
#######################################################
#                                                     #
#                        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   29 (  116),  selected   29 , name T0343AL381_3
# Molecule2: number of CA atoms   94 (  282),  selected   29 , name T0343.pdb
# PARAMETERS: T0343AL381_3.T0343.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:    18        20 - 37          5.00     8.10
  LCS_AVERAGE:     17.61

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        30 - 37          1.58    11.94
  LCS_AVERAGE:      6.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        31 - 36          0.83    12.30
  LONGEST_CONTINUOUS_SEGMENT:     6        32 - 37          0.93    10.10
  LCS_AVERAGE:      4.88

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:   94
LCS_GDT     K       9     K       9      5    7   14     2    3    5    7    7    7    7    9   11   12   13   15   16   17   19   21   23   24   24   25 
LCS_GDT     E      10     E      10      5    7   14     0    3    5    7    7    7    7    9   11   12   12   14   14   16   17   19   20   21   24   25 
LCS_GDT     G      11     G      11      5    7   14     3    4    5    7    7    7    7    9   11   12   13   14   14   16   19   21   23   24   24   25 
LCS_GDT     F      12     F      12      5    7   14     3    4    5    7    7    7    7    9   11   12   13   17   18   19   20   21   23   24   25   26 
LCS_GDT     L      13     L      13      5    7   14     3    4    5    7    7    8    9   12   12   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     D      14     D      14      5    7   14     3    4    5    7    7    8    9   12   12   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     L      15     L      15      5    7   14     3    4    5    7    7    7    8   12   12   13   14   15   16   18   19   21   23   24   25   26 
LCS_GDT     G      16     G      16      4    7   14     3    4    4    6    6    7    7    9   11   12   13   15   16   18   19   21   23   24   25   26 
LCS_GDT     E      17     E      17      4    5   14     3    4    4    5    5    5    5    5    8    9    9   12   13   18   19   19   20   23   25   26 
LCS_GDT     F      18     F      18      4    5   14     3    4    4    5    5    7    7    9   11   12   13   14   15   18   19   19   20   24   25   26 
LCS_GDT     I      19     I      19      3    5   16     0    3    3    5    5    7    8   12   12   13   14   15   16   18   19   21   23   24   25   26 
LCS_GDT     V      20     V      20      3    3   18     1    3    3    4    5    7    8   12   12   13   14   15   16   18   20   21   23   24   25   26 
LCS_GDT     E      21     E      21      3    3   18     3    3    4    4    6    8    9   12   12   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     L      22     L      22      3    3   18     3    3    3    4    4    5    9   12   12   13   14   16   18   19   20   21   23   24   25   26 
LCS_GDT     V      23     V      23      3    3   18     3    3    3    4    6    8    9   12   12   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     Y      24     Y      24      3    3   18     3    4    4    6    8    9   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     I      25     I      25      3    3   18     0    3    3    3    5   10   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     D      26     D      26      3    5   18     0    3    3    7    8   10   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     C      27     C      27      5    6   18     2    3    5    5    5    8   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     P      28     P      28      5    6   18     2    4    5    5    5    6    6    8    9   11   12   15   15   18   19   21   23   24   25   26 
LCS_GDT     C      29     C      29      5    6   18     3    4    5    5    5    7    9   12   13   13   13   15   17   19   20   21   23   24   25   26 
LCS_GDT     E      30     E      30      5    8   18     3    4    5    6    8   10   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     P      31     P      31      6    8   18     3    6    6    7    8   10   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     I      32     I      32      6    8   18     3    6    6    7    8   10   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     P      33     P      33      6    8   18     3    6    6    7    8   10   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     P      34     P      34      6    8   18     3    6    6    7    8   10   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     T      35     T      35      6    8   18     3    6    6    7    8   10   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     L      36     L      36      6    8   18     3    6    6    7    8   10   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_GDT     A      37     A      37      6    8   18     3    3    6    7    8   10   11   12   13   13   16   17   18   19   20   21   23   24   25   26 
LCS_AVERAGE  LCS_A:   9.65  (   4.88    6.46   17.61 )

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      6      6      7      8     10     11     12     13     13     16     17     18     19     20     21     23     24     25     26 
GDT PERCENT_CA   3.19   6.38   6.38   7.45   8.51  10.64  11.70  12.77  13.83  13.83  17.02  18.09  19.15  20.21  21.28  22.34  24.47  25.53  26.60  27.66
GDT RMS_LOCAL    0.10   0.83   0.83   1.19   1.40   1.84   2.09   2.26   2.67   2.67   4.03   4.19   4.35   4.59   4.81   5.07   5.62   5.80   6.04   6.23
GDT RMS_ALL_CA  11.70  12.30  12.30  10.54  10.21  10.90  10.54  10.44  10.54  10.54   8.05   8.10   8.06   7.98   7.84   7.80   7.80   7.74   7.79   7.85

#      Molecule1      Molecule2       DISTANCE
LGA    K       9      K       9          9.295
LGA    E      10      E      10          8.401
LGA    G      11      G      11          7.184
LGA    F      12      F      12          8.947
LGA    L      13      L      13         10.740
LGA    D      14      D      14         14.579
LGA    L      15      L      15         21.116
LGA    G      16      G      16         19.944
LGA    E      17      E      17         19.574
LGA    F      18      F      18         19.891
LGA    I      19      I      19         17.186
LGA    V      20      V      20         13.202
LGA    E      21      E      21          9.725
LGA    L      22      L      22         11.187
LGA    V      23      V      23          8.523
LGA    Y      24      Y      24          3.110
LGA    I      25      I      25          3.385
LGA    D      26      D      26          1.706
LGA    C      27      C      27          3.638
LGA    P      28      P      28          7.986
LGA    C      29      C      29          6.090
LGA    E      30      E      30          2.999
LGA    P      31      P      31          2.334
LGA    I      32      I      32          1.981
LGA    P      33      P      33          1.222
LGA    P      34      P      34          0.654
LGA    T      35      T      35          1.488
LGA    L      36      L      36          0.607
LGA    A      37      A      37          1.012

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   29   94    4.0     12    2.26    12.234    10.890     0.509

LGA_LOCAL      RMSD =  2.258  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.444  Number of atoms =   29 
Std_ALL_ATOMS  RMSD =  7.224  (standard rmsd on all 29 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.652798 * X  +   0.754080 * Y  +  -0.072234 * Z  +  26.303701
  Y_new =  -0.753192 * X  +  -0.656293 * Y  +  -0.044518 * Z  +  26.612165
  Z_new =  -0.080977 * X  +   0.025345 * Y  +   0.996394 * Z  +  24.175716 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.025431   -3.116162  [ DEG:     1.4571   -178.5429 ]
  Theta =   0.081066    3.060527  [ DEG:     4.6447    175.3553 ]
  Phi   =  -2.284911    0.856682  [ DEG:  -130.9158     49.0842 ]
 
# 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: T0343AL381_3                                  
REMARK     2: T0343.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0343AL381_3.T0343.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   29   94   4.0   12   2.26  10.890     7.22
REMARK  ---------------------------------------------------------- 
MOLECULE T0343AL381_3
REMARK Aligment from pdb entry: 1f8hA
ATOM      1  N   LYS     9      31.686  18.210  17.551  1.00  0.00              
ATOM      2  CA  LYS     9      30.761  17.965  18.697  1.00  0.00              
ATOM      3  C   LYS     9      31.561  17.781  19.989  1.00  0.00              
ATOM      4  O   LYS     9      31.301  16.886  20.769  1.00  0.00              
ATOM      5  N   GLU    10      32.533  18.617  20.218  1.00  0.00              
ATOM      6  CA  GLU    10      33.349  18.486  21.458  1.00  0.00              
ATOM      7  C   GLU    10      32.989  19.599  22.440  1.00  0.00              
ATOM      8  O   GLU    10      33.647  19.794  23.444  1.00  0.00              
ATOM      9  N   GLY    11      31.953  20.336  22.157  1.00  0.00              
ATOM     10  CA  GLY    11      31.556  21.437  23.072  1.00  0.00              
ATOM     11  C   GLY    11      32.447  22.655  22.814  1.00  0.00              
ATOM     12  O   GLY    11      32.624  23.493  23.676  1.00  0.00              
ATOM     13  N   PHE    12      32.998  22.769  21.633  1.00  0.00              
ATOM     14  CA  PHE    12      33.867  23.950  21.324  1.00  0.00              
ATOM     15  C   PHE    12      33.833  24.258  19.827  1.00  0.00              
ATOM     16  O   PHE    12      33.478  23.423  19.018  1.00  0.00              
ATOM     17  N   LEU    13      34.219  25.445  19.451  1.00  0.00              
ATOM     18  CA  LEU    13      34.229  25.803  18.004  1.00  0.00              
ATOM     19  C   LEU    13      35.664  26.096  17.553  1.00  0.00              
ATOM     20  O   LEU    13      36.205  27.149  17.825  1.00  0.00              
ATOM     21  N   ASP    14      36.285  25.177  16.864  1.00  0.00              
ATOM     22  CA  ASP    14      37.681  25.417  16.402  1.00  0.00              
ATOM     23  C   ASP    14      37.696  26.495  15.321  1.00  0.00              
ATOM     24  O   ASP    14      36.667  26.953  14.864  1.00  0.00              
ATOM     25  N   LEU    15      38.861  26.906  14.918  1.00  0.00              
ATOM     26  CA  LEU    15      38.961  27.966  13.875  1.00  0.00              
ATOM     27  C   LEU    15      38.082  27.628  12.667  1.00  0.00              
ATOM     28  O   LEU    15      37.553  28.503  12.012  1.00  0.00              
ATOM     29  N   GLY    16      37.919  26.371  12.366  1.00  0.00              
ATOM     30  CA  GLY    16      37.070  25.997  11.200  1.00  0.00              
ATOM     31  C   GLY    16      35.616  25.860  11.644  1.00  0.00              
ATOM     32  O   GLY    16      34.698  26.119  10.893  1.00  0.00              
ATOM     33  N   GLU    17      35.400  25.475  12.869  1.00  0.00              
ATOM     34  CA  GLU    17      34.004  25.344  13.369  1.00  0.00              
ATOM     35  C   GLU    17      33.474  26.728  13.721  1.00  0.00              
ATOM     36  O   GLU    17      32.343  27.066  13.440  1.00  0.00              
ATOM     37  N   PHE    18      34.301  27.541  14.321  1.00  0.00              
ATOM     38  CA  PHE    18      33.866  28.914  14.677  1.00  0.00              
ATOM     39  C   PHE    18      33.559  29.687  13.396  1.00  0.00              
ATOM     40  O   PHE    18      32.791  30.628  13.389  1.00  0.00              
ATOM     41  N   ILE    19      34.152  29.285  12.305  1.00  0.00              
ATOM     42  CA  ILE    19      33.892  29.988  11.017  1.00  0.00              
ATOM     43  C   ILE    19      32.468  29.701  10.543  1.00  0.00              
ATOM     44  O   ILE    19      31.701  30.597  10.237  1.00  0.00              
ATOM     45  N   VAL    20      32.114  28.448  10.482  1.00  0.00              
ATOM     46  CA  VAL    20      30.746  28.078  10.029  1.00  0.00              
ATOM     47  C   VAL    20      29.690  28.752  10.914  1.00  0.00              
ATOM     48  O   VAL    20      28.566  28.971  10.502  1.00  0.00              
ATOM     49  N   GLU    21      30.036  29.067  12.133  1.00  0.00              
ATOM     50  CA  GLU    21      29.043  29.705  13.047  1.00  0.00              
ATOM     51  C   GLU    21      29.065  31.235  12.926  1.00  0.00              
ATOM     52  O   GLU    21      28.261  31.918  13.528  1.00  0.00              
ATOM     53  N   LEU    22      29.969  31.784  12.159  1.00  0.00              
ATOM     54  CA  LEU    22      30.010  33.272  12.022  1.00  0.00              
ATOM     55  C   LEU    22      29.099  33.725  10.884  1.00  0.00              
ATOM     56  O   LEU    22      28.347  34.669  11.022  1.00  0.00              
ATOM     57  N   VAL    23      29.140  33.057   9.769  1.00  0.00              
ATOM     58  CA  VAL    23      28.246  33.465   8.650  1.00  0.00              
ATOM     59  C   VAL    23      26.839  32.952   8.950  1.00  0.00              
ATOM     60  O   VAL    23      25.852  33.471   8.466  1.00  0.00              
ATOM     61  N   TYR    24      26.746  31.945   9.781  1.00  0.00              
ATOM     62  CA  TYR    24      25.414  31.406  10.160  1.00  0.00              
ATOM     63  C   TYR    24      24.748  32.379  11.133  1.00  0.00              
ATOM     64  O   TYR    24      23.542  32.437  11.249  1.00  0.00              
ATOM     65  N   ILE    25      25.540  33.156  11.824  1.00  0.00              
ATOM     66  CA  ILE    25      24.977  34.146  12.782  1.00  0.00              
ATOM     67  C   ILE    25      24.765  35.490  12.085  1.00  0.00              
ATOM     68  O   ILE    25      23.778  36.163  12.299  1.00  0.00              
ATOM     69  N   ASP    26      25.694  35.888  11.261  1.00  0.00              
ATOM     70  CA  ASP    26      25.553  37.195  10.558  1.00  0.00              
ATOM     71  C   ASP    26      24.470  37.114   9.483  1.00  0.00              
ATOM     72  O   ASP    26      23.904  38.115   9.082  1.00  0.00              
ATOM     73  N   CYS    27      24.167  35.938   9.015  1.00  0.00              
ATOM     74  CA  CYS    27      23.115  35.811   7.972  1.00  0.00              
ATOM     75  C   CYS    27      21.735  35.786   8.629  1.00  0.00              
ATOM     76  O   CYS    27      20.733  36.072   8.003  1.00  0.00              
ATOM     77  N   PRO    28      21.675  35.459   9.891  1.00  0.00              
ATOM     78  CA  PRO    28      20.360  35.432  10.586  1.00  0.00              
ATOM     79  C   PRO    28      19.971  36.852  10.985  1.00  0.00              
ATOM     80  O   PRO    28      18.848  37.125  11.358  1.00  0.00              
ATOM     81  N   CYS    29      20.902  37.760  10.907  1.00  0.00              
ATOM     82  CA  CYS    29      20.606  39.168  11.278  1.00  0.00              
ATOM     83  C   CYS    29      20.146  39.964  10.058  1.00  0.00              
ATOM     84  O   CYS    29      19.249  40.780  10.138  1.00  0.00              
ATOM     85  N   GLU    30      20.774  39.755   8.934  1.00  0.00              
ATOM     86  CA  GLU    30      20.391  40.527   7.720  1.00  0.00              
ATOM     87  C   GLU    30      20.057  39.601   6.537  1.00  0.00              
ATOM     88  O   GLU    30      19.578  40.052   5.515  1.00  0.00              
ATOM     89  N   PRO    31      20.309  38.326   6.645  1.00  0.00              
ATOM     90  CA  PRO    31      19.998  37.427   5.489  1.00  0.00              
ATOM     91  C   PRO    31      18.823  36.496   5.799  1.00  0.00              
ATOM     92  O   PRO    31      17.681  36.820   5.536  1.00  0.00              
ATOM     93  N   ILE    32      19.089  35.338   6.339  1.00  0.00              
ATOM     94  CA  ILE    32      17.978  34.388   6.639  1.00  0.00              
ATOM     95  C   ILE    32      18.282  33.583   7.904  1.00  0.00              
ATOM     96  O   ILE    32      19.365  33.658   8.441  1.00  0.00              
ATOM     97  N   PRO    33      17.304  32.831   8.331  1.00  0.00              
ATOM     98  CA  PRO    33      17.457  31.998   9.551  1.00  0.00              
ATOM     99  C   PRO    33      18.470  30.875   9.312  1.00  0.00              
ATOM    100  O   PRO    33      19.179  30.864   8.325  1.00  0.00              
ATOM    101  N   PRO    34      18.551  29.937  10.214  1.00  0.00              
ATOM    102  CA  PRO    34      19.526  28.823  10.049  1.00  0.00              
ATOM    103  C   PRO    34      18.829  27.470  10.202  1.00  0.00              
ATOM    104  O   PRO    34      18.019  27.289  11.089  1.00  0.00              
ATOM    105  N   THR    35      19.181  26.554   9.339  1.00  0.00              
ATOM    106  CA  THR    35      18.598  25.204   9.397  1.00  0.00              
ATOM    107  C   THR    35      19.390  24.376  10.408  1.00  0.00              
ATOM    108  O   THR    35      20.371  24.840  10.947  1.00  0.00              
ATOM    109  N   LEU    36      18.987  23.172  10.684  1.00  0.00              
ATOM    110  CA  LEU    36      19.756  22.362  11.673  1.00  0.00              
ATOM    111  C   LEU    36      20.513  21.244  10.973  1.00  0.00              
ATOM    112  O   LEU    36      20.901  20.270  11.588  1.00  0.00              
ATOM    113  N   ALA    37      20.701  21.344   9.695  1.00  0.00              
ATOM    114  CA  ALA    37      21.405  20.239   8.996  1.00  0.00              
ATOM    115  C   ALA    37      22.765  20.665   8.464  1.00  0.00              
ATOM    116  O   ALA    37      22.885  21.253   7.407  1.00  0.00              
END
