
#######################################################
#                                                     #
#                        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   22 (   88),  selected   22 , name T0289AL380_3-D2
# Molecule2: number of CA atoms   74 (  581),  selected   22 , name T0289_D2.pdb
# PARAMETERS: T0289AL380_3-D2.T0289_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:    16       245 - 294         4.84     7.42
  LCS_AVERAGE:     18.24

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       245 - 251         1.94    11.56
  LCS_AVERAGE:      7.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       245 - 248         0.84    15.35
  LONGEST_CONTINUOUS_SEGMENT:     4       275 - 278         0.35    19.20
  LCS_AVERAGE:      4.55

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:   74
LCS_GDT     I     224     I     224      3    4    6     3    3    3    7    7    7    9   10   11   11   12   14   16   18   19   19   20   20   22   22 
LCS_GDT     M     225     M     225      3    5    7     3    4    5    5    6    7    9   10   11   12   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     E     226     E     226      3    5    7     3    4    4    7    7    7    9   10   11   11   12   16   17   18   19   19   20   20   22   22 
LCS_GDT     K     227     K     227      3    5    7     0    4    4    7    7    7    9   10   11   11   12   16   17   18   19   19   20   20   22   22 
LCS_GDT     V     238     V     238      3    5    7     1    3    3    4    4    5    5    6    6    8    9    9   11   13   15   18   19   20   22   22 
LCS_GDT     A     239     A     239      3    5    7     1    3    3    4    4    5    5    6    6    6    6    8   10   13   13   14   17   19   22   22 
LCS_GDT     N     245     N     245      4    7   16     3    4    5    7    7    8    9   10   11   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     L     246     L     246      4    7   16     3    4    5    5    6    8    9   10   11   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     Q     247     Q     247      4    7   16     3    4    4    5    6    8    9   10   11   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     D     248     D     248      4    7   16     3    3    4    5    6    7    9   10   11   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     Q     249     Q     249      3    7   16     3    4    5    7    7    8    9   10   11   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     D     250     D     250      3    7   16     3    4    5    7    7    8    9   10   11   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     W     251     W     251      3    7   16     3    4    5    7    7    8    9   10   11   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     C     275     C     275      4    5   16     4    4    5    5    6    6    9    9   10   10   12   16   17   18   19   19   20   20   22   22 
LCS_GDT     T     276     T     276      4    5   16     4    4    4    5    6    7    8    9   10   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     V     277     V     277      4    5   16     4    4    5    5    6    7    9    9   10   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     Y     278     Y     278      4    5   16     4    4    5    5    6    7    9    9   10   13   13   15   17   18   19   19   20   20   22   22 
LCS_GDT     P     279     P     279      3    5   16     3    3    5    5    6    8    9    9   10   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     K     291     K     291      3    4   16     0    3    3    4    4    4    4    4    4    5    5    6    6    6   17   18   20   20   22   22 
LCS_GDT     E     292     E     292      3    4   16     3    3    3    4    4    5    6    8    9   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     A     293     A     293      3    4   16     3    3    3    4    5    8    9    9   10   13   13   16   17   18   19   19   20   20   22   22 
LCS_GDT     F     294     F     294      3    4   16     3    3    3    4    4    4    4    4    9   11   12   14   16   16   19   19   20   20   22   22 
LCS_AVERAGE  LCS_A:  10.03  (   4.55    7.31   18.24 )

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      7      7      8      9     10     11     13     13     16     17     18     19     19     20     20     22     22 
GDT PERCENT_CA   5.41   5.41   6.76   9.46   9.46  10.81  12.16  13.51  14.86  17.57  17.57  21.62  22.97  24.32  25.68  25.68  27.03  27.03  29.73  29.73
GDT RMS_LOCAL    0.35   0.35   0.89   1.31   1.31   2.51   2.28   2.51   2.83   3.88   3.88   4.71   4.82   5.00   5.17   5.17   5.46   5.46   6.39   6.39
GDT RMS_ALL_CA  19.20  19.20   8.30   8.62   8.62   8.69   8.23   8.03   8.18   8.02   8.02   6.78   6.78   6.85   6.92   6.92   6.81   6.81   6.39   6.39

#      Molecule1      Molecule2       DISTANCE
LGA    I     224      I     224          2.812
LGA    M     225      M     225          3.343
LGA    E     226      E     226          1.913
LGA    K     227      K     227          2.763
LGA    V     238      V     238         17.223
LGA    A     239      A     239         16.949
LGA    N     245      N     245          1.788
LGA    L     246      L     246          4.520
LGA    Q     247      Q     247          3.641
LGA    D     248      D     248          3.953
LGA    Q     249      Q     249          1.466
LGA    D     250      D     250          0.782
LGA    W     251      W     251          1.483
LGA    C     275      C     275          9.832
LGA    T     276      T     276          8.940
LGA    V     277      V     277          9.183
LGA    Y     278      Y     278         10.124
LGA    P     279      P     279          6.811
LGA    K     291      K     291         10.594
LGA    E     292      E     292          9.831
LGA    A     293      A     293          8.258
LGA    F     294      F     294         10.618

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22   74    4.0     10    2.51    13.514    12.134     0.383

LGA_LOCAL      RMSD =  2.514  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.178  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  6.388  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.920368 * X  +  -0.226736 * Y  +   0.318612 * Z  + -16.105186
  Y_new =   0.350811 * X  +   0.118730 * Y  +  -0.928889 * Z  +  64.226204
  Z_new =   0.172784 * X  +   0.966692 * Y  +   0.188817 * Z  + -20.190186 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.377902   -1.763690  [ DEG:    78.9480   -101.0520 ]
  Theta =  -0.173655   -2.967937  [ DEG:    -9.9497   -170.0503 ]
  Phi   =   0.364164   -2.777429  [ DEG:    20.8650   -159.1350 ]
 
# 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: T0289AL380_3-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0289AL380_3-D2.T0289_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22   74   4.0   10   2.51  12.134     6.39
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL380_3-D2
REMARK Aligment from pdb entry: 2bcoB
ATOM    773  N   ILE   224      25.719  26.677  18.088  1.00  0.00              
ATOM    774  CA  ILE   224      25.050  26.816  19.378  1.00  0.00              
ATOM    775  C   ILE   224      25.031  28.228  19.947  1.00  0.00              
ATOM    776  O   ILE   224      26.021  28.957  19.880  1.00  0.00              
ATOM    777  N   MET   225      23.880  28.597  20.499  1.00  0.00              
ATOM    778  CA  MET   225      23.684  29.906  21.103  1.00  0.00              
ATOM    779  C   MET   225      23.224  29.705  22.542  1.00  0.00              
ATOM    780  O   MET   225      22.124  30.111  22.919  1.00  0.00              
ATOM    781  N   GLU   226      24.070  29.060  23.337  1.00  0.00              
ATOM    782  CA  GLU   226      23.765  28.796  24.736  1.00  0.00              
ATOM    783  C   GLU   226      23.467  30.097  25.473  1.00  0.00              
ATOM    784  O   GLU   226      24.379  30.795  25.917  1.00  0.00              
ATOM    785  N   LYS   227      22.183  30.420  25.596  1.00  0.00              
ATOM    786  CA  LYS   227      21.757  31.638  26.273  1.00  0.00              
ATOM    787  C   LYS   227      21.270  31.347  27.689  1.00  0.00              
ATOM    788  O   LYS   227      21.894  31.759  28.670  1.00  0.00              
ATOM    789  N   VAL   238      31.284  41.108  34.653  1.00  0.00              
ATOM    790  CA  VAL   238      32.648  41.188  35.155  1.00  0.00              
ATOM    791  C   VAL   238      33.475  42.180  34.344  1.00  0.00              
ATOM    792  O   VAL   238      33.987  43.162  34.878  1.00  0.00              
ATOM    793  N   ALA   239      33.595  41.923  33.048  1.00  0.00              
ATOM    794  CA  ALA   239      34.369  42.785  32.163  1.00  0.00              
ATOM    795  C   ALA   239      33.714  44.143  31.942  1.00  0.00              
ATOM    796  O   ALA   239      32.656  44.431  32.502  1.00  0.00              
ATOM    797  N   ASN   245      34.354  44.972  31.123  1.00  0.00              
ATOM    798  CA  ASN   245      33.852  46.310  30.824  1.00  0.00              
ATOM    799  C   ASN   245      33.067  46.330  29.517  1.00  0.00              
ATOM    800  O   ASN   245      32.915  45.301  28.861  1.00  0.00              
ATOM    801  N   LEU   246      32.571  47.507  29.144  1.00  0.00              
ATOM    802  CA  LEU   246      31.808  47.660  27.910  1.00  0.00              
ATOM    803  C   LEU   246      32.717  47.915  26.708  1.00  0.00              
ATOM    804  O   LEU   246      32.244  48.280  25.629  1.00  0.00              
ATOM    805  N   GLN   247      34.019  47.718  26.894  1.00  0.00              
ATOM    806  CA  GLN   247      34.987  47.934  25.820  1.00  0.00              
ATOM    807  C   GLN   247      35.457  46.610  25.218  1.00  0.00              
ATOM    808  O   GLN   247      36.197  46.598  24.235  1.00  0.00              
ATOM    809  N   ASP   248      35.018  45.501  25.808  1.00  0.00              
ATOM    810  CA  ASP   248      35.397  44.166  25.348  1.00  0.00              
ATOM    811  C   ASP   248      34.978  43.851  23.914  1.00  0.00              
ATOM    812  O   ASP   248      34.081  44.488  23.361  1.00  0.00              
ATOM    813  N   GLN   249      35.632  42.851  23.327  1.00  0.00              
ATOM    814  CA  GLN   249      35.355  42.437  21.954  1.00  0.00              
ATOM    815  C   GLN   249      34.493  41.180  21.867  1.00  0.00              
ATOM    816  O   GLN   249      34.491  40.350  22.780  1.00  0.00              
ATOM    817  N   ASP   250      33.764  41.049  20.761  1.00  0.00              
ATOM    818  CA  ASP   250      32.889  39.904  20.534  1.00  0.00              
ATOM    819  C   ASP   250      33.697  38.628  20.339  1.00  0.00              
ATOM    820  O   ASP   250      34.899  38.678  20.077  1.00  0.00              
ATOM    821  N   TRP   251      33.025  37.487  20.468  1.00  0.00              
ATOM    822  CA  TRP   251      33.672  36.185  20.323  1.00  0.00              
ATOM    823  C   TRP   251      34.824  36.041  21.307  1.00  0.00              
ATOM    824  O   TRP   251      34.748  36.523  22.437  1.00  0.00              
ATOM    825  N   CYS   275      33.425  32.883  22.276  1.00  0.00              
ATOM    826  CA  CYS   275      33.229  32.891  23.720  1.00  0.00              
ATOM    827  C   CYS   275      31.893  33.538  24.064  1.00  0.00              
ATOM    828  O   CYS   275      30.915  32.851  24.355  1.00  0.00              
ATOM    829  N   THR   276      31.867  34.866  24.035  1.00  0.00              
ATOM    830  CA  THR   276      30.665  35.633  24.334  1.00  0.00              
ATOM    831  C   THR   276      30.416  36.574  23.158  1.00  0.00              
ATOM    832  O   THR   276      31.361  36.989  22.485  1.00  0.00              
ATOM    833  N   VAL   277      29.154  36.902  22.903  1.00  0.00              
ATOM    834  CA  VAL   277      28.820  37.789  21.796  1.00  0.00              
ATOM    835  C   VAL   277      27.710  38.769  22.160  1.00  0.00              
ATOM    836  O   VAL   277      26.794  38.438  22.910  1.00  0.00              
ATOM    837  N   TYR   278      27.810  39.982  21.629  1.00  0.00              
ATOM    838  CA  TYR   278      26.810  41.023  21.852  1.00  0.00              
ATOM    839  C   TYR   278      26.490  41.391  23.297  1.00  0.00              
ATOM    840  O   TYR   278      25.327  41.637  23.622  1.00  0.00              
ATOM    841  N   PRO   279      27.495  41.440  24.186  1.00  0.00              
ATOM    842  CA  PRO   279      27.180  41.800  25.573  1.00  0.00              
ATOM    843  C   PRO   279      26.779  43.273  25.718  1.00  0.00              
ATOM    844  O   PRO   279      27.401  44.154  25.122  1.00  0.00              
ATOM    845  N   LYS   291      25.740  43.534  26.509  1.00  0.00              
ATOM    846  CA  LYS   291      25.254  44.898  26.724  1.00  0.00              
ATOM    847  C   LYS   291      24.357  44.955  27.959  1.00  0.00              
ATOM    848  O   LYS   291      23.274  44.370  27.980  1.00  0.00              
ATOM    849  N   GLU   292      24.808  45.674  28.982  1.00  0.00              
ATOM    850  CA  GLU   292      24.057  45.791  30.225  1.00  0.00              
ATOM    851  C   GLU   292      23.162  47.030  30.295  1.00  0.00              
ATOM    852  O   GLU   292      22.651  47.367  31.363  1.00  0.00              
ATOM    853  N   ALA   293      22.969  47.707  29.168  1.00  0.00              
ATOM    854  CA  ALA   293      22.131  48.905  29.147  1.00  0.00              
ATOM    855  C   ALA   293      20.797  48.686  28.440  1.00  0.00              
ATOM    856  O   ALA   293      20.110  49.643  28.086  1.00  0.00              
ATOM    857  N   PHE   294      20.434  47.425  28.230  1.00  0.00              
ATOM    858  CA  PHE   294      19.172  47.098  27.577  1.00  0.00              
ATOM    859  C   PHE   294      18.193  46.537  28.598  1.00  0.00              
ATOM    860  O   PHE   294      18.360  46.734  29.804  1.00  0.00              
END
