    944  O   PHE   295      27.425  13.183  14.391  1.00  0.00
ATOM    945  N   THR   296      25.419  14.739  16.588  1.00  0.00
ATOM    946  CA  THR   296      25.344  14.603  18.031  1.00  0.00
ATOM    947  C   THR   296      24.839  15.887  18.656  1.00  0.00
ATOM    948  O   THR   296      25.185  16.223  19.788  1.00  0.00
ATOM    949  N   ARG   297      24.016  16.605  17.904  1.00  0.00
ATOM    950  CA  ARG   297      23.432  17.853  18.371  1.00  0.00
ATOM    951  C   ARG   297      21.974  17.572  18.707  1.00  0.00
ATOM    952  O   ARG   297      21.240  17.010  17.891  1.00  0.00
ATOM    953  N   GLU   298      21.561  17.932  19.913  1.00  0.00
ATOM    954  CA  GLU   298      20.193  17.700  20.325  1.00  0.00
ATOM    955  C   GLU   298      19.288  18.884  20.058  1.00  0.00
ATOM    956  O   GLU   298      19.703  19.894  19.483  1.00  0.00
ATOM    957  N   MET   299      18.031  18.742  20.448  1.00  0.00
ATOM    958  CA  MET   299      17.056  19.805  20.292  1.00  0.00
ATOM    959  C   MET   299      16.454  20.103  21.659  1.00  0.00
ATOM    960  O   MET   299      15.811  19.238  22.266  1.00  0.00
ATOM    961  N   PRO   300      16.782  21.270  22.224  1.00  0.00
ATOM    962  CA  PRO   300      17.675  22.267  21.630  1.00  0.00
ATOM    963  C   PRO   300      19.129  21.878  21.947  1.00  0.00
ATOM    964  O   PRO   300      19.376  20.834  22.559  1.00  0.00
ATOM    965  N   GLU   301      20.108  22.703  21.541  1.00  0.00
ATOM    966  CA  GLU   301      20.006  23.969  20.815  1.00  0.00
ATOM    967  C   GLU   301      19.911  23.853  19.298  1.00  0.00
ATOM    968  O   GLU   301      19.819  24.869  18.603  1.00  0.00
ATOM    969  N   GLU   302      19.948  22.634  18.773  1.00  0.00
ATOM    970  CA  GLU   302      19.845  22.457  17.329  1.00  0.00
ATOM    971  C   GLU   302      18.450  21.941  16.990  1.00  0.00
ATOM    972  O   GLU   302      17.684  21.585  17.883  1.00  0.00
ATOM    973  N   PHE   303      18.103  21.968  15.709  1.00  0.00
ATOM    974  CA  PHE   303      16.817  21.468  15.244  1.00  0.00
ATOM    975  C   PHE   303      17.041  20.046  14.741  1.00  0.00
ATOM    976  O   PHE   303      18.198  19.601  14.598  1.00  0.00
ATOM    977  N   THR   304      15.953  18.753  11.717  1.00  0.00
ATOM    978  CA  THR   304      16.381  18.862  10.335  1.00  0.00
ATOM    979  C   THR   304      17.468  19.931  10.301  1.00  0.00
ATOM    980  O   THR   304      17.591  20.718  11.232  1.00  0.00
ATOM    981  N   LEU   305      18.313  19.890   9.276  1.00  0.00
ATOM    982  CA  LEU   305      19.404  20.842   9.125  1.00  0.00
ATOM    983  C   LEU   305      19.016  22.104   8.370  1.00  0.00
ATOM    984  O   LEU   305      19.744  23.103   8.430  1.00  0.00
ATOM    985  N   GLU   306      17.897  22.050   7.649  1.00  0.00
ATOM    986  CA  GLU   306      17.406  23.183   6.866  1.00  0.00
ATOM    987  C   GLU   306      15.902  23.371   7.081  1.00  0.00
ATOM    988  O   GLU   306      15.207  22.372   7.373  1.00  0.00
TER
END
