
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0335TS307_3u-D1
# Molecule2: number of CA atoms   36 (  584),  selected   34 , name T0335_D1.pdb
# PARAMETERS: T0335TS307_3u-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:    34         5 - 40          4.60     4.60
  LCS_AVERAGE:     94.44

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17         5 - 22          1.31     9.10
  LCS_AVERAGE:     40.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16         5 - 20          0.87     9.46
  LCS_AVERAGE:     28.35

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:   36
LCS_GDT     A       5     A       5     16   17   34    10   13   16   16   16   17   17   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     K       6     K       6     16   17   34    11   13   16   16   16   17   17   17   18   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     I       7     I       7     16   17   34    11   13   16   16   16   17   17   17   18   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     A       8     A       8     16   17   34    11   13   16   16   16   17   17   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     R       9     R       9     16   17   34    11   13   16   16   16   17   17   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     I      10     I      10     16   17   34    11   13   16   16   16   17   17   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     N      11     N      11     16   17   34    11   13   16   16   16   17   17   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     E      12     E      12     16   17   34    11   13   16   16   16   17   17   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     L      13     L      13     16   17   34    11   13   16   16   16   17   17   18   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     A      14     A      14     16   17   34    11   13   16   16   16   17   17   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     A      15     A      15     16   17   34    11   13   16   16   16   17   17   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     K      16     K      16     16   17   34    11   13   16   16   16   17   17   18   21   24   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     A      17     A      17     16   17   34     4   13   16   16   16   17   17   17   21   24   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     K      18     K      18     16   17   34     4   11   16   16   16   17   17   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     A      19     A      19     16   17   34     4    9   16   16   16   17   17   17   17   17   24   29   32   33   33   34   34   34   34   34 
LCS_GDT     G      20     G      20     16   17   34     3    6   16   16   16   17   17   17   17   17   19   20   21   30   31   34   34   34   34   34 
LCS_GDT     I      22     I      22      3   17   34     0    3    4   10   15   17   17   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     T      23     T      23      3    3   34     3    3    4    5    8   12   16   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     E      24     E      24      3    4   34     3    3    4    7    7    8   14   18   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     E      25     E      25      3    8   34     3    3    6    7    8   10   15   16   21   22   25   30   31   33   33   34   34   34   34   34 
LCS_GDT     E      26     E      26      5   14   34     3    4    8   12   12   14   15   18   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     K      27     K      27      7   14   34     3    4    8   12   12   14   16   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     A      28     A      28      7   14   34     3    6    8   12   12   14   16   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     E      29     E      29      7   14   34     4    6    8   12   12   14   16   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     Q      30     Q      30      7   14   34     4    6    8   12   12   14   16   18   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     Q      31     Q      31      7   14   34     4    6    8   12   12   14   16   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     K      32     K      32      7   14   34     4    6    8   12   12   14   16   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     L      33     L      33      7   14   34     4    6    8   12   12   14   16   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     R      34     R      34      5   14   34     4    4    8   12   12   14   16   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     Q      35     Q      35      5   14   34     4    4    6   12   12   14   16   19   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     E      36     E      36      5   14   34     4    4    8   12   12   14   14   15   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_GDT     L      38     L      38      4   14   34     3    4    6    9   11   14   14   15   16   19   23   26   32   33   33   34   34   34   34   34 
LCS_GDT     K      39     K      39      3   14   34     3    6    6    9   11   14   14   15   17   19   22   26   32   33   33   34   34   34   34   34 
LCS_GDT     G      40     G      40      3   14   34     3    6    8   12   12   14   14   15   21   25   27   30   32   33   33   34   34   34   34   34 
LCS_AVERAGE  LCS_A:  54.55  (  28.35   40.85   94.44 )

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     13     16     16     16     17     17     19     21     25     27     30     32     33     33     34     34     34     34     34 
GDT PERCENT_CA  30.56  36.11  44.44  44.44  44.44  47.22  47.22  52.78  58.33  69.44  75.00  83.33  88.89  91.67  91.67  94.44  94.44  94.44  94.44  94.44
GDT RMS_LOCAL    0.25   0.44   0.87   0.87   0.87   1.31   1.31   3.06   3.14   3.56   3.74   4.02   4.32   4.41   4.41   4.60   4.60   4.60   4.60   4.60
GDT RMS_ALL_CA   9.39   9.40   9.46   9.46   9.46   9.10   9.10   4.80   5.11   4.78   4.71   4.70   4.61   4.61   4.61   4.60   4.60   4.60   4.60   4.60

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          3.782
LGA    K       6      K       6          5.155
LGA    I       7      I       7          4.906
LGA    A       8      A       8          2.595
LGA    R       9      R       9          2.885
LGA    I      10      I      10          3.833
LGA    N      11      N      11          2.180
LGA    E      12      E      12          2.746
LGA    L      13      L      13          4.508
LGA    A      14      A      14          2.968
LGA    A      15      A      15          2.986
LGA    K      16      K      16          5.833
LGA    A      17      A      17          5.730
LGA    K      18      K      18          3.008
LGA    A      19      A      19          7.701
LGA    G      20      G      20          9.380
LGA    I      22      I      22          3.940
LGA    T      23      T      23          3.921
LGA    E      24      E      24          5.536
LGA    E      25      E      25          6.366
LGA    E      26      E      26          5.006
LGA    K      27      K      27          2.913
LGA    A      28      A      28          3.470
LGA    E      29      E      29          3.856
LGA    Q      30      Q      30          4.382
LGA    Q      31      Q      31          2.855
LGA    K      32      K      32          2.481
LGA    L      33      L      33          2.938
LGA    R      34      R      34          2.919
LGA    Q      35      Q      35          1.547
LGA    E      36      E      36          4.574
LGA    L      38      L      38          7.340
LGA    K      39      K      39          7.950
LGA    G      40      G      40          5.723

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34   36    4.0     19    3.06    56.944    53.828     0.601

LGA_LOCAL      RMSD =  3.062  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.711  Number of atoms =   34 
Std_ALL_ATOMS  RMSD =  4.596  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.291989 * X  +   0.567355 * Y  +   0.769968 * Z  +   0.101323
  Y_new =  -0.218714 * X  +  -0.744108 * Y  +   0.631242 * Z  +   8.341324
  Z_new =   0.931078 * X  +  -0.352719 * Y  +  -0.093183 * Z  +   5.648819 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.829080    1.312512  [ DEG:  -104.7986     75.2014 ]
  Theta =  -1.197357   -1.944236  [ DEG:   -68.6035   -111.3965 ]
  Phi   =  -0.642892    2.498701  [ DEG:   -36.8350    143.1650 ]
 
# 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_3u-D1                              
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS307_3u-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34   36   4.0   19   3.06  53.828     4.60
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS307_3u-D1
PFRMAT   TS
TARGET   T0335
MODEL    3  UNREFINED
PARENT   1e52_A
ATOM     1   N   ALA     5      -3.905 -12.965  -8.864  1.00                    
ATOM     1   CA  ALA     5      -2.766 -12.777  -7.916  1.00                    
ATOM     1   C   ALA     5      -2.393 -11.295  -7.839  1.00                    
ATOM     1   O   ALA     5      -2.462 -10.678  -6.795  1.00                    
ATOM     1   N   LYS     6      -2.011 -10.719  -8.944  1.00                    
ATOM     1   CA  LYS     6      -1.647  -9.275  -8.945  1.00                    
ATOM     1   C   LYS     6      -2.831  -8.454  -8.414  1.00                    
ATOM     1   O   LYS     6      -2.734  -7.782  -7.407  1.00                    
ATOM     1   N   ILE     7      -3.949  -8.512  -9.086  1.00                    
ATOM     1   CA  ILE     7      -5.145  -7.744  -8.629  1.00                    
ATOM     1   C   ILE     7      -5.405  -7.996  -7.140  1.00                    
ATOM     1   O   ILE     7      -5.849  -7.123  -6.422  1.00                    
ATOM     1   N   ALA     8      -5.128  -9.183  -6.672  1.00                    
ATOM     1   CA  ALA     8      -5.356  -9.485  -5.231  1.00                    
ATOM     1   C   ALA     8      -4.306  -8.774  -4.373  1.00                    
ATOM     1   O   ALA     8      -4.589  -8.309  -3.287  1.00                    
ATOM     1   N   ARG     9      -3.096  -8.687  -4.854  1.00                    
ATOM     1   CA  ARG     9      -2.029  -8.006  -4.067  1.00                    
ATOM     1   C   ARG     9      -2.270  -6.494  -4.054  1.00                    
ATOM     1   O   ARG     9      -2.182  -5.849  -3.028  1.00                    
ATOM     1   N   ILE    10      -2.573  -5.923  -5.188  1.00                    
ATOM     1   CA  ILE    10      -2.821  -4.453  -5.242  1.00                    
ATOM     1   C   ILE    10      -3.902  -4.065  -4.232  1.00                    
ATOM     1   O   ILE    10      -3.701  -3.211  -3.390  1.00                    
ATOM     1   N   ASN    11      -5.048  -4.682  -4.309  1.00                    
ATOM     1   CA  ASN    11      -6.142  -4.346  -3.353  1.00                    
ATOM     1   C   ASN    11      -5.694  -4.626  -1.915  1.00                    
ATOM     1   O   ASN    11      -6.229  -4.078  -0.971  1.00                    
ATOM     1   N   GLU    12      -4.720  -5.475  -1.743  1.00                    
ATOM     1   CA  GLU    12      -4.240  -5.791  -0.366  1.00                    
ATOM     1   C   GLU    12      -3.293  -4.695   0.134  1.00                    
ATOM     1   O   GLU    12      -3.373  -4.263   1.266  1.00                    
ATOM     1   N   LEU    13      -2.397  -4.245  -0.701  1.00                    
ATOM     1   CA  LEU    13      -1.443  -3.181  -0.271  1.00                    
ATOM     1   C   LEU    13      -2.169  -1.840  -0.121  1.00                    
ATOM     1   O   LEU    13      -1.954  -1.113   0.828  1.00                    
ATOM     1   N   ALA    14      -3.026  -1.509  -1.047  1.00                    
ATOM     1   CA  ALA    14      -3.762  -0.214  -0.952  1.00                    
ATOM     1   C   ALA    14      -4.615  -0.179   0.319  1.00                    
ATOM     1   O   ALA    14      -4.662   0.812   1.019  1.00                    
ATOM     1   N   ALA    15      -5.291  -1.254   0.620  1.00                    
ATOM     1   CA  ALA    15      -6.141  -1.281   1.844  1.00                    
ATOM     1   C   ALA    15      -5.258  -1.183   3.089  1.00                    
ATOM     1   O   ALA    15      -5.706  -0.795   4.149  1.00                    
ATOM     1   N   LYS    16      -4.006  -1.531   2.972  1.00                    
ATOM     1   CA  LYS    16      -3.098  -1.457   4.154  1.00                    
ATOM     1   C   LYS    16      -2.748   0.001   4.464  1.00                    
ATOM     1   O   LYS    16      -2.682   0.404   5.610  1.00                    
ATOM     1   N   ALA    17      -2.522   0.797   3.455  1.00                    
ATOM     1   CA  ALA    17      -2.177   2.228   3.693  1.00                    
ATOM     1   C   ALA    17      -3.224   2.886   4.597  1.00                    
ATOM     1   O   ALA    17      -2.901   3.505   5.591  1.00                    
ATOM     1   N   LYS    18      -4.479   2.761   4.253  1.00                    
ATOM     1   CA  LYS    18      -5.553   3.383   5.084  1.00                    
ATOM     1   C   LYS    18      -5.365   3.029   6.563  1.00                    
ATOM     1   O   LYS    18      -5.469   3.873   7.431  1.00                    
ATOM     1   N   ALA    19      -5.092   1.788   6.857  1.00                    
ATOM     1   CA  ALA    19      -4.901   1.381   8.279  1.00                    
ATOM     1   C   ALA    19      -3.873   2.291   8.962  1.00                    
ATOM     1   O   ALA    19      -4.214   3.143   9.757  1.00                    
ATOM     1   N   GLY    20      -2.616   2.108   8.664  1.00                    
ATOM     1   CA  GLY    20      -1.565   2.954   9.300  1.00                    
ATOM     1   C   GLY    20      -1.858   4.441   9.079  1.00                    
ATOM     1   O   GLY    20      -1.935   5.209  10.017  1.00                    
ATOM     1   N   ILE    22      -2.021   4.854   7.846  1.00                    
ATOM     1   CA  ILE    22      -2.311   6.295   7.562  1.00                    
ATOM     1   C   ILE    22      -3.414   6.805   8.497  1.00                    
ATOM     1   O   ILE    22      -3.443   7.960   8.871  1.00                    
ATOM     1   N   THR    23      -4.311   5.940   8.889  1.00                    
ATOM     1   CA  THR    23      -5.399   6.364   9.816  1.00                    
ATOM     1   C   THR    23      -4.859   6.396  11.248  1.00                    
ATOM     1   O   THR    23      -5.234   7.230  12.048  1.00                    
ATOM     1   N   GLU    24      -3.967   5.498  11.568  1.00                    
ATOM     1   CA  GLU    24      -3.384   5.477  12.939  1.00                    
ATOM     1   C   GLU    24      -2.062   6.248  12.948  1.00                    
ATOM     1   O   GLU    24      -1.199   6.019  13.772  1.00                    
ATOM     1   N   GLU    25      -1.901   7.161  12.029  1.00                    
ATOM     1   CA  GLU    25      -0.643   7.960  11.964  1.00                    
ATOM     1   C   GLU    25       0.579   7.042  11.874  1.00                    
ATOM     1   O   GLU    25       1.655   7.380  12.328  1.00                    
ATOM     1   N   GLU    26       0.429   5.892  11.278  1.00                    
ATOM     1   CA  GLU    26       1.590   4.964  11.145  1.00                    
ATOM     1   C   GLU    26       2.029   4.887   9.678  1.00                    
ATOM     1   O   GLU    26       2.677   3.949   9.261  1.00                    
ATOM     1   N   LYS    27       1.668   5.872   8.896  1.00                    
ATOM     1   CA  LYS    27       2.038   5.881   7.453  1.00                    
ATOM     1   C   LYS    27       3.556   5.891   7.248  1.00                    
ATOM     1   O   LYS    27       4.022   5.740   6.140  1.00                    
ATOM     1   N   ALA    28       4.341   6.066   8.284  1.00                    
ATOM     1   CA  ALA    28       5.824   6.074   8.092  1.00                    
ATOM     1   C   ALA    28       6.236   4.858   7.258  1.00                    
ATOM     1   O   ALA    28       6.637   4.978   6.116  1.00                    
ATOM     1   N   GLU    29       6.107   3.693   7.814  1.00                    
ATOM     1   CA  GLU    29       6.450   2.460   7.053  1.00                    
ATOM     1   C   GLU    29       5.278   2.074   6.140  1.00                    
ATOM     1   O   GLU    29       5.429   1.319   5.200  1.00                    
ATOM     1   N   GLN    30       4.102   2.578   6.428  1.00                    
ATOM     1   CA  GLN    30       2.906   2.234   5.602  1.00                    
ATOM     1   C   GLN    30       2.897   3.002   4.276  1.00                    
ATOM     1   O   GLN    30       2.737   2.425   3.220  1.00                    
ATOM     1   N   GLN    31       3.048   4.298   4.317  1.00                    
ATOM     1   CA  GLN    31       3.027   5.089   3.052  1.00                    
ATOM     1   C   GLN    31       4.001   4.496   2.033  1.00                    
ATOM     1   O   GLN    31       3.850   4.679   0.843  1.00                    
ATOM     1   N   LYS    32       4.992   3.776   2.483  1.00                    
ATOM     1   CA  LYS    32       5.955   3.169   1.519  1.00                    
ATOM     1   C   LYS    32       5.192   2.332   0.492  1.00                    
ATOM     1   O   LYS    32       5.577   2.236  -0.657  1.00                    
ATOM     1   N   LEU    33       4.101   1.736   0.895  1.00                    
ATOM     1   CA  LEU    33       3.302   0.917  -0.061  1.00                    
ATOM     1   C   LEU    33       2.960   1.762  -1.288  1.00                    
ATOM     1   O   LEU    33       2.800   1.257  -2.382  1.00                    
ATOM     1   N   ARG    34       2.861   3.053  -1.111  1.00                    
ATOM     1   CA  ARG    34       2.546   3.953  -2.262  1.00                    
ATOM     1   C   ARG    34       3.462   3.618  -3.448  1.00                    
ATOM     1   O   ARG    34       3.068   3.706  -4.593  1.00                    
ATOM     1   N   GLN    35       4.676   3.227  -3.176  1.00                    
ATOM     1   CA  GLN    35       5.610   2.878  -4.284  1.00                    
ATOM     1   C   GLN    35       5.185   1.553  -4.922  1.00                    
ATOM     1   O   GLN    35       5.268   1.374  -6.120  1.00                    
ATOM     1   N   GLU    36       4.723   0.625  -4.127  1.00                    
ATOM     1   CA  GLU    36       4.286  -0.685  -4.686  1.00                    
ATOM     1   C   GLU    36       2.879  -0.559  -5.276  1.00                    
ATOM     1   O   GLU    36       2.551  -1.182  -6.267  1.00                    
ATOM     1   N   LEU    38       2.044   0.245  -4.674  1.00                    
ATOM     1   CA  LEU    38       0.658   0.413  -5.197  1.00                    
ATOM     1   C   LEU    38       0.690   1.103  -6.564  1.00                    
ATOM     1   O   LEU    38      -0.088   0.794  -7.444  1.00                    
ATOM     1   N   LYS    39       1.584   2.035  -6.747  1.00                    
ATOM     1   CA  LYS    39       1.664   2.745  -8.056  1.00                    
ATOM     1   C   LYS    39       2.355   1.859  -9.096  1.00                    
ATOM     1   O   LYS    39       1.914   1.750 -10.223  1.00                    
ATOM     1   N   GLY    40       3.437   1.229  -8.729  1.00                    
ATOM     1   CA  GLY    40       4.156   0.353  -9.698  1.00                    
ATOM     1   C   GLY    40       3.269  -0.829 -10.100  1.00                    
ATOM     1   O   GLY    40       3.173  -1.179 -11.260  1.00                    
TER
END
