
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0363AL243_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   27 , name T0363_D1.pdb
# PARAMETERS: T0363AL243_1-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:    27        28 - 56          4.09     4.09
  LCS_AVERAGE:     58.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        28 - 49          1.97     4.32
  LCS_AVERAGE:     38.24

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        28 - 43          0.97     4.79
  LONGEST_CONTINUOUS_SEGMENT:    16        29 - 44          1.00     4.88
  LCS_AVERAGE:     27.05

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     K      28     K      28     16   20   27     4    9   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     S      29     S      29     16   20   27     6   11   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     F      30     F      30     16   20   27     4   11   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     Q      31     Q      31     16   20   27     4   10   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     V      32     V      32     16   20   27     4    9   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     D      33     D      33     16   20   27     5   11   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     E      34     E      34     16   20   27     3    8   16   17   19   19   21   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     G      35     G      35     16   20   27     5   11   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     I      36     I      36     16   20   27     6   11   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     T      37     T      37     16   20   27     7   11   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     V      38     V      38     16   20   27     7   11   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     Q      39     Q      39     16   20   27     7   11   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     T      40     T      40     16   20   27     7   11   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     A      41     A      41     16   20   27     7   11   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     I      42     I      42     16   20   27     7   11   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     T      43     T      43     16   20   27     7   10   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     Q      44     Q      44     16   20   27     7   10   16   17   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     I      47     I      47      8   20   27     6    8    9   10   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     L      48     L      48      8   20   27     6    8    9   13   19   19   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     S      49     S      49      8   20   27     6    8    9   10   14   17   19   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     Q      50     Q      50      8   15   27     6    8    9   10   14   17   19   23   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     F      51     F      51      8   15   27     6    8    9   10   14   17   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     P      52     P      52      8   15   27     6    8    9   10   14   17   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     E      53     E      53      8   15   27     6    8    9   10   14   17   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     I      54     I      54      8   15   27     5    8    9   11   14   18   22   24   25   25   25   25   25   25   25   25   25   25   27   27 
LCS_GDT     D      55     D      55      0    0   27     0    0    0    0    0    0    0    0    0    0   18   19   20   20   20   22   22   25   27   27 
LCS_GDT     L      56     L      56      0    0   27     0    0    0    0    1    1    1    1    1    1    3    7   10   10   14   21   22   25   27   27 
LCS_AVERAGE  LCS_A:  41.33  (  27.05   38.24   58.70 )

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      7     11     16     17     19     19     22     24     25     25     25     25     25     25     25     25     25     25     27     27 
GDT PERCENT_CA  15.22  23.91  34.78  36.96  41.30  41.30  47.83  52.17  54.35  54.35  54.35  54.35  54.35  54.35  54.35  54.35  54.35  54.35  58.70  58.70
GDT RMS_LOCAL    0.33   0.74   0.97   1.02   1.51   1.51   2.34   2.52   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   4.09   4.09
GDT RMS_ALL_CA   6.07   4.88   4.79   4.80   4.47   4.47   4.34   4.32   4.34   4.34   4.34   4.34   4.34   4.34   4.34   4.34   4.34   4.34   4.09   4.09

#      Molecule1      Molecule2       DISTANCE
LGA    K      28      K      28          2.295
LGA    S      29      S      29          1.749
LGA    F      30      F      30          3.164
LGA    Q      31      Q      31          3.276
LGA    V      32      V      32          2.913
LGA    D      33      D      33          3.320
LGA    E      34      E      34          3.504
LGA    G      35      G      35          1.985
LGA    I      36      I      36          0.993
LGA    T      37      T      37          0.599
LGA    V      38      V      38          0.857
LGA    Q      39      Q      39          1.235
LGA    T      40      T      40          0.841
LGA    A      41      A      41          2.176
LGA    I      42      I      42          2.649
LGA    T      43      T      43          1.339
LGA    Q      44      Q      44          3.266
LGA    I      47      I      47          3.022
LGA    L      48      L      48          1.485
LGA    S      49      S      49          3.990
LGA    Q      50      Q      50          4.574
LGA    F      51      F      51          3.308
LGA    P      52      P      52          3.109
LGA    E      53      E      53          3.314
LGA    I      54      I      54          2.047
LGA    D      55      D      55         13.460
LGA    L      56      L      56         11.701

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   46    4.0     24    2.52    41.848    43.114     0.917

LGA_LOCAL      RMSD =  2.518  Number of atoms =   24  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.283  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  4.089  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.448609 * X  +  -0.824559 * Y  +  -0.344750 * Z  +  50.949757
  Y_new =   0.884583 * X  +   0.354613 * Y  +   0.302922 * Z  + -26.561424
  Z_new =  -0.127525 * X  +  -0.440853 * Y  +   0.888474 * Z  +  31.077169 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.460596    2.680996  [ DEG:   -26.3902    153.6098 ]
  Theta =   0.127873    3.013720  [ DEG:     7.3266    172.6734 ]
  Phi   =   1.101452   -2.040140  [ DEG:    63.1086   -116.8914 ]
 
# 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: T0363AL243_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL243_1-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   46   4.0   24   2.52  43.114     4.09
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL243_1-D1
REMARK Aligment from pdb entry: 1vjkA
ATOM      1  N   LYS    28      23.329  17.753  -0.497  1.00  0.00              
ATOM      2  CA  LYS    28      23.428  16.381  -0.950  1.00  0.00              
ATOM      3  C   LYS    28      22.798  15.449   0.046  1.00  0.00              
ATOM      4  O   LYS    28      22.849  15.701   1.257  1.00  0.00              
ATOM      5  N   SER    29      22.182  14.396  -0.449  1.00  0.00              
ATOM      6  CA  SER    29      21.636  13.349   0.379  1.00  0.00              
ATOM      7  C   SER    29      22.685  12.312   0.636  1.00  0.00              
ATOM      8  O   SER    29      23.313  11.802  -0.317  1.00  0.00              
ATOM      9  N   PHE    30      22.868  11.939   1.891  1.00  0.00              
ATOM     10  CA  PHE    30      23.854  10.949   2.248  1.00  0.00              
ATOM     11  C   PHE    30      23.192   9.800   2.991  1.00  0.00              
ATOM     12  O   PHE    30      22.610   9.978   4.080  1.00  0.00              
ATOM     13  N   GLN    31      23.249   8.622   2.392  1.00  0.00              
ATOM     14  CA  GLN    31      22.742   7.400   3.004  1.00  0.00              
ATOM     15  C   GLN    31      23.824   6.816   3.911  1.00  0.00              
ATOM     16  O   GLN    31      24.973   6.643   3.495  1.00  0.00              
ATOM     17  N   VAL    32      23.446   6.537   5.156  1.00  0.00              
ATOM     18  CA  VAL    32      24.355   6.057   6.173  1.00  0.00              
ATOM     19  C   VAL    32      23.817   4.761   6.749  1.00  0.00              
ATOM     20  O   VAL    32      22.615   4.543   6.729  1.00  0.00              
ATOM     21  N   ASP    33      24.687   3.882   7.257  1.00  0.00              
ATOM     22  CA  ASP    33      24.223   2.642   7.874  1.00  0.00              
ATOM     23  C   ASP    33      23.443   2.894   9.154  1.00  0.00              
ATOM     24  O   ASP    33      23.619   3.918   9.825  1.00  0.00              
ATOM     25  N   GLU    34      22.579   1.943   9.479  1.00  0.00              
ATOM     26  CA  GLU    34      21.873   1.915  10.741  1.00  0.00              
ATOM     27  C   GLU    34      22.820   2.252  11.898  1.00  0.00              
ATOM     28  O   GLU    34      23.937   1.748  11.958  1.00  0.00              
ATOM     29  N   GLY    35      22.356   3.122  12.793  1.00  0.00              
ATOM     30  CA  GLY    35      23.113   3.484  13.985  1.00  0.00              
ATOM     31  C   GLY    35      24.085   4.630  13.766  1.00  0.00              
ATOM     32  O   GLY    35      24.829   5.015  14.683  1.00  0.00              
ATOM     33  N   ILE    36      24.097   5.187  12.563  1.00  0.00              
ATOM     34  CA  ILE    36      25.042   6.249  12.267  1.00  0.00              
ATOM     35  C   ILE    36      24.911   7.410  13.206  1.00  0.00              
ATOM     36  O   ILE    36      23.800   7.821  13.581  1.00  0.00              
ATOM     37  N   THR    37      26.074   7.959  13.549  1.00  0.00              
ATOM     38  CA  THR    37      26.185   9.116  14.416  1.00  0.00              
ATOM     39  C   THR    37      26.731  10.314  13.643  1.00  0.00              
ATOM     40  O   THR    37      27.289  10.177  12.542  1.00  0.00              
ATOM     41  N   VAL    38      26.630  11.505  14.222  1.00  0.00              
ATOM     42  CA  VAL    38      27.212  12.699  13.610  1.00  0.00              
ATOM     43  C   VAL    38      28.679  12.478  13.192  1.00  0.00              
ATOM     44  O   VAL    38      29.085  12.841  12.065  1.00  0.00              
ATOM     45  N   GLN    39      29.484  11.852  14.062  1.00  0.00              
ATOM     46  CA  GLN    39      30.885  11.633  13.697  1.00  0.00              
ATOM     47  C   GLN    39      31.037  10.764  12.421  1.00  0.00              
ATOM     48  O   GLN    39      31.985  10.958  11.642  1.00  0.00              
ATOM     49  N   THR    40      30.114   9.817  12.217  1.00  0.00              
ATOM     50  CA  THR    40      30.177   8.953  11.016  1.00  0.00              
ATOM     51  C   THR    40      29.841   9.756   9.796  1.00  0.00              
ATOM     52  O   THR    40      30.456   9.560   8.740  1.00  0.00              
ATOM     53  N   ALA    41      28.892  10.669   9.923  1.00  0.00              
ATOM     54  CA  ALA    41      28.559  11.551   8.804  1.00  0.00              
ATOM     55  C   ALA    41      29.739  12.455   8.430  1.00  0.00              
ATOM     56  O   ALA    41      30.045  12.606   7.233  1.00  0.00              
ATOM     57  N   ILE    42      30.430  13.004   9.429  1.00  0.00              
ATOM     58  CA  ILE    42      31.602  13.827   9.158  1.00  0.00              
ATOM     59  C   ILE    42      32.649  13.013   8.402  1.00  0.00              
ATOM     60  O   ILE    42      33.244  13.502   7.407  1.00  0.00              
ATOM     61  N   THR    43      32.894  11.763   8.833  1.00  0.00              
ATOM     62  CA  THR    43      33.842  10.930   8.083  1.00  0.00              
ATOM     63  C   THR    43      33.419  10.660   6.658  1.00  0.00              
ATOM     64  O   THR    43      34.282  10.608   5.754  1.00  0.00              
ATOM     65  N   GLN    44      32.125  10.493   6.431  1.00  0.00              
ATOM     66  CA  GLN    44      31.638  10.258   5.084  1.00  0.00              
ATOM     67  C   GLN    44      31.771  11.513   4.221  1.00  0.00              
ATOM     68  O   GLN    44      32.104  11.392   3.036  1.00  0.00              
ATOM     69  N   ILE    47      31.538  12.712   4.787  1.00  0.00              
ATOM     70  CA  ILE    47      31.741  13.950   4.024  1.00  0.00              
ATOM     71  C   ILE    47      33.196  14.041   3.560  1.00  0.00              
ATOM     72  O   ILE    47      33.461  14.346   2.378  1.00  0.00              
ATOM     73  N   LEU    48      34.117  13.731   4.468  1.00  0.00              
ATOM     74  CA  LEU    48      35.549  13.743   4.147  1.00  0.00              
ATOM     75  C   LEU    48      35.920  12.699   3.084  1.00  0.00              
ATOM     76  O   LEU    48      36.809  12.956   2.238  1.00  0.00              
ATOM     77  N   SER    49      35.254  11.549   3.110  1.00  0.00              
ATOM     78  CA  SER    49      35.498  10.502   2.133  1.00  0.00              
ATOM     79  C   SER    49      34.997  10.913   0.752  1.00  0.00              
ATOM     80  O   SER    49      35.641  10.610  -0.264  1.00  0.00              
ATOM     81  N   GLN    50      33.847  11.580   0.686  1.00  0.00              
ATOM     82  CA  GLN    50      33.287  11.988  -0.591  1.00  0.00              
ATOM     83  C   GLN    50      34.009  13.190  -1.183  1.00  0.00              
ATOM     84  O   GLN    50      34.066  13.366  -2.398  1.00  0.00              
ATOM     85  N   PHE    51      34.482  14.058  -0.301  1.00  0.00              
ATOM     86  CA  PHE    51      35.022  15.350  -0.704  1.00  0.00              
ATOM     87  C   PHE    51      36.324  15.579   0.018  1.00  0.00              
ATOM     88  O   PHE    51      36.349  16.165   1.129  1.00  0.00              
ATOM     89  N   PRO    52      37.414  15.147  -0.615  1.00  0.00              
ATOM     90  CA  PRO    52      38.713  15.094   0.060  1.00  0.00              
ATOM     91  C   PRO    52      39.204  16.441   0.573  1.00  0.00              
ATOM     92  O   PRO    52      40.005  16.473   1.503  1.00  0.00              
ATOM     93  N   GLU    53      38.721  17.539  -0.003  1.00  0.00              
ATOM     94  CA  GLU    53      39.152  18.872   0.478  1.00  0.00              
ATOM     95  C   GLU    53      38.701  19.130   1.915  1.00  0.00              
ATOM     96  O   GLU    53      39.266  19.999   2.596  1.00  0.00              
ATOM     97  N   ILE    54      37.712  18.369   2.412  1.00  0.00              
ATOM     98  CA  ILE    54      37.295  18.507   3.807  1.00  0.00              
ATOM     99  C   ILE    54      38.219  17.805   4.801  1.00  0.00              
ATOM    100  O   ILE    54      38.100  18.016   6.016  1.00  0.00              
ATOM    101  N   ASP    55      34.032  28.288  17.801  1.00  0.00              
ATOM    102  CA  ASP    55      34.472  29.367  16.908  1.00  0.00              
ATOM    103  C   ASP    55      35.885  29.152  16.375  1.00  0.00              
ATOM    104  O   ASP    55      36.279  29.779  15.382  1.00  0.00              
ATOM    105  N   LEU    56      36.640  28.254  17.006  1.00  0.00              
ATOM    106  CA  LEU    56      38.036  28.023  16.601  1.00  0.00              
ATOM    107  C   LEU    56      38.178  26.972  15.491  1.00  0.00              
ATOM    108  O   LEU    56      39.231  26.862  14.859  1.00  0.00              
END
