
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0363AL316_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   35 , name T0363_D1.pdb
# PARAMETERS: T0363AL316_3-D1.T0363_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:    28        18 - 56          4.90     7.05
  LCS_AVERAGE:     53.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        29 - 45          1.72     6.82
  LONGEST_CONTINUOUS_SEGMENT:    17        30 - 46          1.96     6.97
  LCS_AVERAGE:     25.22

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        34 - 44          0.76     6.85
  LCS_AVERAGE:     14.29

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:   46
LCS_GDT     N      11     N      11      5    8   11     3    4    6    7    7    8    8    9   12   16   20   24   27   28   29   30   31   31   32   32 
LCS_GDT     Q      12     Q      12      5    8   11     4    5    6    7    7    8    8    9   12   16   20   24   27   28   29   30   31   31   32   32 
LCS_GDT     I      13     I      13      5    8   11     4    5    6    7    7    8    8    9    9   16   19   21   22   25   29   29   31   31   32   32 
LCS_GDT     N      14     N      14      5    8   11     4    5    6    7    7    8    8    9   12   16   19   21   27   28   29   30   31   31   32   32 
LCS_GDT     I      15     I      15      5    8   11     4    5    6    7    7    8    9   10   12   16   19   21   22   28   29   30   31   31   32   32 
LCS_GDT     E      16     E      16      5    8   11     4    5    6    7    7   10   10   11   12   16   19   24   27   28   29   30   31   31   32   32 
LCS_GDT     I      17     I      17      5    8   11     3    4    5    7    7    8    8    9   10   13   19   24   27   28   29   30   31   31   32   32 
LCS_GDT     A      18     A      18      4    8   28     3    4    5    5    6    8    8   13   18   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     Y      19     Y      19      3    5   28     3    3    4    4    4    5   17   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     A      20     A      20      3    5   28     3    3    9   13   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     F      21     F      21      3    5   28     3    3    4   11   13   17   19   19   20   20   22   22   24   25   25   26   28   30   32   32 
LCS_GDT     P      22     P      22      3    5   28     3    3    4    4    4    5    6    6   11   13   21   22   22   25   25   26   27   27   28   30 
LCS_GDT     E      23     E      23      3    4   28     3    3    3    4    4    5    6    6    8    9    9    9   15   19   24   25   27   27   27   28 
LCS_GDT     R      24     R      24      3    3   28     0    3    3    4    4    4    6    6    8    9    9   12   15   23   25   26   27   27   27   28 
LCS_GDT     S      29     S      29      5   17   28     4    5    5   10   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     F      30     F      30      5   17   28     4    5   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     Q      31     Q      31      5   17   28     4    9   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     V      32     V      32      6   17   28     4    5   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     D      33     D      33      8   17   28     4    9   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     E      34     E      34     11   17   28     6   10   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     G      35     G      35     11   17   28     3   10   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     I      36     I      36     11   17   28     6   10   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     T      37     T      37     11   17   28     6   10   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     V      38     V      38     11   17   28     6   10   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     Q      39     Q      39     11   17   28     6   10   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     T      40     T      40     11   17   28     6   10   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     A      41     A      41     11   17   28     6   10   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     I      42     I      42     11   17   28     6   10   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     T      43     T      43     11   17   28     4   10   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     Q      44     Q      44     11   17   28     6    9   13   15   17   18   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     S      45     S      45      9   17   28     3    4    8    9   11   16   19   19   20   21   22   24   27   28   29   30   31   31   32   32 
LCS_GDT     G      46     G      46      5   17   28     3    4    6    9    9   10   15   19   20   21   22   22   27   28   29   30   31   31   32   32 
LCS_GDT     I      54     I      54      3    3   28     0    3    3    3    3    3    4    5   11   13   16   22   24   25   28   30   31   31   32   32 
LCS_GDT     D      55     D      55      3    3   28     1    3    3    4    4    4    5    7   11   13   21   22   24   25   27   30   31   31   32   32 
LCS_GDT     L      56     L      56      3    3   28     1    5    8   12   16   18   19   19   20   21   22   22   27   28   29   30   31   31   32   32 
LCS_AVERAGE  LCS_A:  30.99  (  14.29   25.22   53.48 )

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      6     10     13     15     17     18     19     19     20     21     22     24     27     28     29     30     31     31     32     32 
GDT PERCENT_CA  13.04  21.74  28.26  32.61  36.96  39.13  41.30  41.30  43.48  45.65  47.83  52.17  58.70  60.87  63.04  65.22  67.39  67.39  69.57  69.57
GDT RMS_LOCAL    0.29   0.66   0.99   1.19   1.56   1.64   1.94   1.92   2.14   2.45   2.82   4.16   4.40   4.60   4.77   4.94   5.10   5.10   5.36   5.36
GDT RMS_ALL_CA   6.70   6.81   6.98   7.04   6.71   6.73   6.86   6.67   6.69   6.64   6.65   6.82   6.90   7.01   7.10   6.99   7.07   7.07   6.84   6.84

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          9.212
LGA    Q      12      Q      12          9.658
LGA    I      13      I      13         11.155
LGA    N      14      N      14         10.763
LGA    I      15      I      15         11.332
LGA    E      16      E      16         10.283
LGA    I      17      I      17         10.106
LGA    A      18      A      18          7.388
LGA    Y      19      Y      19          4.473
LGA    A      20      A      20          2.452
LGA    F      21      F      21          6.104
LGA    P      22      P      22         10.223
LGA    E      23      E      23         13.317
LGA    R      24      R      24         12.912
LGA    S      29      S      29          2.469
LGA    F      30      F      30          1.660
LGA    Q      31      Q      31          1.464
LGA    V      32      V      32          2.631
LGA    D      33      D      33          1.642
LGA    E      34      E      34          2.087
LGA    G      35      G      35          2.551
LGA    I      36      I      36          1.756
LGA    T      37      T      37          1.061
LGA    V      38      V      38          1.093
LGA    Q      39      Q      39          0.982
LGA    T      40      T      40          0.600
LGA    A      41      A      41          0.532
LGA    I      42      I      42          0.986
LGA    T      43      T      43          1.430
LGA    Q      44      Q      44          0.898
LGA    S      45      S      45          3.953
LGA    G      46      G      46          5.827
LGA    I      54      I      54          7.775
LGA    D      55      D      55          8.094
LGA    L      56      L      56          3.150

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   35   46    4.0     19    1.92    40.217    37.311     0.941

LGA_LOCAL      RMSD =  1.919  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.652  Number of atoms =   35 
Std_ALL_ATOMS  RMSD =  6.545  (standard rmsd on all 35 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.649552 * X  +   0.040013 * Y  +  -0.759264 * Z  +  22.629400
  Y_new =   0.742644 * X  +   0.247450 * Y  +  -0.622293 * Z  +   5.075387
  Z_new =   0.162980 * X  +  -0.968074 * Y  +  -0.190447 * Z  +   3.751243 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.765043    1.376549  [ DEG:  -101.1295     78.8705 ]
  Theta =  -0.163711   -2.977882  [ DEG:    -9.3799   -170.6201 ]
  Phi   =   2.289427   -0.852166  [ DEG:   131.1745    -48.8255 ]
 
# 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: T0363AL316_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL316_3-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   35   46   4.0   19   1.92  37.311     6.54
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL316_3-D1
REMARK Aligment from pdb entry: 1rws_A
ATOM      1  N   ASN    11      22.490   3.073   6.327  1.00  0.00              
ATOM      2  CA  ASN    11      22.700   4.545   6.425  1.00  0.00              
ATOM      3  C   ASN    11      23.889   4.958   5.568  1.00  0.00              
ATOM      4  O   ASN    11      25.011   4.530   5.753  1.00  0.00              
ATOM      5  N   GLN    12      23.606   5.784   4.610  1.00  0.00              
ATOM      6  CA  GLN    12      24.653   6.262   3.672  1.00  0.00              
ATOM      7  C   GLN    12      24.846   7.764   3.876  1.00  0.00              
ATOM      8  O   GLN    12      24.027   8.440   4.465  1.00  0.00              
ATOM      9  N   ILE    13      25.984   8.254   3.485  1.00  0.00              
ATOM     10  CA  ILE    13      26.321   9.681   3.749  1.00  0.00              
ATOM     11  C   ILE    13      26.419  10.472   2.443  1.00  0.00              
ATOM     12  O   ILE    13      26.522   9.928   1.361  1.00  0.00              
ATOM     13  N   ASN    14      26.405  11.775   2.571  1.00  0.00              
ATOM     14  CA  ASN    14      26.513  12.706   1.409  1.00  0.00              
ATOM     15  C   ASN    14      27.457  13.804   1.846  1.00  0.00              
ATOM     16  O   ASN    14      27.538  14.144   3.004  1.00  0.00              
ATOM     17  N   ILE    15      28.270  14.245   0.941  1.00  0.00              
ATOM     18  CA  ILE    15      29.341  15.222   1.292  1.00  0.00              
ATOM     19  C   ILE    15      29.343  16.403   0.313  1.00  0.00              
ATOM     20  O   ILE    15      29.252  16.229  -0.885  1.00  0.00              
ATOM     21  N   GLU    16      29.492  17.605   0.817  1.00  0.00              
ATOM     22  CA  GLU    16      29.554  18.803  -0.072  1.00  0.00              
ATOM     23  C   GLU    16      30.564  19.801   0.495  1.00  0.00              
ATOM     24  O   GLU    16      30.926  19.741   1.650  1.00  0.00              
ATOM     25  N   ILE    17      31.121  20.649  -0.332  1.00  0.00              
ATOM     26  CA  ILE    17      32.167  21.603   0.125  1.00  0.00              
ATOM     27  C   ILE    17      31.532  22.883   0.609  1.00  0.00              
ATOM     28  O   ILE    17      30.460  23.232   0.158  1.00  0.00              
ATOM     29  N   ALA    18      31.948  23.264   1.787  1.00  0.00              
ATOM     30  CA  ALA    18      31.021  24.177   2.543  1.00  0.00              
ATOM     31  C   ALA    18      30.075  24.819   1.516  1.00  0.00              
ATOM     32  O   ALA    18      30.544  25.381   0.546  1.00  0.00              
ATOM     33  N   TYR    19      28.773  24.864   1.735  1.00  0.00              
ATOM     34  CA  TYR    19      27.934  25.603   0.748  1.00  0.00              
ATOM     35  C   TYR    19      28.478  25.380  -0.662  1.00  0.00              
ATOM     36  O   TYR    19      28.708  26.308  -1.414  1.00  0.00              
ATOM     37  N   ALA    20      28.651  24.146  -1.028  1.00  0.00              
ATOM     38  CA  ALA    20      29.142  23.814  -2.397  1.00  0.00              
ATOM     39  C   ALA    20      27.992  23.325  -3.275  1.00  0.00              
ATOM     40  O   ALA    20      28.102  23.298  -4.485  1.00  0.00              
ATOM     41  N   PHE    21      26.863  23.006  -2.698  1.00  0.00              
ATOM     42  CA  PHE    21      25.667  22.602  -3.474  1.00  0.00              
ATOM     43  C   PHE    21      25.645  21.102  -3.735  1.00  0.00              
ATOM     44  O   PHE    21      25.606  20.684  -4.875  1.00  0.00              
ATOM     45  N   PRO    22      25.760  20.285  -2.731  1.00  0.00              
ATOM     46  CA  PRO    22      25.843  18.829  -3.046  1.00  0.00              
ATOM     47  C   PRO    22      24.781  18.002  -2.328  1.00  0.00              
ATOM     48  O   PRO    22      24.961  17.463  -1.254  1.00  0.00              
ATOM     49  N   GLU    23      23.693  17.869  -3.024  1.00  0.00              
ATOM     50  CA  GLU    23      22.493  17.061  -2.634  1.00  0.00              
ATOM     51  C   GLU    23      22.560  15.653  -3.211  1.00  0.00              
ATOM     52  O   GLU    23      22.823  15.461  -4.382  1.00  0.00              
ATOM     53  N   ARG    24      22.245  14.668  -2.410  1.00  0.00              
ATOM     54  CA  ARG    24      22.200  13.272  -2.910  1.00  0.00              
ATOM     55  C   ARG    24      21.375  12.482  -1.890  1.00  0.00              
ATOM     56  O   ARG    24      21.895  12.187  -0.834  1.00  0.00              
ATOM     57  N   SER    29      20.086  12.327  -2.037  1.00  0.00              
ATOM     58  CA  SER    29      19.320  11.745  -0.884  1.00  0.00              
ATOM     59  C   SER    29      20.146  10.637  -0.223  1.00  0.00              
ATOM     60  O   SER    29      21.216  10.296  -0.684  1.00  0.00              
ATOM     61  N   PHE    30      19.747  10.172   0.946  1.00  0.00              
ATOM     62  CA  PHE    30      20.709   9.284   1.699  1.00  0.00              
ATOM     63  C   PHE    30      19.985   8.431   2.766  1.00  0.00              
ATOM     64  O   PHE    30      19.375   9.025   3.632  1.00  0.00              
ATOM     65  N   GLN    31      19.901   7.113   2.762  1.00  0.00              
ATOM     66  CA  GLN    31      19.073   6.389   3.786  1.00  0.00              
ATOM     67  C   GLN    31      19.526   6.797   5.197  1.00  0.00              
ATOM     68  O   GLN    31      19.774   7.953   5.478  1.00  0.00              
ATOM     69  N   VAL    32      19.633   5.846   6.085  1.00  0.00              
ATOM     70  CA  VAL    32      20.062   6.116   7.492  1.00  0.00              
ATOM     71  C   VAL    32      20.058   4.748   8.188  1.00  0.00              
ATOM     72  O   VAL    32      20.124   3.752   7.494  1.00  0.00              
ATOM     73  N   ASP    33      20.207   4.610   9.488  1.00  0.00              
ATOM     74  CA  ASP    33      20.493   3.211   9.944  1.00  0.00              
ATOM     75  C   ASP    33      20.225   2.926  11.442  1.00  0.00              
ATOM     76  O   ASP    33      19.086   3.023  11.856  1.00  0.00              
ATOM     77  N   GLU    34      21.171   2.510  12.278  1.00  0.00              
ATOM     78  CA  GLU    34      20.771   2.172  13.686  1.00  0.00              
ATOM     79  C   GLU    34      22.014   1.777  14.505  1.00  0.00              
ATOM     80  O   GLU    34      22.661   0.786  14.231  1.00  0.00              
ATOM     81  N   GLY    35      22.377   2.582  15.478  1.00  0.00              
ATOM     82  CA  GLY    35      23.610   2.289  16.277  1.00  0.00              
ATOM     83  C   GLY    35      24.738   3.257  15.879  1.00  0.00              
ATOM     84  O   GLY    35      25.644   3.542  16.638  1.00  0.00              
ATOM     85  N   ILE    36      24.677   3.724  14.668  1.00  0.00              
ATOM     86  CA  ILE    36      25.746   4.659  14.149  1.00  0.00              
ATOM     87  C   ILE    36      25.398   6.021  14.743  1.00  0.00              
ATOM     88  O   ILE    36      24.904   6.173  15.843  1.00  0.00              
ATOM     89  N   THR    37      26.143   6.881  14.188  1.00  0.00              
ATOM     90  CA  THR    37      26.474   8.225  14.712  1.00  0.00              
ATOM     91  C   THR    37      26.635   9.232  13.554  1.00  0.00              
ATOM     92  O   THR    37      27.126   8.859  12.508  1.00  0.00              
ATOM     93  N   VAL    38      26.550  10.528  13.801  1.00  0.00              
ATOM     94  CA  VAL    38      27.097  11.518  12.816  1.00  0.00              
ATOM     95  C   VAL    38      28.499  11.116  12.371  1.00  0.00              
ATOM     96  O   VAL    38      28.785  11.025  11.193  1.00  0.00              
ATOM     97  N   GLN    39      29.415  11.062  13.298  1.00  0.00              
ATOM     98  CA  GLN    39      30.842  10.887  12.940  1.00  0.00              
ATOM     99  C   GLN    39      30.951   9.872  11.805  1.00  0.00              
ATOM    100  O   GLN    39      31.349  10.193  10.703  1.00  0.00              
ATOM    101  N   THR    40      30.547   8.655  12.056  1.00  0.00              
ATOM    102  CA  THR    40      30.590   7.650  10.933  1.00  0.00              
ATOM    103  C   THR    40      30.092   8.259   9.619  1.00  0.00              
ATOM    104  O   THR    40      30.834   8.298   8.658  1.00  0.00              
ATOM    105  N   ALA    41      28.845   8.622   9.489  1.00  0.00              
ATOM    106  CA  ALA    41      28.396   9.081   8.139  1.00  0.00              
ATOM    107  C   ALA    41      29.493   9.975   7.551  1.00  0.00              
ATOM    108  O   ALA    41      29.848   9.892   6.391  1.00  0.00              
ATOM    109  N   ILE    42      30.067  10.765   8.393  1.00  0.00              
ATOM    110  CA  ILE    42      31.210  11.641   7.991  1.00  0.00              
ATOM    111  C   ILE    42      32.424  10.757   7.683  1.00  0.00              
ATOM    112  O   ILE    42      33.108  10.941   6.696  1.00  0.00              
ATOM    113  N   THR    43      32.567   9.695   8.422  1.00  0.00              
ATOM    114  CA  THR    43      33.588   8.657   8.086  1.00  0.00              
ATOM    115  C   THR    43      33.372   8.140   6.662  1.00  0.00              
ATOM    116  O   THR    43      34.319   7.817   5.972  1.00  0.00              
ATOM    117  N   GLN    44      32.152   8.076   6.192  1.00  0.00              
ATOM    118  CA  GLN    44      31.964   7.592   4.774  1.00  0.00              
ATOM    119  C   GLN    44      32.659   8.599   3.856  1.00  0.00              
ATOM    120  O   GLN    44      33.030   8.316   2.735  1.00  0.00              
ATOM    121  N   SER    45      32.959   9.720   4.427  1.00  0.00              
ATOM    122  CA  SER    45      33.778  10.703   3.674  1.00  0.00              
ATOM    123  C   SER    45      35.245  10.392   3.971  1.00  0.00              
ATOM    124  O   SER    45      36.136  11.010   3.422  1.00  0.00              
ATOM    125  N   GLY    46      35.505   9.559   4.946  1.00  0.00              
ATOM    126  CA  GLY    46      36.911   9.369   5.386  1.00  0.00              
ATOM    127  C   GLY    46      37.240  10.624   6.181  1.00  0.00              
ATOM    128  O   GLY    46      38.330  11.159   6.122  1.00  0.00              
ATOM    129  N   ILE    54      36.217  11.190   6.775  1.00  0.00              
ATOM    130  CA  ILE    54      36.325  12.530   7.429  1.00  0.00              
ATOM    131  C   ILE    54      35.306  12.562   8.583  1.00  0.00              
ATOM    132  O   ILE    54      34.196  13.011   8.385  1.00  0.00              
ATOM    133  N   ASP    55      35.725  12.385   9.807  1.00  0.00              
ATOM    134  CA  ASP    55      34.852  12.822  10.944  1.00  0.00              
ATOM    135  C   ASP    55      34.632  14.336  10.832  1.00  0.00              
ATOM    136  O   ASP    55      34.943  15.097  11.727  1.00  0.00              
ATOM    137  N   LEU    56      34.310  14.769   9.644  1.00  0.00              
ATOM    138  CA  LEU    56      34.319  16.250   9.389  1.00  0.00              
ATOM    139  C   LEU    56      35.664  16.828   9.835  1.00  0.00              
ATOM    140  O   LEU    56      35.727  17.301  10.953  1.00  0.00              
END
