
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0335TS307_5u-D1
# Molecule2: number of CA atoms   36 (  584),  selected   32 , name T0335_D1.pdb
# PARAMETERS: T0335TS307_5u-D1.T0335_D1.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:    32         5 - 40          4.74     4.74
  LCS_AVERAGE:     88.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19         5 - 23          1.95     6.49
  LCS_AVERAGE:     47.14

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15         5 - 19          0.69     7.71
  LCS_AVERAGE:     35.24

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:   36
LCS_GDT     A       5     A       5     15   19   32     8   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     K       6     K       6     15   19   32     9   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     I       7     I       7     15   19   32     9   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     A       8     A       8     15   19   32     9   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     R       9     R       9     15   19   32     9   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     I      10     I      10     15   19   32     9   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     N      11     N      11     15   19   32     9   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     E      12     E      12     15   19   32     9   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     L      13     L      13     15   19   32     9   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     A      14     A      14     15   19   32     9   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     A      15     A      15     15   19   32     8   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     K      16     K      16     15   19   32     8   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     A      17     A      17     15   19   32     8   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     K      18     K      18     15   19   32     5   14   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     A      19     A      19     15   19   32     4   10   15   15   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     G      20     G      20      3   19   32     3    3    3    4    4   14   18   19   19   19   19   27   30   32   32   32   32   32   32   32 
LCS_GDT     V      21     V      21      3   19   32     3    3    4   14   16   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     I      22     I      22      3   19   32     3    3    3    5   15   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     T      23     T      23      3   19   32     3    3    4   10   15   18   18   19   19   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     A      28     A      28     13   14   32    11   13   13   13   13   13   13   15   16   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     E      29     E      29     13   14   32    11   13   13   13   13   13   13   15   16   21   25   27   30   32   32   32   32   32   32   32 
LCS_GDT     Q      30     Q      30     13   14   32    11   13   13   13   13   13   13   15   16   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     Q      31     Q      31     13   14   32    10   13   13   13   13   13   13   15   17   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     K      32     K      32     13   14   32    10   13   13   13   13   13   13   15   15   21   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     L      33     L      33     13   14   32    11   13   13   13   13   13   13   15   16   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     R      34     R      34     13   14   32    11   13   13   13   13   13   13   15   15   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     Q      35     Q      35     13   14   32    11   13   13   13   13   13   13   15   15   18   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     E      36     E      36     13   14   32    11   13   13   13   13   13   13   15   17   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     Y      37     Y      37     13   14   32    11   13   13   13   13   13   13   15   17   22   26   28   30   32   32   32   32   32   32   32 
LCS_GDT     L      38     L      38     13   14   32    11   13   13   13   13   13   13   15   15   16   19   22   29   32   32   32   32   32   32   32 
LCS_GDT     K      39     K      39     13   14   32    11   13   13   13   13   13   13   15   15   16   17   21   26   32   32   32   32   32   32   32 
LCS_GDT     G      40     G      40     13   14   32    11   13   13   13   13   13   13   15   17   22   26   28   30   32   32   32   32   32   32   32 
LCS_AVERAGE  LCS_A:  57.09  (  35.24   47.14   88.89 )

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     11     14     15     15     16     18     18     19     19     22     26     28     30     32     32     32     32     32     32     32 
GDT PERCENT_CA  30.56  38.89  41.67  41.67  44.44  50.00  50.00  52.78  52.78  61.11  72.22  77.78  83.33  88.89  88.89  88.89  88.89  88.89  88.89  88.89
GDT RMS_LOCAL    0.25   0.51   0.69   0.69   1.17   1.71   1.71   1.95   1.95   3.53   4.12   4.30   4.52   4.74   4.74   4.74   4.74   4.74   4.74   4.74
GDT RMS_ALL_CA  13.29   7.61   7.71   7.71   7.07   6.44   6.44   6.49   6.49   5.12   4.82   4.78   4.76   4.74   4.74   4.74   4.74   4.74   4.74   4.74

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          1.761
LGA    K       6      K       6          1.466
LGA    I       7      I       7          1.419
LGA    A       8      A       8          1.101
LGA    R       9      R       9          1.194
LGA    I      10      I      10          1.436
LGA    N      11      N      11          1.280
LGA    E      12      E      12          0.790
LGA    L      13      L      13          1.184
LGA    A      14      A      14          1.453
LGA    A      15      A      15          1.149
LGA    K      16      K      16          1.068
LGA    A      17      A      17          1.984
LGA    K      18      K      18          0.758
LGA    A      19      A      19          2.025
LGA    G      20      G      20          3.979
LGA    V      21      V      21          2.605
LGA    I      22      I      22          2.973
LGA    T      23      T      23          3.811
LGA    A      28      A      28         10.756
LGA    E      29      E      29         11.457
LGA    Q      30      Q      30          9.450
LGA    Q      31      Q      31          9.258
LGA    K      32      K      32         11.143
LGA    L      33      L      33         10.220
LGA    R      34      R      34          8.779
LGA    Q      35      Q      35          8.941
LGA    E      36      E      36          9.602
LGA    Y      37      Y      37          8.992
LGA    L      38      L      38          8.969
LGA    K      39      K      39          9.392
LGA    G      40      G      40          8.801

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32   36    4.0     19    1.95    55.556    54.060     0.928

LGA_LOCAL      RMSD =  1.947  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.378  Number of atoms =   32 
Std_ALL_ATOMS  RMSD =  4.736  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.990445 * X  +   0.000691 * Y  +  -0.137905 * Z  +   1.042810
  Y_new =   0.072210 * X  +  -0.854543 * Y  +   0.514336 * Z  +  -1.367384
  Z_new =  -0.117490 * X  +  -0.519380 * Y  +  -0.846428 * Z  +   0.896448 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.591223    0.550369  [ DEG:  -148.4662     31.5338 ]
  Theta =   0.117762    3.023831  [ DEG:     6.7473    173.2527 ]
  Phi   =   0.072778   -3.068815  [ DEG:     4.1699   -175.8301 ]
 
# 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: T0335TS307_5u-D1                              
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS307_5u-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32   36   4.0   19   1.95  54.060     4.74
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS307_5u-D1
PFRMAT   TS
TARGET   T0335
MODEL    5  UNREFINED
PARENT   1ywm_A
ATOM    814  N   ALA     5      -1.123 -11.295  -8.365  1.00 18.74           N  
ATOM    815  CA  ALA     5      -1.325 -11.457  -6.918  1.00 23.45           C  
ATOM    816  C   ALA     5      -0.823 -10.235  -6.141  1.00 20.91           C  
ATOM    817  O   ALA     5      -1.457  -9.794  -5.170  1.00 18.80           O  
ATOM    821  N   LYS     6       0.334  -9.708  -6.547  1.00 16.56           N  
ATOM    822  CA  LYS     6       0.814  -8.453  -5.979  1.00 15.55           C  
ATOM    823  C   LYS     6      -0.239  -7.369  -6.104  1.00 17.28           C  
ATOM    824  O   LYS     6      -0.527  -6.655  -5.123  1.00 16.00           O  
ATOM    829  N   ILE     7      -0.841  -7.239  -7.285  1.00 14.20           N  
ATOM    830  CA  ILE     7      -1.811  -6.155  -7.482  1.00 16.86           C  
ATOM    831  C   ILE     7      -3.056  -6.345  -6.604  1.00 17.32           C  
ATOM    832  O   ILE     7      -3.589  -5.387  -6.053  1.00 16.45           O  
ATOM    840  N   ALA     8      -3.493  -7.595  -6.454  1.00 14.80           N  
ATOM    841  CA  ALA     8      -4.608  -7.914  -5.564  1.00 17.33           C  
ATOM    842  C   ALA     8      -4.238  -7.586  -4.134  1.00 17.72           C  
ATOM    843  O   ALA     8      -5.031  -6.990  -3.414  1.00 15.55           O  
ATOM    848  N   ARG     9      -3.051  -8.009  -3.721  1.00 13.75           N  
ATOM    849  CA  ARG     9      -2.565  -7.709  -2.369  1.00 20.31           C  
ATOM    850  C   ARG     9      -2.531  -6.204  -2.100  1.00 16.34           C  
ATOM    851  O   ARG     9      -2.928  -5.722  -1.016  1.00 13.68           O  
ATOM    857  N   ILE    10      -2.012  -5.455  -3.057  1.00 14.00           N  
ATOM    858  CA  ILE    10      -1.976  -4.021  -2.915  1.00 15.11           C  
ATOM    859  C   ILE    10      -3.372  -3.443  -2.710  1.00 16.46           C  
ATOM    860  O   ILE    10      -3.556  -2.569  -1.852  1.00 14.51           O  
ATOM    865  N   ASN    11      -4.359  -3.919  -3.479  1.00 13.04           N  
ATOM    866  CA  ASN    11      -5.730  -3.385  -3.343  1.00 12.82           C  
ATOM    867  C   ASN    11      -6.340  -3.783  -2.000  1.00 14.24           C  
ATOM    868  O   ASN    11      -7.083  -3.006  -1.405  1.00 13.15           O  
ATOM    874  N   GLU    12      -5.995  -4.966  -1.512  1.00 16.54           N  
ATOM    875  CA  GLU    12      -6.496  -5.413  -0.198  1.00 16.86           C  
ATOM    876  C   GLU    12      -5.947  -4.542   0.940  1.00 16.71           C  
ATOM    877  O   GLU    12      -6.705  -4.143   1.859  1.00 14.00           O  
ATOM    883  N   LEU    13      -4.658  -4.206   0.875  1.00 14.44           N  
ATOM    884  CA  LEU    13      -4.052  -3.348   1.913  1.00 17.60           C  
ATOM    885  C   LEU    13      -4.601  -1.927   1.787  1.00 16.18           C  
ATOM    886  O   LEU    13      -4.846  -1.256   2.786  1.00 14.16           O  
ATOM    890  N   ALA    14      -4.771  -1.449   0.555  1.00 10.98           N  
ATOM    891  CA  ALA    14      -5.358  -0.140   0.330  1.00 11.62           C  
ATOM    892  C   ALA    14      -6.742  -0.061   0.987  1.00 15.73           C  
ATOM    893  O   ALA    14      -7.079   0.924   1.678  1.00 17.35           O  
ATOM    901  N   ALA    15      -7.551  -1.098   0.766  1.00 13.16           N  
ATOM    902  CA  ALA    15      -8.917  -1.114   1.284  1.00 15.03           C  
ATOM    903  C   ALA    15      -8.867  -1.093   2.822  1.00 17.22           C  
ATOM    904  O   ALA    15      -9.561  -0.323   3.473  1.00 15.39           O  
ATOM    908  N   LYS    16      -8.023  -1.945   3.374  1.00 10.96           N  
ATOM    909  CA  LYS    16      -7.813  -1.975   4.815  1.00 15.18           C  
ATOM    910  C   LYS    16      -7.363  -0.603   5.352  1.00 17.06           C  
ATOM    911  O   LYS    16      -7.954  -0.078   6.319  1.00 13.18           O  
ATOM    916  N   ALA    17      -6.332  -0.027   4.731  1.00 15.43           N  
ATOM    917  CA  ALA    17      -5.753   1.231   5.193  1.00 17.89           C  
ATOM    918  C   ALA    17      -6.788   2.362   5.214  1.00 18.60           C  
ATOM    919  O   ALA    17      -6.691   3.254   6.048  1.00 13.87           O  
ATOM    921  N   LYS    18      -7.768   2.308   4.312  1.00 13.05           N  
ATOM    922  CA  LYS    18      -8.788   3.359   4.211  1.00 14.24           C  
ATOM    923  C   LYS    18      -9.866   3.314   5.290  1.00 11.86           C  
ATOM    924  O   LYS    18     -10.670   4.239   5.412  1.00 12.63           O  
ATOM    929  N   ALA    19      -9.830   2.277   6.111  1.00 12.04           N  
ATOM    930  CA  ALA    19     -10.755   2.178   7.243  1.00 14.23           C  
ATOM    931  C   ALA    19     -10.467   3.335   8.243  1.00 11.95           C  
ATOM    932  O   ALA    19      -9.327   3.477   8.684  1.00 12.62           O  
ATOM    937  N   GLY    20     -11.458   4.153   8.601  1.00 13.05           N  
ATOM    938  CA  GLY    20     -11.222   5.238   9.550  1.00 15.08           C  
ATOM    939  C   GLY    20     -10.780   4.805  10.938  1.00 13.92           C  
ATOM    940  O   GLY    20     -10.397   5.697  11.702  1.00 16.96           O  
ATOM    944  N   VAL    21     -10.744   3.508  11.255  1.00 10.20           N  
ATOM    945  CA  VAL    21     -10.241   3.118  12.584  1.00 10.33           C  
ATOM    946  C   VAL    21      -8.707   3.347  12.752  1.00 14.81           C  
ATOM    947  O   VAL    21      -8.194   3.393  13.878  1.00 11.35           O  
ATOM    953  N   ILE    22      -7.992   3.466  11.623  1.00 12.20           N  
ATOM    954  CA  ILE    22      -6.544   3.690  11.602  1.00 11.20           C  
ATOM    955  C   ILE    22      -6.228   5.174  11.660  1.00  7.51           C  
ATOM    956  O   ILE    22      -6.976   5.996  11.132  1.00 12.56           O  
ATOM    967  N   THR    23      -5.133   5.534  12.324  1.00  8.21           N  
ATOM    968  CA  THR    23      -4.702   6.928  12.326  1.00 13.83           C  
ATOM    969  C   THR    23      -4.497   7.429  10.896  1.00 12.74           C  
ATOM    970  O   THR    23      -4.046   6.679  10.023  1.00 13.22           O  
ATOM    974  N   ALA    28      -4.792   8.701  10.665  1.00 11.34           N  
ATOM    975  CA  ALA    28      -4.521   9.252   9.332  1.00 15.90           C  
ATOM    976  C   ALA    28      -3.014   9.188   8.995  1.00 13.75           C  
ATOM    977  O   ALA    28      -2.625   8.895   7.861  1.00 17.03           O  
ATOM    983  N   GLU    29      -2.170   9.430   9.985  1.00 15.38           N  
ATOM    984  CA  GLU    29      -0.725   9.440   9.768  1.00 15.35           C  
ATOM    985  C   GLU    29      -0.218   8.051   9.319  1.00 20.44           C  
ATOM    986  O   GLU    29       0.615   7.947   8.397  1.00 18.18           O  
ATOM    992  N   GLN    30      -0.698   6.987   9.965  1.00 13.69           N  
ATOM    993  CA  GLN    30      -0.299   5.650   9.509  1.00 15.09           C  
ATOM    994  C   GLN    30      -0.904   5.279   8.129  1.00 13.36           C  
ATOM    995  O   GLN    30      -0.201   4.694   7.270  1.00 13.06           O  
ATOM    998  N   GLN    31      -2.172   5.614   7.916  1.00 10.56           N  
ATOM    999  CA  GLN    31      -2.798   5.382   6.607  1.00 13.00           C  
ATOM   1000  C   GLN    31      -1.935   6.007   5.504  1.00 12.17           C  
ATOM   1001  O   GLN    31      -1.667   5.389   4.468  1.00  9.95           O  
ATOM   1009  N   LYS    32      -1.542   7.254   5.719  1.00 10.59           N  
ATOM   1010  CA  LYS    32      -0.834   8.000   4.693  1.00 14.09           C  
ATOM   1011  C   LYS    32       0.520   7.365   4.398  1.00 12.93           C  
ATOM   1012  O   LYS    32       0.933   7.274   3.238  1.00  9.40           O  
ATOM   1016  N   LEU    33       1.213   6.922   5.441  1.00  8.69           N  
ATOM   1017  CA  LEU    33       2.514   6.292   5.239  1.00 10.85           C  
ATOM   1018  C   LEU    33       2.361   4.993   4.470  1.00 12.13           C  
ATOM   1019  O   LEU    33       3.155   4.692   3.573  1.00 11.96           O  
ATOM   1025  N   ARG    34       1.337   4.218   4.818  1.00  6.96           N  
ATOM   1026  CA  ARG    34       1.090   2.946   4.136  1.00 10.84           C  
ATOM   1027  C   ARG    34       0.706   3.193   2.660  1.00 10.17           C  
ATOM   1028  O   ARG    34       1.271   2.566   1.736  1.00 13.04           O  
ATOM   1032  N   GLN    35      -0.209   4.125   2.427  1.00  8.99           N  
ATOM   1033  CA  GLN    35      -0.614   4.394   1.022  1.00  8.55           C  
ATOM   1034  C   GLN    35       0.529   4.925   0.188  1.00 11.03           C  
ATOM   1035  O   GLN    35       0.612   4.669  -1.047  1.00 11.70           O  
ATOM   1040  N   GLU    36       1.424   5.688   0.816  1.00  8.16           N  
ATOM   1041  CA  GLU    36       2.582   6.211   0.093  1.00  9.85           C  
ATOM   1042  C   GLU    36       3.453   5.061  -0.431  1.00 12.98           C  
ATOM   1043  O   GLU    36       3.945   5.083  -1.578  1.00 13.99           O  
ATOM   1047  N   TYR    37       3.657   4.066   0.420  1.00 12.14           N  
ATOM   1048  CA  TYR    37       4.477   2.916   0.045  1.00 16.99           C  
ATOM   1049  C   TYR    37       3.796   2.084  -1.042  1.00 15.30           C  
ATOM   1050  O   TYR    37       4.442   1.605  -2.012  1.00 14.35           O  
ATOM   1051  N   LEU    38       2.499   1.867  -0.881  1.00 10.68           N  
ATOM   1052  CA  LEU    38       1.752   1.174  -1.934  1.00 12.08           C  
ATOM   1053  C   LEU    38       1.812   1.919  -3.282  1.00 12.54           C  
ATOM   1054  O   LEU    38       1.930   1.281  -4.339  1.00 10.82           O  
ATOM   1059  N   LYS    39       1.648   3.244  -3.263  1.00 13.30           N  
ATOM   1060  CA  LYS    39       1.729   4.043  -4.485  1.00 15.42           C  
ATOM   1061  C   LYS    39       3.077   3.937  -5.174  1.00 13.38           C  
ATOM   1062  O   LYS    39       3.142   3.893  -6.402  1.00 11.76           O  
ATOM   1067  N   GLY    40       4.139   3.898  -4.388  1.00 14.43           N  
ATOM   1068  CA  GLY    40       5.487   3.767  -4.935  1.00 17.65           C  
ATOM   1069  C   GLY    40       5.651   2.419  -5.675  1.00 14.53           C  
ATOM   1070  O   GLY    40       6.141   2.364  -6.829  1.00 15.01           O  
TER
END
