
#######################################################
#                                                     #
#                        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   85 (   85),  selected   42 , name T0335TS393_1
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS393_1.T0335.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:    42         1 - 42          3.50     3.50
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39         4 - 42          1.87     3.78
  LCS_AVERAGE:     88.78

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23        19 - 41          0.97     3.72
  LCS_AVERAGE:     44.39

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:   42
LCS_GDT     M       1     M       1      3    4   42     3    3    3    4    5    5   10   10   13   14   19   19   21   21   21   22   22   22   41   41 
LCS_GDT     I       2     I       2      4    4   42     3    3    4    4    5    6   11   17   18   19   19   20   21   21   21   40   41   41   41   41 
LCS_GDT     S       3     S       3      4   37   42     3    3    4    4   15   17   31   38   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     N       4     N       4     16   39   42     4   12   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A       5     A       5     16   39   42     6   13   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K       6     K       6     16   39   42     7   13   22   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     I       7     I       7     16   39   42     7   13   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A       8     A       8     16   39   42     7   13   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     R       9     R       9     16   39   42     7   13   20   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     I      10     I      10     16   39   42     7   13   16   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     N      11     N      11     16   39   42     7   13   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      12     E      12     16   39   42     7   13   20   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      13     L      13     16   39   42     7   13   16   22   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      14     A      14     16   39   42     7   13   16   21   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      15     A      15     16   39   42     7   13   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      16     K      16     16   39   42     7   13   16   19   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      17     A      17     16   39   42     7   13   16   16   16   32   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      18     K      18     16   39   42     7   13   16   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      19     A      19     23   39   42     7   13   16   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     G      20     G      20     23   39   42     8   20   22   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     V      21     V      21     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     I      22     I      22     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     T      23     T      23     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      24     E      24     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      25     E      25     23   39   42    11   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      26     E      26     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      27     K      27     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      28     A      28     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      29     E      29     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      30     Q      30     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      31     Q      31     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      32     K      32     23   39   42     4   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      33     L      33     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     R      34     R      34     23   39   42    12   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      35     Q      35     23   39   42     9   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      36     E      36     23   39   42     9   20   22   29   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Y      37     Y      37     23   39   42     9   20   22   29   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      38     L      38     23   39   42     9   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      39     K      39     23   39   42     9   17   22   29   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     G      40     G      40     23   39   42     8   15   22   22   33   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     F      41     F      41     23   39   42     8   20   23   30   34   37   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     R      42     R      42      3   39   42     3    3    3   21   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_AVERAGE  LCS_A:  77.72  (  44.39   88.78  100.00 )

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     20     23     30     34     37     38     39     39     39     40     40     40     40     40     40     41     41     41     41 
GDT PERCENT_CA  28.57  47.62  54.76  71.43  80.95  88.10  90.48  92.86  92.86  92.86  95.24  95.24  95.24  95.24  95.24  95.24  97.62  97.62  97.62  97.62
GDT RMS_LOCAL    0.36   0.66   1.09   1.34   1.50   1.69   1.78   1.87   1.87   1.87   2.10   2.10   2.10   2.10   2.10   2.10   2.75   2.75   2.75   2.75
GDT RMS_ALL_CA   4.14   3.86   3.81   3.86   3.76   3.72   3.78   3.78   3.78   3.78   3.69   3.69   3.69   3.69   3.69   3.69   3.57   3.57   3.57   3.57

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         16.381
LGA    I       2      I       2         12.398
LGA    S       3      S       3          6.522
LGA    N       4      N       4          1.285
LGA    A       5      A       5          1.750
LGA    K       6      K       6          1.741
LGA    I       7      I       7          1.431
LGA    A       8      A       8          1.293
LGA    R       9      R       9          1.995
LGA    I      10      I      10          1.988
LGA    N      11      N      11          1.463
LGA    E      12      E      12          1.775
LGA    L      13      L      13          3.040
LGA    A      14      A      14          2.302
LGA    A      15      A      15          1.333
LGA    K      16      K      16          2.825
LGA    A      17      A      17          3.831
LGA    K      18      K      18          1.914
LGA    A      19      A      19          2.139
LGA    G      20      G      20          1.591
LGA    V      21      V      21          1.281
LGA    I      22      I      22          1.448
LGA    T      23      T      23          1.425
LGA    E      24      E      24          1.066
LGA    E      25      E      25          0.455
LGA    E      26      E      26          0.663
LGA    K      27      K      27          0.955
LGA    A      28      A      28          0.344
LGA    E      29      E      29          0.710
LGA    Q      30      Q      30          1.447
LGA    Q      31      Q      31          1.065
LGA    K      32      K      32          1.380
LGA    L      33      L      33          1.501
LGA    R      34      R      34          1.122
LGA    Q      35      Q      35          0.767
LGA    E      36      E      36          2.054
LGA    Y      37      Y      37          2.160
LGA    L      38      L      38          0.939
LGA    K      39      K      39          2.477
LGA    G      40      G      40          3.483
LGA    F      41      F      41          1.240
LGA    R      42      R      42          3.665

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   85   42    4.0     39    1.87    76.786    83.242     1.984

LGA_LOCAL      RMSD =  1.866  Number of atoms =   39  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.781  Number of atoms =   42 
Std_ALL_ATOMS  RMSD =  3.505  (standard rmsd on all 42 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.253590 * X  +   0.383247 * Y  +   0.888152 * Z  +   4.353767
  Y_new =   0.897596 * X  +  -0.435484 * Y  +  -0.068370 * Z  +   1.399942
  Z_new =   0.360574 * X  +   0.814540 * Y  +  -0.454436 * Z  +  -6.854937 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.079688   -1.061905  [ DEG:   119.1573    -60.8426 ]
  Theta =  -0.368883   -2.772710  [ DEG:   -21.1354   -158.8646 ]
  Phi   =   1.295451   -1.846141  [ DEG:    74.2239   -105.7761 ]
 
# 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: T0335TS393_1                                  
REMARK     2: T0335.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS393_1.T0335.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   85   42   4.0   39   1.87  83.242     3.50
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS393_1
PFRMAT TS
TARGET T0335
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      -1.365 -19.005  -9.698  1.00 25.00           C
ATOM      2  CA  ILE     2      -3.855 -16.220 -10.223  1.00 25.00           C
ATOM      3  CA  SER     3      -1.643 -13.616 -11.812  1.00 25.00           C
ATOM      4  CA  ASN     4      -0.804 -10.370 -10.051  1.00 25.00           C
ATOM      5  CA  ALA     5       0.510 -10.849  -6.486  1.00 25.00           C
ATOM      6  CA  LYS     6       1.872  -7.269  -6.481  1.00 25.00           C
ATOM      7  CA  ILE     7      -1.511  -5.954  -7.698  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.296  -7.909  -4.930  1.00 25.00           C
ATOM      9  CA  ARG     9      -0.889  -6.466  -2.325  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.538  -2.931  -3.648  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.316  -3.522  -3.445  1.00 25.00           C
ATOM     12  CA  GLU    12      -4.951  -4.772   0.157  1.00 25.00           C
ATOM     13  CA  LEU    13      -2.897  -1.666   1.052  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.572   0.584  -0.512  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.295  -1.223   1.486  1.00 25.00           C
ATOM     16  CA  LYS    16      -6.271  -0.766   4.705  1.00 25.00           C
ATOM     17  CA  ALA    17      -5.848   2.963   3.939  1.00 25.00           C
ATOM     18  CA  LYS    18      -9.615   3.292   3.335  1.00 25.00           C
ATOM     19  CA  ALA    19     -10.327   1.529   6.660  1.00 25.00           C
ATOM     20  CA  GLY    20     -11.404   2.394  10.174  1.00 25.00           C
ATOM     21  CA  VAL    21      -8.602   4.278  12.000  1.00 25.00           C
ATOM     22  CA  ILE    22      -5.103   4.121  10.379  1.00 25.00           C
ATOM     23  CA  THR    23      -1.800   4.694  12.259  1.00 25.00           C
ATOM     24  CA  GLU    24       1.494   6.273  11.100  1.00 25.00           C
ATOM     25  CA  GLU    25       3.375   2.988  10.520  1.00 25.00           C
ATOM     26  CA  GLU    26       0.447   1.650   8.443  1.00 25.00           C
ATOM     27  CA  LYS    27       0.419   4.868   6.366  1.00 25.00           C
ATOM     28  CA  ALA    28       4.191   4.554   5.785  1.00 25.00           C
ATOM     29  CA  GLU    29       3.745   0.913   4.686  1.00 25.00           C
ATOM     30  CA  GLN    30       0.963   1.958   2.270  1.00 25.00           C
ATOM     31  CA  GLN    31       3.212   4.704   0.830  1.00 25.00           C
ATOM     32  CA  LYS    32       6.048   2.172   0.367  1.00 25.00           C
ATOM     33  CA  LEU    33       3.651  -0.228  -1.411  1.00 25.00           C
ATOM     34  CA  ARG    34       2.482   2.605  -3.710  1.00 25.00           C
ATOM     35  CA  GLN    35       6.121   3.488  -4.512  1.00 25.00           C
ATOM     36  CA  GLU    36       6.862  -0.183  -5.313  1.00 25.00           C
ATOM     37  CA  TYR    37       3.801  -0.324  -7.611  1.00 25.00           C
ATOM     38  CA  LEU    38       4.960   2.863  -9.390  1.00 25.00           C
ATOM     39  CA  LYS    39       8.453   1.364  -9.853  1.00 25.00           C
ATOM     40  CA  GLY    40       6.917  -1.836 -11.291  1.00 25.00           C
ATOM     41  CA  PHE    41       4.793   0.242 -13.707  1.00 25.00           C
ATOM     42  CA  ARG    42       7.902   2.187 -14.808  1.00 25.00           C
ATOM     43  CA  SER    43       9.782  -1.099 -15.388  1.00 25.00           C
ATOM     44  CA  SER    44       6.856  -2.436 -17.465  1.00 25.00           C
ATOM     45  CA  MET    45       6.828   0.782 -19.542  1.00 25.00           C
ATOM     46  CA  LYS    46      10.600   0.469 -20.123  1.00 25.00           C
ATOM     47  CA  ASN    47      10.154  -3.172 -21.223  1.00 25.00           C
ATOM     48  CA  THR    48       7.372  -2.128 -23.639  1.00 25.00           C
ATOM     49  CA  LEU    49       9.620   0.617 -25.079  1.00 25.00           C
ATOM     50  CA  LYS    50       7.696   3.872 -24.954  1.00 25.00           C
ATOM     51  CA  SER    51       4.182   2.944 -23.809  1.00 25.00           C
ATOM     52  CA  VAL    52       1.329   3.372 -21.293  1.00 25.00           C
ATOM     53  CA  LYS    53      -1.558   0.922 -21.596  1.00 25.00           C
ATOM     54  CA  ILE    54      -3.333   1.819 -18.311  1.00 25.00           C
ATOM     55  CA  ILE    55      -6.122   2.831 -15.907  1.00 25.00           C
ATOM     56  CA  ASP    56      -5.042   5.890 -13.927  1.00 25.00           C
ATOM     57  CA  PRO    57      -7.881   8.264 -14.580  1.00 25.00           C
ATOM     58  CA  GLU    58      -8.750  11.760 -15.678  1.00 25.00           C
ATOM     59  CA  GLY    59      -6.748  12.710 -18.772  1.00 25.00           C
ATOM     60  CA  ASN    60      -4.066  13.642 -16.240  1.00 25.00           C
ATOM     61  CA  ASP    61      -2.305  11.637 -13.597  1.00 25.00           C
ATOM     62  CA  VAL    62      -0.339   8.707 -15.130  1.00 25.00           C
ATOM     63  CA  THR    63       2.451  11.326 -15.299  1.00 25.00           C
ATOM     64  CA  PRO    64       5.740   9.626 -16.344  1.00 25.00           C
ATOM     65  CA  GLU    65       7.613  12.608 -14.839  1.00 25.00           C
ATOM     66  CA  LYS    66       7.935  10.754 -11.503  1.00 25.00           C
ATOM     67  CA  LEU    67       9.285   7.666 -13.321  1.00 25.00           C
ATOM     68  CA  LYS    68      11.829   9.842 -15.181  1.00 25.00           C
ATOM     69  CA  ARG    69      12.931  11.424 -11.871  1.00 25.00           C
ATOM     70  CA  GLU    70      13.338   7.947 -10.317  1.00 25.00           C
ATOM     71  CA  GLN    71      15.430   6.823 -13.321  1.00 25.00           C
ATOM     72  CA  ARG    72      17.630   9.939 -12.987  1.00 25.00           C
ATOM     73  CA  ASN    73      18.109   9.232  -9.254  1.00 25.00           C
ATOM     74  CA  ASN    74      19.077   5.610 -10.038  1.00 25.00           C
ATOM     75  CA  LYS    75      22.768   5.942  -9.318  1.00 25.00           C
ATOM     76  CA  LEU    76      23.167   2.220 -10.260  1.00 25.00           C
ATOM     77  CA  HIS    77      22.532  -0.413  -7.544  1.00 25.00           C
ATOM     78  CA  LEU    78      24.261  -2.376  -4.861  1.00 25.00           C
ATOM     79  CA  GLU    79      22.213  -5.625  -5.057  1.00 25.00           C
ATOM     80  CA  HIS    80      19.108  -5.978  -2.891  1.00 25.00           C
ATOM     81  CA  HIS    81      17.155  -3.961  -0.324  1.00 25.00           C
ATOM     82  CA  HIS    82      17.684  -1.829   2.710  1.00 25.00           C
ATOM     83  CA  HIS    83      17.393  -4.351   5.518  1.00 25.00           C
ATOM     84  CA  HIS    84      14.399  -5.159   7.768  1.00 25.00           C
ATOM     85  CA  HIS    85      15.686  -8.657   8.756  1.00 25.00           C
TER
END
