
#######################################################
#                                                     #
#                        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 (  153),  selected   31 , name T0386TS239_1_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   31 , name T0386_D2.pdb
# PARAMETERS: T0386TS239_1_1-D2.T0386_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:    27       222 - 248         4.92     6.55
  LCS_AVERAGE:     31.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       222 - 231         1.50     7.83
  LONGEST_CONTINUOUS_SEGMENT:    10       230 - 239         1.99    15.22
  LCS_AVERAGE:      9.80

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       222 - 230         0.40     8.14
  LCS_AVERAGE:      6.97

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:   81
LCS_GDT     K     222     K     222      9   10   27     8    9    9   10   11   13   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     I     223     I     223      9   10   27     8    9    9   10   11   13   15   19   21   22   23   24   25   25   28   28   30   30   31   31 
LCS_GDT     R     224     R     224      9   10   27     8    9    9   10   11   13   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     L     225     L     225      9   10   27     8    9    9   10   11   13   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     L     226     L     226      9   10   27     8    9    9   10   11   13   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     K     227     K     227      9   10   27     8    9    9   10   11   13   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     E     228     E     228      9   10   27     8    9    9   10   11   13   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     F     229     F     229      9   10   27     8    9    9   10   11   13   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     M     230     M     230      9   10   27     7    9    9   10   11   13   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     H     231     H     231      4   10   27     3    4    4    6   10   13   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     T     232     T     232      4   10   27     3    4    4    6    8   10   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     M     233     M     233      5   10   27     3    4    5    6    9   13   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     K     234     K     234      5   10   27     4    4    5    6    9   11   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     N     235     N     235      5   10   27     4    4    5    6    9   11   15   19   21   22   23   24   25   25   28   28   30   30   31   31 
LCS_GDT     T     236     T     236      5   10   27     4    4    5    6    9   11   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     G     237     G     237      5   10   27     4    4    5    6    9   11   15   18   21   22   23   24   25   25   27   28   30   30   31   31 
LCS_GDT     R     238     R     238      5   10   27     3    4    5    6    8   11   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     N     239     N     239      3   10   27     3    3    4    6    8   13   15   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     V     240     V     240      5    6   27     4    4    5   10   11   13   14   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     N     241     N     241      5    6   27     4    4    5    6    7    9   12   17   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     D     242     D     242      5    6   27     4    4    5    6    7   10   15   18   21   22   23   24   25   25   27   27   30   30   31   31 
LCS_GDT     R     243     R     243      5    6   27     4    4    5   10   11   13   14   19   21   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     P     244     P     244      5    6   27     1    3    5    9   11   13   14   16   19   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     V     245     V     245      3    3   27     0    3    3    3    4    5    8   10   14   21   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     M     246     M     246      3    4   27     0    3    3    3    4    5    8   12   16   22   23   24   25   26   28   28   30   30   31   31 
LCS_GDT     V     247     V     247      4    5   27     2    4    4    5    5    7   10   11   14   17   20   24   24   26   28   28   30   30   31   31 
LCS_GDT     A     248     A     248      4    5   27     2    4    4    5    5    5    6   10   11   13   15   19   22   26   28   28   30   30   31   31 
LCS_GDT     K     249     K     249      4    5   19     3    4    4    5    5    7   10   11   14   17   20   24   24   26   28   28   30   30   31   31 
LCS_GDT     E     250     E     250      4    5   17     3    4    4    5    5    7   10   11   13   15   16   20   23   26   28   28   30   30   31   31 
LCS_GDT     G     251     G     251      3    5   14     3    3    3    4    4    5   10   11   12   13   15   17   19   23   23   24   25   28   31   31 
LCS_GDT     E     252     E     252      3    4   14     3    3    3    3    4    7   10   11   14   15   16   19   23   26   28   28   30   30   31   31 
LCS_AVERAGE  LCS_A:  16.12  (   6.97    9.80   31.58 )

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      8      9      9     10     11     13     15     19     21     22     23     24     25     26     28     28     30     30     31     31 
GDT PERCENT_CA   9.88  11.11  11.11  12.35  13.58  16.05  18.52  23.46  25.93  27.16  28.40  29.63  30.86  32.10  34.57  34.57  37.04  37.04  38.27  38.27
GDT RMS_LOCAL    0.33   0.40   0.40   1.05   1.43   1.74   2.55   3.16   3.34   3.41   3.61   3.82   4.00   5.06   5.24   5.20   5.54   5.54   5.81   5.81
GDT RMS_ALL_CA   8.29   8.14   8.14   7.79   7.34   7.71   8.84   8.52   9.36   9.09   8.44   8.02   7.70   5.83   5.82   5.93   5.85   5.85   5.81   5.81

#      Molecule1      Molecule2       DISTANCE
LGA    K     222      K     222          3.734
LGA    I     223      I     223          2.499
LGA    R     224      R     224          3.069
LGA    L     225      L     225          3.236
LGA    L     226      L     226          2.011
LGA    K     227      K     227          3.399
LGA    E     228      E     228          3.842
LGA    F     229      F     229          1.723
LGA    M     230      M     230          2.988
LGA    H     231      H     231          2.466
LGA    T     232      T     232          3.991
LGA    M     233      M     233          3.335
LGA    K     234      K     234          1.887
LGA    N     235      N     235          3.802
LGA    T     236      T     236          3.775
LGA    G     237      G     237          4.824
LGA    R     238      R     238          3.375
LGA    N     239      N     239          3.744
LGA    V     240      V     240          2.786
LGA    N     241      N     241          4.441
LGA    D     242      D     242          4.774
LGA    R     243      R     243          3.896
LGA    P     244      P     244          6.302
LGA    V     245      V     245          8.135
LGA    M     246      M     246          7.625
LGA    V     247      V     247         12.080
LGA    A     248      A     248         16.745
LGA    K     249      K     249         15.539
LGA    E     250      E     250         19.222
LGA    G     251      G     251         22.398
LGA    E     252      E     252         18.363

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31   81    4.0     19    3.16    20.370    17.930     0.582

LGA_LOCAL      RMSD =  3.163  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.617  Number of atoms =   31 
Std_ALL_ATOMS  RMSD =  5.808  (standard rmsd on all 31 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.184593 * X  +   0.757353 * Y  +  -0.626372 * Z  + -18.412504
  Y_new =   0.300674 * X  +  -0.650285 * Y  +  -0.697657 * Z  + 105.998878
  Z_new =  -0.935692 * X  +  -0.059551 * Y  +  -0.347755 * Z  +  55.863636 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.971992    0.169600  [ DEG:  -170.2826      9.7174 ]
  Theta =   1.210217    1.931376  [ DEG:    69.3403    110.6597 ]
  Phi   =   1.020197   -2.121396  [ DEG:    58.4530   -121.5470 ]
 
# 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: T0386TS239_1_1-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS239_1_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31   81   4.0   19   3.16  17.930     5.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS239_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0386
PARENT 2f6s_A
ATOM    724  N   LYS   222       4.184  57.538  74.841  1.00  9.99
ATOM    725  CA  LYS   222       4.989  58.508  74.135  1.00  9.99
ATOM    726  C   LYS   222       4.713  59.917  74.650  1.00  9.99
ATOM    727  O   LYS   222       5.651  60.683  74.843  1.00  9.99
ATOM    728  CB  LYS   222       4.879  58.398  72.573  1.00  9.99
ATOM    729  N   ILE   223       3.446  60.252  74.903  1.00  9.99
ATOM    730  CA  ILE   223       3.115  61.584  75.426  1.00  9.99
ATOM    731  C   ILE   223       3.825  61.826  76.749  1.00  9.99
ATOM    732  O   ILE   223       4.415  62.878  76.947  1.00  9.99
ATOM    733  CB  ILE   223       1.614  61.771  75.630  1.00  9.99
ATOM    734  N   ARG   224       3.786  60.843  77.646  1.00  9.99
ATOM    735  CA  ARG   224       4.389  60.970  78.973  1.00  9.99
ATOM    736  C   ARG   224       5.903  61.065  78.872  1.00  9.99
ATOM    737  O   ARG   224       6.531  61.875  79.560  1.00  9.99
ATOM    738  CB  ARG   224       4.000  59.759  79.865  1.00  9.99
ATOM    739  N   LEU   225       6.487  60.238  78.012  1.00  9.99
ATOM    740  CA  LEU   225       7.928  60.154  77.876  1.00  9.99
ATOM    741  C   LEU   225       8.487  61.471  77.363  1.00  9.99
ATOM    742  O   LEU   225       9.447  62.008  77.927  1.00  9.99
ATOM    743  CB  LEU   225       8.296  59.018  76.927  1.00  9.99
ATOM    744  N   LEU   226       7.879  61.991  76.297  1.00  9.99
ATOM    745  CA  LEU   226       8.290  63.275  75.728  1.00  9.99
ATOM    746  C   LEU   226       8.077  64.450  76.668  1.00  9.99
ATOM    747  O   LEU   226       8.949  65.306  76.772  1.00  9.99
ATOM    748  CB  LEU   226       7.590  63.537  74.392  1.00  9.99
ATOM    749  N   LYS   227       6.941  64.488  77.365  1.00  9.99
ATOM    750  CA  LYS   227       6.621  65.646  78.212  1.00  9.99
ATOM    751  C   LYS   227       7.658  65.865  79.306  1.00  9.99
ATOM    752  O   LYS   227       7.858  66.980  79.752  1.00  9.99
ATOM    753  CB  LYS   227       5.226  65.543  78.811  1.00  9.99
ATOM    754  N   GLU   228       8.334  64.794  79.703  1.00  9.99
ATOM    755  CA  GLU   228       9.309  64.833  80.794  1.00  9.99
ATOM    756  C   GLU   228      10.713  65.277  80.391  1.00  9.99
ATOM    757  O   GLU   228      11.562  65.438  81.251  1.00  9.99
ATOM    758  CB  GLU   228       9.402  63.459  81.458  1.00  9.99
ATOM    759  N   PHE   229      10.966  65.444  79.097  1.00  9.99
ATOM    760  CA  PHE   229      12.300  65.751  78.615  1.00  9.99
ATOM    761  C   PHE   229      12.250  66.853  77.584  1.00  9.99
ATOM    762  O   PHE   229      12.858  66.762  76.521  1.00  9.99
ATOM    763  CB  PHE   229      12.978  64.492  78.070  1.00  9.99
ATOM    764  N   MET   230      11.512  67.902  77.912  1.00  9.99
ATOM    765  CA  MET   230      11.461  69.100  77.091  1.00  9.99
ATOM    766  C   MET   230      12.424  70.158  77.622  1.00  9.99
ATOM    767  O   MET   230      12.700  70.203  78.820  1.00  9.99
ATOM    768  CB  MET   230      10.042  69.659  77.073  1.00  9.99
ATOM    769  N   HIS   231      12.935  71.002  76.727  1.00  9.99
ATOM    770  CA  HIS   231      13.823  72.098  77.111  1.00  9.99
ATOM    771  C   HIS   231      13.415  73.389  76.422  1.00  9.99
ATOM    772  O   HIS   231      12.950  73.363  75.271  1.00  9.99
ATOM    773  CB  HIS   231      15.266  71.764  76.743  1.00  9.99
ATOM    774  N   THR   232      13.598  74.509  77.129  1.00  9.99
ATOM    775  CA  THR   232      13.415  75.853  76.564  1.00  9.99
ATOM    776  C   THR   232      14.632  76.329  75.769  1.00  9.99
ATOM    777  O   THR   232      14.564  77.314  75.042  1.00  9.99
ATOM    778  CB  THR   232      13.084  76.859  77.662  1.00  9.99
ATOM    779  N   MET   233      15.732  75.603  75.900  1.00  9.99
ATOM    780  CA  MET   233      16.980  75.963  75.268  1.00  9.99
ATOM    781  C   MET   233      17.032  75.519  73.805  1.00  9.99
ATOM    782  O   MET   233      17.880  74.712  73.406  1.00  9.99
ATOM    783  CB  MET   233      18.123  75.339  76.061  1.00  9.99
ATOM    784  N   LYS   234      16.140  76.079  73.002  1.00  9.99
ATOM    785  CA  LYS   234      15.853  75.530  71.675  1.00  9.99
ATOM    786  C   LYS   234      16.925  75.820  70.633  1.00  9.99
ATOM    787  O   LYS   234      16.843  75.333  69.498  1.00  9.99
ATOM    788  CB  LYS   234      14.501  76.053  71.133  1.00  9.99
ATOM    789  N   ASN   235      17.914  76.623  71.011  1.00  9.99
ATOM    790  CA  ASN   235      18.856  77.164  70.045  1.00  9.99
ATOM    791  C   ASN   235      20.306  76.785  70.308  1.00  9.99
ATOM    792  O   ASN   235      21.158  77.007  69.449  1.00  9.99
ATOM    793  CB  ASN   235      18.721  78.693  69.956  1.00  9.99
ATOM    794  N   THR   236      20.588  76.230  71.487  1.00  9.99
ATOM    795  CA  THR   236      21.933  75.773  71.802  1.00  9.99
ATOM    796  C   THR   236      22.394  74.658  70.836  1.00  9.99
ATOM    797  O   THR   236      21.815  73.552  70.832  1.00  9.99
ATOM    798  CB  THR   236      22.014  75.281  73.233  1.00  9.99
ATOM    799  N   GLY   237      23.432  74.933  70.003  1.00  9.99
ATOM    800  CA  GLY   237      23.722  73.868  69.026  1.00  9.99
ATOM    801  C   GLY   237      24.387  72.628  69.665  1.00  9.99
ATOM    802  O   GLY   237      24.251  71.530  69.111  1.00  9.99
ATOM    803  N   ARG   238      25.048  72.780  70.821  1.00  9.99
ATOM    804  CA  ARG   238      25.556  71.602  71.553  1.00  9.99
ATOM    805  C   ARG   238      24.393  70.666  71.942  1.00  9.99
ATOM    806  O   ARG   238      24.423  69.457  71.658  1.00  9.99
ATOM    807  CB  ARG   238      26.381  71.993  72.790  1.00  9.99
ATOM    808  N   ASN   239      23.368  71.243  72.571  1.00  9.99
ATOM    809  CA  ASN   239      22.148  70.532  72.943  1.00  9.99
ATOM    810  C   ASN   239      21.504  69.850  71.728  1.00  9.99
ATOM    811  O   ASN   239      21.074  68.702  71.806  1.00  9.99
ATOM    812  CB  ASN   239      21.138  71.504  73.586  1.00  9.99
ATOM    813  N   VAL   240      21.466  70.566  70.611  1.00  9.99
ATOM    814  CA  VAL   240      20.843  70.075  69.398  1.00  9.99
ATOM    815  C   VAL   240      21.629  68.909  68.798  1.00  9.99
ATOM    816  O   VAL   240      21.042  67.916  68.372  1.00  9.99
ATOM    817  CB  VAL   240      20.683  71.221  68.397  1.00  9.99
ATOM    818  N   ASN   241      22.952  69.021  68.792  1.00  9.99
ATOM    819  CA  ASN   241      23.815  67.961  68.279  1.00  9.99
ATOM    820  C   ASN   241      23.727  66.701  69.152  1.00  9.99
ATOM    821  O   ASN   241      23.598  65.598  68.623  1.00  9.99
ATOM    822  CB  ASN   241      25.299  68.446  68.090  1.00  9.99
ATOM    823  N   ASP   242      23.776  66.869  70.473  1.00  9.99
ATOM    824  CA  ASP   242      23.538  65.759  71.395  1.00  9.99
ATOM    825  C   ASP   242      22.206  65.069  71.117  1.00  9.99
ATOM    826  O   ASP   242      22.121  63.839  71.125  1.00  9.99
ATOM    827  CB  ASP   242      23.564  66.226  72.839  1.00  9.99
ATOM    828  N   ARG   243      21.180  65.872  70.851  1.00  9.99
ATOM    829  CA  ARG   243      19.874  65.377  70.499  1.00  9.99
ATOM    830  C   ARG   243      19.880  64.541  69.234  1.00  9.99
ATOM    831  O   ARG   243      19.330  63.426  69.208  1.00  9.99
ATOM    832  CB  ARG   243      18.917  66.573  70.364  1.00  9.99
ATOM    833  N   PRO   244      20.500  65.062  68.180  1.00  9.99
ATOM    834  CA  PRO   244      20.483  64.372  66.897  1.00  9.99
ATOM    835  C   PRO   244      21.349  63.124  66.932  1.00  9.99
ATOM    836  O   PRO   244      21.011  62.134  66.312  1.00  9.99
ATOM    837  CB  PRO   244      20.878  65.306  65.742  1.00  9.99
ATOM    838  N   VAL   245      22.454  63.165  67.676  1.00  9.99
ATOM    839  CA  VAL   245      23.295  61.995  67.862  1.00  9.99
ATOM    840  C   VAL   245      22.466  60.871  68.498  1.00  9.99
ATOM    841  O   VAL   245      22.590  59.715  68.119  1.00  9.99
ATOM    842  CB  VAL   245      24.545  62.327  68.719  1.00  9.99
ATOM    843  N   MET   246      21.609  61.209  69.453  1.00  9.99
ATOM    844  CA  MET   246      20.796  60.208  70.117  1.00  9.99
ATOM    845  C   MET   246      19.737  59.673  69.158  1.00  9.99
ATOM    846  O   MET   246      19.473  58.464  69.125  1.00  9.99
ATOM    847  CB  MET   246      20.132  60.794  71.341  1.00  9.99
ATOM    848  N   VAL   247      19.152  60.573  68.363  1.00  9.99
ATOM    849  CA  VAL   247      18.183  60.181  67.362  1.00  9.99
ATOM    850  C   VAL   247      18.780  59.101  66.447  1.00  9.99
ATOM    851  O   VAL   247      18.131  58.094  66.163  1.00  9.99
ATOM    852  CB  VAL   247      17.736  61.401  66.550  1.00  9.99
ATOM    853  N   ALA   248      20.017  59.314  65.994  1.00  9.99
ATOM    854  CA  ALA   248      20.711  58.341  65.141  1.00  9.99
ATOM    855  C   ALA   248      21.076  57.071  65.901  1.00  9.99
ATOM    856  O   ALA   248      21.098  55.973  65.331  1.00  9.99
ATOM    857  CB  ALA   248      21.950  58.968  64.503  1.00  9.99
ATOM    858  N   LYS   249      18.457  54.349  65.900  1.00  9.99
ATOM    859  CA  LYS   249      18.461  53.535  64.703  1.00  9.99
ATOM    860  C   LYS   249      19.640  52.554  64.671  1.00  9.99
ATOM    861  O   LYS   249      19.836  51.862  63.668  1.00  9.99
ATOM    862  CB  LYS   249      18.514  54.437  63.473  1.00  9.99
ATOM    863  N   GLU   250      20.427  52.498  65.753  1.00  9.99
ATOM    864  CA  GLU   250      21.555  51.566  65.856  1.00  9.99
ATOM    865  C   GLU   250      22.940  52.100  65.504  1.00  9.99
ATOM    866  O   GLU   250      23.888  51.324  65.354  1.00  9.99
ATOM    867  CB  GLU   250      21.232  50.350  64.973  1.00  9.99
ATOM    868  N   GLY   251      23.076  53.417  65.363  1.00  9.99
ATOM    869  CA  GLY   251      24.390  54.020  65.121  1.00  9.99
ATOM    870  C   GLY   251      25.103  54.287  66.446  1.00  9.99
ATOM    871  O   GLY   251      24.623  55.076  67.264  1.00  9.99
ATOM    872  N   GLU   252      26.250  53.630  66.653  1.00  9.99
ATOM    873  CA  GLU   252      26.941  53.647  67.948  1.00  9.99
ATOM    874  C   GLU   252      28.282  54.356  67.897  1.00  9.99
ATOM    875  O   GLU   252      28.343  55.589  67.828  1.00  9.99
ATOM    876  CB  GLU   252      27.117  52.200  68.439  1.00  9.99
TER
END
