
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0386AL380_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   33 , name T0386_D2.pdb
# PARAMETERS: T0386AL380_2-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:    14       231 - 246         4.83    13.07
  LCS_AVERAGE:     15.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       228 - 237         1.51    24.28
  LCS_AVERAGE:      7.97

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       228 - 234         0.76    24.85
  LCS_AVERAGE:      5.35

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     E     228     E     228      7   10   13     4    7    7    8   10   10   10   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     F     229     F     229      7   10   13     4    7    7    9   10   10   10   11   11   12   15   15   17   18   19   20   21   21   24   25 
LCS_GDT     M     230     M     230      7   10   13     4    7    7    9   10   10   10   11   11   11   11   14   14   15   17   18   21   21   22   24 
LCS_GDT     H     231     H     231      7   10   14     4    7    7    9   10   10   10   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     T     232     T     232      7   10   14     4    7    7    9   10   10   10   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     M     233     M     233      7   10   14     4    7    7    9   10   10   10   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     K     234     K     234      7   10   14     4    7    7    9   10   10   10   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     N     235     N     235      4   10   14     3    4    5    9   10   10   10   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     T     236     T     236      4   10   14     3    6    7    9   10   10   11   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     G     237     G     237      4   10   14     0    4    5    9   10   10   11   11   11   12   15   16   17   18   19   20   21   21   22   25 
LCS_GDT     R     238     R     238      4    6   14     0    4    4    6    7    7   11   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     N     239     N     239      4    6   14     3    4    4    7    7    9   11   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     V     240     V     240      4    6   14     3    4    4    6    7    9   11   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     N     241     N     241      4    6   14     3    4    4    7    7    9   11   11   11   12   14   16   17   18   19   20   21   21   24   25 
LCS_GDT     D     242     D     242      4    6   14     3    4    4    7    7    9   11   11   11   12   14   16   17   18   19   20   21   21   24   25 
LCS_GDT     R     243     R     243      3    6   14     3    3    4    7    7    9   11   11   11   12   14   16   17   18   19   20   21   21   24   25 
LCS_GDT     M     246     M     246      3    4   14     0    3    4    5    6    6    6    7    9   10   11   12   13   14   14   17   19   20   24   25 
LCS_GDT     V     247     V     247      3    4   12     2    3    4    5    6    6    6    7    7    8   10   12   13   15   16   17   18   19   20   24 
LCS_GDT     A     248     A     248      3    4   11     2    3    4    5    6    6    6    7    7    8   10   12   13   15   16   17   19   20   24   25 
LCS_GDT     K     249     K     249      4    5   12     3    4    4    4    5    5    6    7    7    8   10   12   13   15   16   17   19   20   24   25 
LCS_GDT     E     250     E     250      4    5   12     3    4    4    4    5    5    5    6    7    8   10   11   13   15   16   17   17   18   20   21 
LCS_GDT     G     251     G     251      4    5   12     3    4    4    4    5    5    5    6    7    8    9   11   13   15   15   16   16   18   20   20 
LCS_GDT     E     252     E     252      4    5   12     3    4    4    4    5    5    6    7    7    8    9   11   13   15   16   17   18   19   24   25 
LCS_GDT     T     253     T     253      3    5   12     0    3    3    3    5    5    6    7    7    8   10   12   13   15   16   17   21   21   24   25 
LCS_GDT     Y     254     Y     254      3    3   12     0    3    3    4    4    5    6    7    7    8   10   12   13   15   16   17   21   21   24   25 
LCS_GDT     T     255     T     255      3    4   12     0    3    3    3    6    6    6    6    7    8   10   12   13   15   16   20   21   21   24   25 
LCS_GDT     G     256     G     256      3    4   12     0    3    4    6    7    9   11   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     T     257     T     257      3    4   12     3    3    4    7    7    9   11   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     Y     258     Y     258      4    5   12     3    4    4    7    7    9   11   11   11   12   15   16   17   18   19   20   21   21   24   25 
LCS_GDT     R     259     R     259      4    5   12     3    4    4    4    5    6    6    6    6    8   10   11   14   18   19   20   21   21   22   22 
LCS_GDT     G     260     G     260      4    5   12     3    4    4    4    5    6    6    6    6    8   10   11   13   18   19   19   21   21   22   24 
LCS_GDT     A     261     A     261      4    5   11     0    4    4    4    5    6    6    6    6    8   10   11   13   15   15   15   17   18   22   22 
LCS_GDT     G     262     G     262      3    5   11     0    3    3    3    5    6    6    6    6    7   10   11   13   15   15   15   16   16   17   17 
LCS_AVERAGE  LCS_A:   9.73  (   5.35    7.97   15.86 )

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      7      7      9     10     10     11     11     11     12     15     16     17     18     19     20     21     21     24     25 
GDT PERCENT_CA   4.94   8.64   8.64  11.11  12.35  12.35  13.58  13.58  13.58  14.81  18.52  19.75  20.99  22.22  23.46  24.69  25.93  25.93  29.63  30.86
GDT RMS_LOCAL    0.16   0.76   0.76   1.35   1.51   1.51   2.33   2.33   2.33   2.93   3.99   4.37   4.57   4.75   4.95   5.22   5.51   5.46   7.56   7.60
GDT RMS_ALL_CA  23.61  24.85  24.85  24.27  24.28  24.28  12.28  12.28  12.28  11.81  12.94  11.44  11.41  11.60  11.78  11.68  11.84  11.79   9.88   9.90

#      Molecule1      Molecule2       DISTANCE
LGA    E     228      E     228         14.943
LGA    F     229      F     229         14.076
LGA    M     230      M     230         17.583
LGA    H     231      H     231         15.059
LGA    T     232      T     232          7.791
LGA    M     233      M     233          8.964
LGA    K     234      K     234         11.702
LGA    N     235      N     235          9.481
LGA    T     236      T     236          2.403
LGA    G     237      G     237          3.201
LGA    R     238      R     238          3.476
LGA    N     239      N     239          1.225
LGA    V     240      V     240          2.681
LGA    N     241      N     241          0.397
LGA    D     242      D     242          1.515
LGA    R     243      R     243          1.987
LGA    M     246      M     246         13.838
LGA    V     247      V     247         16.801
LGA    A     248      A     248         14.776
LGA    K     249      K     249         16.432
LGA    E     250      E     250         22.484
LGA    G     251      G     251         21.909
LGA    E     252      E     252         15.268
LGA    T     253      T     253         13.158
LGA    Y     254      Y     254         11.667
LGA    T     255      T     255          8.644
LGA    G     256      G     256          2.779
LGA    T     257      T     257          1.570
LGA    Y     258      Y     258          2.544
LGA    R     259      R     259          8.514
LGA    G     260      G     260         12.604
LGA    A     261      A     261         16.484
LGA    G     262      G     262         22.843

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33   81    4.0     11    2.33    14.506    12.762     0.452

LGA_LOCAL      RMSD =  2.333  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.278  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  9.547  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.539259 * X  +   0.687804 * Y  +  -0.485928 * Z  + -23.629642
  Y_new =  -0.798198 * X  +  -0.601403 * Y  +   0.034549 * Z  +  82.425194
  Z_new =  -0.268476 * X  +   0.406497 * Y  +   0.873316 * Z  +  51.367973 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.435640   -2.705953  [ DEG:    24.9603   -155.0397 ]
  Theta =   0.271811    2.869782  [ DEG:    15.5736    164.4264 ]
  Phi   =  -2.164955    0.976638  [ DEG:  -124.0428     55.9572 ]
 
# 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: T0386AL380_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL380_2-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33   81   4.0   11   2.33  12.762     9.55
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL380_2-D2
REMARK Aligment from pdb entry: 2f6sA
ATOM    541  N   GLU   228      17.879  76.786  89.637  1.00  0.00              
ATOM    542  CA  GLU   228      17.754  75.862  88.532  1.00  0.00              
ATOM    543  C   GLU   228      17.498  76.611  87.228  1.00  0.00              
ATOM    544  O   GLU   228      18.093  76.271  86.211  1.00  0.00              
ATOM    545  N   PHE   229      16.648  77.640  87.255  1.00  0.00              
ATOM    546  CA  PHE   229      16.379  78.419  86.039  1.00  0.00              
ATOM    547  C   PHE   229      17.665  79.025  85.502  1.00  0.00              
ATOM    548  O   PHE   229      17.935  78.943  84.312  1.00  0.00              
ATOM    549  N   MET   230      18.470  79.616  86.382  1.00  0.00              
ATOM    550  CA  MET   230      19.713  80.278  85.985  1.00  0.00              
ATOM    551  C   MET   230      20.723  79.267  85.465  1.00  0.00              
ATOM    552  O   MET   230      21.394  79.508  84.458  1.00  0.00              
ATOM    553  N   HIS   231      20.825  78.135  86.152  1.00  0.00              
ATOM    554  CA  HIS   231      21.808  77.120  85.826  1.00  0.00              
ATOM    555  C   HIS   231      21.534  76.542  84.447  1.00  0.00              
ATOM    556  O   HIS   231      22.442  76.446  83.614  1.00  0.00              
ATOM    557  N   THR   232      20.277  76.166  84.208  1.00  0.00              
ATOM    558  CA  THR   232      19.868  75.634  82.908  1.00  0.00              
ATOM    559  C   THR   232      19.990  76.640  81.776  1.00  0.00              
ATOM    560  O   THR   232      20.457  76.285  80.699  1.00  0.00              
ATOM    561  N   MET   233      19.597  77.892  82.015  1.00  0.00              
ATOM    562  CA  MET   233      19.587  78.892  80.936  1.00  0.00              
ATOM    563  C   MET   233      20.973  79.116  80.345  1.00  0.00              
ATOM    564  O   MET   233      21.099  79.476  79.188  1.00  0.00              
ATOM    565  N   LYS   234      22.004  78.863  81.140  1.00  0.00              
ATOM    566  CA  LYS   234      23.391  79.100  80.738  1.00  0.00              
ATOM    567  C   LYS   234      24.036  77.969  79.941  1.00  0.00              
ATOM    568  O   LYS   234      25.151  78.122  79.475  1.00  0.00              
ATOM    569  N   ASN   235      23.355  76.835  79.807  1.00  0.00              
ATOM    570  CA  ASN   235      23.935  75.669  79.166  1.00  0.00              
ATOM    571  C   ASN   235      22.949  75.046  78.208  1.00  0.00              
ATOM    572  O   ASN   235      22.742  73.835  78.200  1.00  0.00              
ATOM    573  N   THR   236      22.337  75.893  77.394  1.00  0.00              
ATOM    574  CA  THR   236      21.456  75.444  76.329  1.00  0.00              
ATOM    575  C   THR   236      22.205  75.386  75.000  1.00  0.00              
ATOM    576  O   THR   236      23.152  76.143  74.786  1.00  0.00              
ATOM    577  N   GLY   237      21.782  74.485  74.116  1.00  0.00              
ATOM    578  CA  GLY   237      22.373  74.365  72.785  1.00  0.00              
ATOM    579  C   GLY   237      21.292  74.253  71.723  1.00  0.00              
ATOM    580  O   GLY   237      20.233  73.653  71.970  1.00  0.00              
ATOM    581  N   ARG   238      21.569  74.826  70.547  1.00  0.00              
ATOM    582  CA  ARG   238      20.715  74.675  69.360  1.00  0.00              
ATOM    583  C   ARG   238      20.967  73.363  68.616  1.00  0.00              
ATOM    584  O   ARG   238      20.192  72.971  67.751  1.00  0.00              
ATOM    585  N   ASN   239      22.044  72.685  68.981  1.00  0.00              
ATOM    586  CA  ASN   239      22.453  71.464  68.326  1.00  0.00              
ATOM    587  C   ASN   239      21.685  70.248  68.847  1.00  0.00              
ATOM    588  O   ASN   239      22.266  69.308  69.403  1.00  0.00              
ATOM    589  N   VAL   240      20.378  70.257  68.631  1.00  0.00              
ATOM    590  CA  VAL   240      19.480  69.344  69.340  1.00  0.00              
ATOM    591  C   VAL   240      19.519  67.908  68.833  1.00  0.00              
ATOM    592  O   VAL   240      18.873  67.023  69.409  1.00  0.00              
ATOM    593  N   ASN   241      20.259  67.684  67.753  1.00  0.00              
ATOM    594  CA  ASN   241      20.186  66.420  67.038  1.00  0.00              
ATOM    595  C   ASN   241      21.507  65.669  66.961  1.00  0.00              
ATOM    596  O   ASN   241      21.522  64.503  66.569  1.00  0.00              
ATOM    597  N   ASP   242      22.608  66.331  67.319  1.00  0.00              
ATOM    598  CA  ASP   242      23.906  65.676  67.343  1.00  0.00              
ATOM    599  C   ASP   242      23.931  64.502  68.348  1.00  0.00              
ATOM    600  O   ASP   242      23.808  64.720  69.571  1.00  0.00              
ATOM    601  N   ARG   243      24.084  63.247  67.850  1.00  0.00              
ATOM    602  CA  ARG   243      23.964  62.178  68.857  1.00  0.00              
ATOM    603  C   ARG   243      25.186  62.097  69.799  1.00  0.00              
ATOM    604  O   ARG   243      25.033  61.616  70.930  1.00  0.00              
ATOM    605  N   MET   246      26.356  62.595  69.375  1.00  0.00              
ATOM    606  CA  MET   246      27.506  62.693  70.297  1.00  0.00              
ATOM    607  C   MET   246      27.161  63.600  71.496  1.00  0.00              
ATOM    608  O   MET   246      27.330  63.209  72.662  1.00  0.00              
ATOM    609  N   VAL   247      26.660  64.798  71.192  1.00  0.00              
ATOM    610  CA  VAL   247      26.202  65.756  72.195  1.00  0.00              
ATOM    611  C   VAL   247      25.150  65.135  73.125  1.00  0.00              
ATOM    612  O   VAL   247      25.197  65.318  74.338  1.00  0.00              
ATOM    613  N   ALA   248      24.221  64.389  72.538  1.00  0.00              
ATOM    614  CA  ALA   248      23.135  63.781  73.279  1.00  0.00              
ATOM    615  C   ALA   248      23.641  62.679  74.211  1.00  0.00              
ATOM    616  O   ALA   248      23.215  62.592  75.362  1.00  0.00              
ATOM    617  N   LYS   249      24.568  61.863  73.723  1.00  0.00              
ATOM    618  CA  LYS   249      25.156  60.794  74.525  1.00  0.00              
ATOM    619  C   LYS   249      25.985  61.362  75.686  1.00  0.00              
ATOM    620  O   LYS   249      25.855  60.895  76.817  1.00  0.00              
ATOM    621  N   GLU   250      26.810  62.370  75.410  1.00  0.00              
ATOM    622  CA  GLU   250      27.522  63.089  76.468  1.00  0.00              
ATOM    623  C   GLU   250      26.565  63.619  77.531  1.00  0.00              
ATOM    624  O   GLU   250      26.841  63.522  78.730  1.00  0.00              
ATOM    625  N   GLY   251      25.436  64.156  77.082  1.00  0.00              
ATOM    626  CA  GLY   251      24.399  64.638  77.959  1.00  0.00              
ATOM    627  C   GLY   251      23.829  63.553  78.851  1.00  0.00              
ATOM    628  O   GLY   251      23.715  63.735  80.077  1.00  0.00              
ATOM    629  N   GLU   252      23.472  62.419  78.256  1.00  0.00              
ATOM    630  CA  GLU   252      22.834  61.354  79.018  1.00  0.00              
ATOM    631  C   GLU   252      23.822  60.681  79.956  1.00  0.00              
ATOM    632  O   GLU   252      23.452  60.289  81.047  1.00  0.00              
ATOM    633  N   THR   253      25.083  60.570  79.541  1.00  0.00              
ATOM    634  CA  THR   253      26.128  60.040  80.401  1.00  0.00              
ATOM    635  C   THR   253      26.233  60.905  81.664  1.00  0.00              
ATOM    636  O   THR   253      26.395  60.389  82.761  1.00  0.00              
ATOM    637  N   TYR   254      26.123  62.219  81.516  1.00  0.00              
ATOM    638  CA  TYR   254      26.224  63.111  82.655  1.00  0.00              
ATOM    639  C   TYR   254      24.993  62.965  83.545  1.00  0.00              
ATOM    640  O   TYR   254      25.108  62.952  84.777  1.00  0.00              
ATOM    641  N   THR   255      23.823  62.833  82.916  1.00  0.00              
ATOM    642  CA  THR   255      22.592  62.616  83.646  1.00  0.00              
ATOM    643  C   THR   255      22.739  61.401  84.575  1.00  0.00              
ATOM    644  O   THR   255      22.360  61.459  85.745  1.00  0.00              
ATOM    645  N   GLY   256      23.292  60.307  84.049  1.00  0.00              
ATOM    646  CA  GLY   256      23.519  59.092  84.843  1.00  0.00              
ATOM    647  C   GLY   256      24.608  59.289  85.891  1.00  0.00              
ATOM    648  O   GLY   256      24.561  58.696  86.976  1.00  0.00              
ATOM    649  N   THR   257      25.572  60.145  85.566  1.00  0.00              
ATOM    650  CA  THR   257      26.600  60.504  86.508  1.00  0.00              
ATOM    651  C   THR   257      26.036  61.231  87.727  1.00  0.00              
ATOM    652  O   THR   257      26.582  61.096  88.827  1.00  0.00              
ATOM    653  N   TYR   258      24.949  61.995  87.527  1.00  0.00              
ATOM    654  CA  TYR   258      24.312  62.754  88.598  1.00  0.00              
ATOM    655  C   TYR   258      23.785  61.796  89.670  1.00  0.00              
ATOM    656  O   TYR   258      23.668  62.167  90.829  1.00  0.00              
ATOM    657  N   ARG   259      23.443  60.578  89.245  1.00  0.00              
ATOM    658  CA  ARG   259      22.909  59.550  90.112  1.00  0.00              
ATOM    659  C   ARG   259      24.009  58.664  90.711  1.00  0.00              
ATOM    660  O   ARG   259      23.704  57.681  91.391  1.00  0.00              
ATOM    661  N   GLY   260      25.280  58.999  90.453  1.00  0.00              
ATOM    662  CA  GLY   260      26.416  58.256  91.010  1.00  0.00              
ATOM    663  C   GLY   260      27.054  57.188  90.127  1.00  0.00              
ATOM    664  O   GLY   260      27.858  56.381  90.606  1.00  0.00              
ATOM    665  N   ALA   261      26.708  57.161  88.841  1.00  0.00              
ATOM    666  CA  ALA   261      27.345  56.231  87.906  1.00  0.00              
ATOM    667  C   ALA   261      28.629  56.841  87.343  1.00  0.00              
ATOM    668  O   ALA   261      28.584  57.870  86.666  1.00  0.00              
ATOM    669  N   GLY   262      29.769  56.201  87.623  1.00  0.00              
ATOM    670  CA  GLY   262      31.086  56.769  87.308  1.00  0.00              
ATOM    671  C   GLY   262      31.835  55.983  86.248  1.00  0.00              
ATOM    672  O   GLY   262      31.502  56.047  85.060  1.00  0.00              
END
