
#######################################################
#                                                     #
#                        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   27 (  135),  selected   27 , name T0297TS239_3_2
# Molecule2: number of CA atoms  211 ( 1703),  selected   27 , name T0297.pdb
# PARAMETERS: T0297TS239_3_2.T0297.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:    21         7 - 27          4.42    11.65
  LCS_AVERAGE:      9.04

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        12 - 27          1.85    14.34
  LCS_AVERAGE:      5.28

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        14 - 27          0.40    13.18
  LCS_AVERAGE:      4.27

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:  211
LCS_GDT     M       1     M       1      4    4   11     3    3    4    4    4    4    6    7    8   10   11   12   13   15   15   16   18   19   19   20 
LCS_GDT     A       2     A       2      4    4   11     3    3    4    4    4    4    5    7    8   10   11   11   13   15   15   16   18   19   19   20 
LCS_GDT     V       3     V       3      4    4   13     3    3    4    4    4    4    7    7    8   10   10   12   13   15   15   16   18   19   19   20 
LCS_GDT     Q       4     Q       4      4    4   13     3    3    4    4    4    4    7    7    7    9   10   12   13   15   15   16   18   19   19   20 
LCS_GDT     L       5     L       5      3    3   13     0    3    3    3    4    4    7    7    8   10   11   12   13   15   15   17   18   20   21   21 
LCS_GDT     L       6     L       6      3    3   13     0    3    3    3    4    4    7    7    8   10   11   12   13   15   15   17   19   20   21   21 
LCS_GDT     E       7     E       7      3    3   21     3    3    3    3    4    6    7    7    8   10   11   12   14   15   18   19   19   20   21   21 
LCS_GDT     N       8     N       8      3    5   21     3    3    3    3    5    6    6    9   14   15   18   18   18   18   20   20   20   20   21   21 
LCS_GDT     W       9     W       9      4    5   21     4    4    4    4    5    7   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     L      10     L      10      4    5   21     4    4    4    4   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     L      11     L      11      4    5   21     4    4    4    4    5   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     K      12     K      12      4   16   21     4    4    4    4    5    7    9   15   16   17   19   19   19   19   20   20   20   20   20   21 
LCS_GDT     E      13     E      13      3   16   21     3    3    4    4    5    7   11   14   16   17   19   19   19   19   20   20   20   20   20   21 
LCS_GDT     Q      14     Q      14     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     E      15     E      15     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     K      16     K      16     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     I      17     I      17     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     Q      18     Q      18     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     T      19     T      19     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     K      20     K      20     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     Y      21     Y      21     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     R      22     R      22     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     H      23     H      23     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     L      24     L      24     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     N      25     N      25     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     H      26     H      26     14   16   21     3   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_GDT     I      27     I      27     14   16   21    12   14   14   14   15   16   17   17   17   17   19   19   19   19   20   20   20   20   21   21 
LCS_AVERAGE  LCS_A:   6.20  (   4.27    5.28    9.04 )

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     12     14     14     14     15     16     17     17     17     17     19     19     19     19     20     20     20     20     21     21 
GDT PERCENT_CA   5.69   6.64   6.64   6.64   7.11   7.58   8.06   8.06   8.06   8.06   9.00   9.00   9.00   9.00   9.48   9.48   9.48   9.48   9.95   9.95
GDT RMS_LOCAL    0.21   0.40   0.40   0.40   0.91   1.13   1.58   1.58   1.58   1.58   2.56   2.56   2.56   2.56   3.38   3.38   3.38   3.38   5.52   4.42
GDT RMS_ALL_CA  13.32  13.18  13.18  13.18  12.74  12.62  12.42  12.42  12.42  12.42  13.17  13.17  13.17  13.17  12.42  12.42  12.42  12.42   9.62  11.65

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         28.444
LGA    A       2      A       2         28.561
LGA    V       3      V       3         27.642
LGA    Q       4      Q       4         26.554
LGA    L       5      L       5         19.467
LGA    L       6      L       6         16.272
LGA    E       7      E       7         14.185
LGA    N       8      N       8          9.451
LGA    W       9      W       9          3.783
LGA    L      10      L      10          3.936
LGA    L      11      L      11          3.218
LGA    K      12      K      12          5.952
LGA    E      13      E      13          7.287
LGA    Q      14      Q      14          1.147
LGA    E      15      E      15          1.135
LGA    K      16      K      16          1.348
LGA    I      17      I      17          0.780
LGA    Q      18      Q      18          0.163
LGA    T      19      T      19          0.640
LGA    K      20      K      20          0.661
LGA    Y      21      Y      21          0.759
LGA    R      22      R      22          0.742
LGA    H      23      H      23          0.487
LGA    L      24      L      24          1.007
LGA    N      25      N      25          1.183
LGA    H      26      H      26          0.865
LGA    I      27      I      27          0.567

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27  211    4.0     17    1.58     7.701     7.174     1.014

LGA_LOCAL      RMSD =  1.576  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.424  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  8.455  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.828236 * X  +   0.128303 * Y  +   0.545494 * Z  + -24.822193
  Y_new =  -0.189355 * X  +  -0.852103 * Y  +   0.487920 * Z  +  88.515244
  Z_new =   0.527419 * X  +  -0.507405 * Y  +  -0.681447 * Z  + -14.456548 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.501557    0.640036  [ DEG:  -143.3287     36.6713 ]
  Theta =  -0.555560   -2.586033  [ DEG:   -31.8312   -148.1688 ]
  Phi   =  -0.224761    2.916831  [ DEG:   -12.8779    167.1221 ]
 
# 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: T0297TS239_3_2                                
REMARK     2: T0297.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0297TS239_3_2.T0297.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27  211   4.0   17   1.58   7.174     8.45
REMARK  ---------------------------------------------------------- 
MOLECULE T0297TS239_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0297
PARENT 1wab
ATOM      1  N   MET     1      17.878 105.658   0.179  1.00  9.99
ATOM      2  CA  MET     1      19.097 105.378   0.992  1.00  9.99
ATOM      3  C   MET     1      18.815 105.416   2.502  1.00  9.99
ATOM      4  O   MET     1      19.652 104.891   3.261  1.00  9.99
ATOM      5  CB  MET     1      20.193 106.372   0.609  1.00  9.99
ATOM      6  N   ALA     2      17.683 106.040   2.869  1.00  9.99
ATOM      7  CA  ALA     2      17.391 106.183   4.313  1.00  9.99
ATOM      8  C   ALA     2      16.113 105.435   4.655  1.00  9.99
ATOM      9  O   ALA     2      15.675 105.652   5.810  1.00  9.99
ATOM     10  CB  ALA     2      17.391 107.664   4.698  1.00  9.99
ATOM     11  N   VAL     3      15.584 104.650   3.735  1.00  9.99
ATOM     12  CA  VAL     3      14.378 103.840   4.098  1.00  9.99
ATOM     13  C   VAL     3      14.922 102.466   4.451  1.00  9.99
ATOM     14  O   VAL     3      15.322 101.737   3.549  1.00  9.99
ATOM     15  CB  VAL     3      13.473 103.794   2.885  1.00  9.99
ATOM     16  N   GLN     4      14.823 102.074   5.711  1.00  9.99
ATOM     17  CA  GLN     4      15.465 100.799   6.115  1.00  9.99
ATOM     18  C   GLN     4      14.821  99.633   5.405  1.00  9.99
ATOM     19  O   GLN     4      13.585  99.560   5.367  1.00  9.99
ATOM     20  CB  GLN     4      15.353 100.759   7.643  1.00  9.99
ATOM     21  N   LEU     5      15.651  98.746   4.867  1.00  9.99
ATOM     22  CA  LEU     5      15.111  97.579   4.167  1.00  9.99
ATOM     23  C   LEU     5      16.173  96.505   4.180  1.00  9.99
ATOM     24  O   LEU     5      17.384  96.844   4.126  1.00  9.99
ATOM     25  CB  LEU     5      14.667  97.947   2.707  1.00  9.99
ATOM     26  N   LEU     6      15.758  95.279   4.355  1.00  9.99
ATOM     27  CA  LEU     6      16.705  94.177   4.345  1.00  9.99
ATOM     28  C   LEU     6      17.072  93.843   2.910  1.00  9.99
ATOM     29  O   LEU     6      16.371  94.262   1.974  1.00  9.99
ATOM     30  CB  LEU     6      15.980  93.020   5.041  1.00  9.99
ATOM     31  N   GLU     7      18.167  93.105   2.760  1.00  9.99
ATOM     32  CA  GLU     7      18.441  92.578   1.379  1.00  9.99
ATOM     33  C   GLU     7      17.518  91.400   1.134  1.00  9.99
ATOM     34  O   GLU     7      17.481  90.404   1.888  1.00  9.99
ATOM     35  CB  GLU     7      19.929  92.274   1.264  1.00  9.99
ATOM     36  N   ASN     8      16.865  91.473  -0.019  1.00  9.99
ATOM     37  CA  ASN     8      15.940  90.392  -0.447  1.00  9.99
ATOM     38  C   ASN     8      16.778  89.240  -0.998  1.00  9.99
ATOM     39  O   ASN     8      17.680  89.519  -1.824  1.00  9.99
ATOM     40  CB  ASN     8      15.051  90.946  -1.570  1.00  9.99
ATOM     41  N   TRP     9      16.429  88.026  -0.600  1.00  9.99
ATOM     42  CA  TRP     9      17.195  86.860  -1.056  1.00  9.99
ATOM     43  C   TRP     9      16.688  86.496  -2.473  1.00  9.99
ATOM     44  O   TRP     9      15.514  86.017  -2.539  1.00  9.99
ATOM     45  CB  TRP     9      17.089  85.694  -0.083  1.00  9.99
ATOM     46  N   LEU    10      17.507  86.773  -3.483  1.00  9.99
ATOM     47  CA  LEU    10      17.068  86.283  -4.822  1.00  9.99
ATOM     48  C   LEU    10      17.939  85.127  -5.306  1.00  9.99
ATOM     49  O   LEU    10      17.900  84.853  -6.532  1.00  9.99
ATOM     50  CB  LEU    10      17.042  87.430  -5.829  1.00  9.99
ATOM     51  N   LEU    11      18.725  84.559  -4.397  1.00  9.99
ATOM     52  CA  LEU    11      19.695  83.498  -4.801  1.00  9.99
ATOM     53  C   LEU    11      19.175  82.211  -4.175  1.00  9.99
ATOM     54  O   LEU    11      19.214  81.122  -4.829  1.00  9.99
ATOM     55  CB  LEU    11      21.129  83.838  -4.404  1.00  9.99
ATOM     56  N   LYS    12      18.838  82.219  -2.885  1.00  9.99
ATOM     57  CA  LYS    12      18.120  81.064  -2.279  1.00  9.99
ATOM     58  C   LYS    12      18.806  80.480  -1.070  1.00  9.99
ATOM     59  O   LYS    12      18.165  79.615  -0.382  1.00  9.99
ATOM     60  CB  LYS    12      17.931  79.973  -3.346  1.00  9.99
ATOM     61  N   GLU    13      19.990  80.955  -0.673  1.00  9.99
ATOM     62  CA  GLU    13      20.722  80.330   0.442  1.00  9.99
ATOM     63  C   GLU    13      20.609  81.162   1.743  1.00  9.99
ATOM     64  O   GLU    13      21.213  80.689   2.753  1.00  9.99
ATOM     65  CB  GLU    13      22.174  80.067   0.018  1.00  9.99
ATOM     66  N   GLN    14      19.940  82.297   1.698  1.00  9.99
ATOM     67  CA  GLN    14      19.612  83.010   2.971  1.00  9.99
ATOM     68  C   GLN    14      20.862  83.568   3.643  1.00  9.99
ATOM     69  O   GLN    14      20.780  83.849   4.886  1.00  9.99
ATOM     70  CB  GLN    14      18.870  82.055   3.922  1.00  9.99
ATOM     71  N   GLU    15      21.960  83.863   2.938  1.00  9.99
ATOM     72  CA  GLU    15      23.197  84.191   3.643  1.00  9.99
ATOM     73  C   GLU    15      23.114  85.544   4.355  1.00  9.99
ATOM     74  O   GLU    15      23.734  85.667   5.423  1.00  9.99
ATOM     75  CB  GLU    15      24.413  84.202   2.663  1.00  9.99
ATOM     76  N   LYS    16      22.466  86.515   3.707  1.00  9.99
ATOM     77  CA  LYS    16      22.440  87.853   4.355  1.00  9.99
ATOM     78  C   LYS    16      21.700  87.800   5.681  1.00  9.99
ATOM     79  O   LYS    16      22.215  88.349   6.689  1.00  9.99
ATOM     80  CB  LYS    16      21.775  88.830   3.376  1.00  9.99
ATOM     81  N   ILE    17      20.567  87.120   5.698  1.00  9.99
ATOM     82  CA  ILE    17      19.807  86.996   6.991  1.00  9.99
ATOM     83  C   ILE    17      20.596  86.132   7.970  1.00  9.99
ATOM     84  O   ILE    17      20.541  86.453   9.170  1.00  9.99
ATOM     85  CB  ILE    17      18.416  86.499   6.697  1.00  9.99
ATOM     86  N   GLN    18      21.348  85.129   7.530  1.00  9.99
ATOM     87  CA  GLN    18      22.199  84.383   8.453  1.00  9.99
ATOM     88  C   GLN    18      23.226  85.280   9.155  1.00  9.99
ATOM     89  O   GLN    18      23.504  85.122  10.352  1.00  9.99
ATOM     90  CB  GLN    18      22.891  83.216   7.755  1.00  9.99
ATOM     91  N   THR    19      23.852  86.131   8.332  1.00  9.99
ATOM     92  CA  THR    19      24.818  87.094   8.886  1.00  9.99
ATOM     93  C   THR    19      24.155  88.023   9.909  1.00  9.99
ATOM     94  O   THR    19      24.694  88.140  11.022  1.00  9.99
ATOM     95  CB  THR    19      25.428  87.876   7.708  1.00  9.99
ATOM     96  N   LYS    20      23.052  88.619   9.533  1.00  9.99
ATOM     97  CA  LYS    20      22.299  89.488  10.462  1.00  9.99
ATOM     98  C   LYS    20      21.996  88.744  11.765  1.00  9.99
ATOM     99  O   LYS    20      22.255  89.262  12.863  1.00  9.99
ATOM    100  CB  LYS    20      21.022  89.996   9.782  1.00  9.99
ATOM    101  N   TYR    21      21.483  87.533  11.603  1.00  9.99
ATOM    102  CA  TYR    21      21.145  86.733  12.830  1.00  9.99
ATOM    103  C   TYR    21      22.360  86.400  13.664  1.00  9.99
ATOM    104  O   TYR    21      22.268  86.426  14.928  1.00  9.99
ATOM    105  CB  TYR    21      20.328  85.471  12.498  1.00  9.99
ATOM    106  N   ARG    22      23.500  86.142  13.022  1.00  9.99
ATOM    107  CA  ARG    22      24.738  85.914  13.772  1.00  9.99
ATOM    108  C   ARG    22      25.084  87.144  14.613  1.00  9.99
ATOM    109  O   ARG    22      25.481  87.061  15.768  1.00  9.99
ATOM    110  CB  ARG    22      25.933  85.509  12.915  1.00  9.99
ATOM    111  N   HIS    23      24.999  88.330  13.973  1.00  9.99
ATOM    112  CA  HIS    23      25.338  89.588  14.647  1.00  9.99
ATOM    113  C   HIS    23      24.394  89.895  15.801  1.00  9.99
ATOM    114  O   HIS    23      24.868  90.376  16.849  1.00  9.99
ATOM    115  CB  HIS    23      25.297  90.706  13.576  1.00  9.99
ATOM    116  N   LEU    24      23.117  89.619  15.584  1.00  9.99
ATOM    117  CA  LEU    24      22.096  89.783  16.634  1.00  9.99
ATOM    118  C   LEU    24      22.538  88.907  17.821  1.00  9.99
ATOM    119  O   LEU    24      22.524  89.361  18.979  1.00  9.99
ATOM    120  CB  LEU    24      20.693  89.474  16.138  1.00  9.99
ATOM    121  N   ASN    25      22.886  87.684  17.507  1.00  9.99
ATOM    122  CA  ASN    25      23.331  86.754  18.588  1.00  9.99
ATOM    123  C   ASN    25      24.582  87.262  19.267  1.00  9.99
ATOM    124  O   ASN    25      24.741  87.130  20.501  1.00  9.99
ATOM    125  CB  ASN    25      23.459  85.334  18.024  1.00  9.99
ATOM    126  N   HIS    26      25.519  87.820  18.518  1.00  9.99
ATOM    127  CA  HIS    26      26.764  88.408  19.022  1.00  9.99
ATOM    128  C   HIS    26      26.451  89.496  20.049  1.00  9.99
ATOM    129  O   HIS    26      27.035  89.531  21.158  1.00  9.99
ATOM    130  CB  HIS    26      27.621  88.981  17.909  1.00  9.99
ATOM    131  N   ILE    27      25.528  90.377  19.639  1.00  9.99
ATOM    132  CA  ILE    27      25.169  91.498  20.534  1.00  9.99
ATOM    133  C   ILE    27      24.434  90.972  21.769  1.00  9.99
ATOM    134  O   ILE    27      24.623  91.579  22.854  1.00  9.99
ATOM    135  CB  ILE    27      24.330  92.551  19.802  1.00  9.99
TER
END
