
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0360AL381_5
# Molecule2: number of CA atoms  116 (  917),  selected   33 , name T0360.pdb
# PARAMETERS: T0360AL381_5.T0360.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:    22        40 - 61          4.99     8.39
  LCS_AVERAGE:     18.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        44 - 57          1.70    11.06
  LONGEST_CONTINUOUS_SEGMENT:    14        45 - 58          1.88    11.30
  LCS_AVERAGE:      8.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        47 - 57          0.68    12.21
  LCS_AVERAGE:      5.77

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:  116
LCS_GDT     Y      35     Y      35      3    7   18     3    3    3    3    3    5    7    7    9   12   13   15   18   20   20   21   21   24   24   24 
LCS_GDT     D      36     D      36      6    7   20     4    6    6    6    6    6    7    7   10   12   13   15   18   20   20   23   23   24   24   24 
LCS_GDT     V      37     V      37      6    7   21     5    6    6    6    6    6    7    7    8    9   13   15   18   20   20   23   23   24   24   25 
LCS_GDT     F      38     F      38      6    7   21     5    6    6    6    6    6    7    7    8   10   13   15   18   20   20   23   23   24   24   24 
LCS_GDT     K      39     K      39      6    7   21     5    6    6    6    6    6    7    7    8    9   13   14   18   20   20   23   23   24   24   24 
LCS_GDT     R      40     R      40      6    7   22     5    6    6    6    7    8   10   13   16   17   18   19   20   20   21   23   25   25   28   28 
LCS_GDT     F      41     F      41      6    7   22     5    6    6    6    7    8   11   13   16   17   18   19   20   20   21   23   25   25   28   28 
LCS_GDT     K      42     K      42      3    4   22     3    4    4    6    7    8   10   13   16   17   18   19   20   20   21   23   25   25   28   28 
LCS_GDT     P      43     P      43      3    4   22     3    4    4    4    5    5   10   13   16   17   18   19   20   20   21   23   25   25   28   28 
LCS_GDT     L      44     L      44      3   14   22     3    6    8   12   12   13   14   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     A      45     A      45      5   14   22     3    4    6   10   13   13   15   16   16   16   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     L      46     L      46      5   14   22     3    6   11   12   13   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     G      47     G      47     11   14   22     3   10   10   12   13   13   15   16   16   16   17   19   21   21   21   23   24   25   28   28 
LCS_GDT     I      48     I      48     11   14   22     9   10   11   12   13   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     D      49     D      49     11   14   22     9   10   11   12   13   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     Q      50     Q      50     11   14   22     9   10   11   12   13   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     D      51     D      51     11   14   22     9   10   11   12   13   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     L      52     L      52     11   14   22     9   10   11   12   13   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     I      53     I      53     11   14   22     9   10   11   12   13   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     A      54     A      54     11   14   22     9   10   11   12   13   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     A      55     A      55     11   14   22     9   10   11   12   13   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     L      56     L      56     11   14   22     9   10   11   12   13   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     P      57     P      57     11   14   22     4    9   11   12   13   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     Q      58     Q      58      5   14   22     3    3    7    7    8   13   15   16   16   17   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     Y      59     Y      59      5   12   22     3    4    7    7   12   13   15   16   16   16   18   19   21   21   21   23   25   25   28   28 
LCS_GDT     D      60     D      60      5    9   22     4    4    7    7    8   10   10   12   15   16   17   19   21   21   21   23   25   25   28   28 
LCS_GDT     A      61     A      61      5    9   22     4    4    6    7    8    9   10   11   11   13   14   16   17   19   20   23   25   25   28   28 
LCS_GDT     A      62     A      62      5    9   21     4    4    7    7    8   10   10   11   12   14   15   16   17   19   20   23   24   24   28   28 
LCS_GDT     L      63     L      63      5    9   21     4    4    7    7    8   10   10   11   13   15   17   19   21   21   21   23   25   25   28   28 
LCS_GDT     I      64     I      64      3    9   21     2    3    4    7    8   10   10   11   13   15   17   19   21   21   21   23   25   25   28   28 
LCS_GDT     A      65     A      65      3    3   20     1    3    3    3    3    4    4    5   12   14   15   16   17   19   20   23   24   24   28   28 
LCS_GDT     R      66     R      66      3    3   20     0    3    3    3    3    3    7   11   13   15   17   19   21   21   21   23   25   25   28   28 
LCS_GDT     V      67     V      67      3    3   20     0    3    3    3    3    3    4   11   13   15   17   19   21   21   21   23   25   25   28   28 
LCS_AVERAGE  LCS_A:  10.99  (   5.77    8.70   18.50 )

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      9     10     11     12     13     13     15     16     16     17     18     19     21     21     21     23     25     25     28     28 
GDT PERCENT_CA   7.76   8.62   9.48  10.34  11.21  11.21  12.93  13.79  13.79  14.66  15.52  16.38  18.10  18.10  18.10  19.83  21.55  21.55  24.14  24.14
GDT RMS_LOCAL    0.23   0.41   0.89   1.21   1.38   1.34   2.06   2.25   2.25   3.35   3.52   3.71   4.45   4.45   4.45   5.18   5.87   5.72   6.36   6.36
GDT RMS_ALL_CA  12.30  12.40  11.45  10.73  11.91  11.04  11.16  10.40  10.40   8.87   8.79   8.86  10.09  10.09  10.09  10.27   8.22   8.24   8.35   8.35

#      Molecule1      Molecule2       DISTANCE
LGA    Y      35      Y      35         20.152
LGA    D      36      D      36         19.273
LGA    V      37      V      37         13.734
LGA    F      38      F      38         17.592
LGA    K      39      K      39         20.406
LGA    R      40      R      40         14.915
LGA    F      41      F      41         11.610
LGA    K      42      K      42         11.476
LGA    P      43      P      43          9.207
LGA    L      44      L      44          3.457
LGA    A      45      A      45          2.992
LGA    L      46      L      46          0.993
LGA    G      47      G      47          3.122
LGA    I      48      I      48          1.479
LGA    D      49      D      49          1.086
LGA    Q      50      Q      50          1.059
LGA    D      51      D      51          0.769
LGA    L      52      L      52          1.073
LGA    I      53      I      53          1.226
LGA    A      54      A      54          1.189
LGA    A      55      A      55          2.021
LGA    L      56      L      56          2.729
LGA    P      57      P      57          0.873
LGA    Q      58      Q      58          3.690
LGA    Y      59      Y      59          3.804
LGA    D      60      D      60          8.593
LGA    A      61      A      61         11.998
LGA    A      62      A      62         14.295
LGA    L      63      L      63         10.636
LGA    I      64      I      64         10.335
LGA    A      65      A      65         15.369
LGA    R      66      R      66         13.657
LGA    V      67      V      67         12.617

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  116    4.0     16    2.25    13.147    12.028     0.680

LGA_LOCAL      RMSD =  2.252  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.402  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  7.812  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.064761 * X  +  -0.172791 * Y  +  -0.982827 * Z  + -38.753010
  Y_new =  -0.972302 * X  +   0.210724 * Y  +  -0.101115 * Z  +   5.541860
  Z_new =   0.224577 * X  +   0.962153 * Y  +  -0.154358 * Z  + -15.759353 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.729871   -1.411722  [ DEG:    99.1143    -80.8857 ]
  Theta =  -0.226509   -2.915084  [ DEG:   -12.9780   -167.0220 ]
  Phi   =  -1.504289    1.637304  [ DEG:   -86.1894     93.8106 ]
 
# 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: T0360AL381_5                                  
REMARK     2: T0360.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0360AL381_5.T0360.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  116   4.0   16   2.25  12.028     7.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0360AL381_5
REMARK Aligment from pdb entry: 2awhA
ATOM      1  N   TYR    35     -61.123  -8.373 -31.306  1.00  0.00              
ATOM      2  CA  TYR    35     -60.956  -6.974 -31.694  1.00  0.00              
ATOM      3  C   TYR    35     -59.910  -6.369 -30.772  1.00  0.00              
ATOM      4  O   TYR    35     -59.709  -6.842 -29.652  1.00  0.00              
ATOM      5  N   ASP    36     -59.209  -5.358 -31.244  1.00  0.00              
ATOM      6  CA  ASP    36     -58.282  -4.668 -30.374  1.00  0.00              
ATOM      7  C   ASP    36     -59.101  -4.104 -29.206  1.00  0.00              
ATOM      8  O   ASP    36     -60.269  -3.723 -29.373  1.00  0.00              
ATOM      9  N   VAL    37     -58.471  -4.063 -28.036  1.00  0.00              
ATOM     10  CA  VAL    37     -59.102  -3.639 -26.805  1.00  0.00              
ATOM     11  C   VAL    37     -59.685  -2.230 -26.927  1.00  0.00              
ATOM     12  O   VAL    37     -60.717  -1.938 -26.327  1.00  0.00              
ATOM     13  N   PHE    38     -59.039  -1.356 -27.701  1.00  0.00              
ATOM     14  CA  PHE    38     -59.587  -0.007 -27.890  1.00  0.00              
ATOM     15  C   PHE    38     -60.905  -0.032 -28.666  1.00  0.00              
ATOM     16  O   PHE    38     -61.809   0.755 -28.374  1.00  0.00              
ATOM     17  N   LYS    39     -61.016  -0.917 -29.656  1.00  0.00              
ATOM     18  CA  LYS    39     -62.311  -1.074 -30.350  1.00  0.00              
ATOM     19  C   LYS    39     -63.401  -1.658 -29.466  1.00  0.00              
ATOM     20  O   LYS    39     -64.551  -1.233 -29.567  1.00  0.00              
ATOM     21  N   ARG    40     -63.062  -2.645 -28.609  1.00  0.00              
ATOM     22  CA  ARG    40     -64.006  -3.203 -27.652  1.00  0.00              
ATOM     23  C   ARG    40     -64.577  -2.115 -26.748  1.00  0.00              
ATOM     24  O   ARG    40     -65.801  -2.087 -26.504  1.00  0.00              
ATOM     25  N   PHE    41     -63.706  -1.222 -26.271  1.00  0.00              
ATOM     26  CA  PHE    41     -64.105  -0.077 -25.411  1.00  0.00              
ATOM     27  C   PHE    41     -65.038   0.952 -26.096  1.00  0.00              
ATOM     28  O   PHE    41     -66.009   1.438 -25.488  1.00  0.00              
ATOM     29  N   LYS    42     -64.732   1.290 -27.349  1.00  0.00              
ATOM     30  CA  LYS    42     -65.622   2.124 -28.166  1.00  0.00              
ATOM     31  C   LYS    42     -67.003   1.466 -28.361  1.00  0.00              
ATOM     32  O   LYS    42     -68.020   2.126 -28.257  1.00  0.00              
ATOM     33  N   PRO    43     -67.027   0.163 -28.640  1.00  0.00              
ATOM     34  CA  PRO    43     -68.297  -0.560 -28.825  1.00  0.00              
ATOM     35  C   PRO    43     -69.148  -0.555 -27.565  1.00  0.00              
ATOM     36  O   PRO    43     -70.366  -0.358 -27.622  1.00  0.00              
ATOM     37  N   LEU    44     -68.536  -0.790 -26.418  1.00  0.00              
ATOM     38  CA  LEU    44     -69.276  -0.755 -25.140  1.00  0.00              
ATOM     39  C   LEU    44     -69.684   0.686 -24.808  1.00  0.00              
ATOM     40  O   LEU    44     -70.838   0.966 -24.481  1.00  0.00              
ATOM     41  N   ALA    45     -68.751   1.618 -24.958  1.00  0.00              
ATOM     42  CA  ALA    45     -69.066   3.034 -24.691  1.00  0.00              
ATOM     43  C   ALA    45     -70.351   3.443 -25.381  1.00  0.00              
ATOM     44  O   ALA    45     -71.268   3.903 -24.727  1.00  0.00              
ATOM     45  N   LEU    46     -70.432   3.256 -26.692  1.00  0.00              
ATOM     46  CA  LEU    46     -71.598   3.707 -27.474  1.00  0.00              
ATOM     47  C   LEU    46     -72.781   2.757 -27.563  1.00  0.00              
ATOM     48  O   LEU    46     -73.887   3.176 -27.938  1.00  0.00              
ATOM     49  N   GLY    47     -72.570   1.487 -27.181  1.00  0.00              
ATOM     50  CA  GLY    47     -73.647   0.496 -27.210  1.00  0.00              
ATOM     51  C   GLY    47     -74.324   0.093 -25.900  1.00  0.00              
ATOM     52  O   GLY    47     -75.482  -0.349 -25.937  1.00  0.00              
ATOM     53  N   ILE    48     -73.655   0.241 -24.746  1.00  0.00              
ATOM     54  CA  ILE    48     -74.222  -0.306 -23.485  1.00  0.00              
ATOM     55  C   ILE    48     -75.569   0.257 -23.101  1.00  0.00              
ATOM     56  O   ILE    48     -76.450  -0.509 -22.737  1.00  0.00              
ATOM     57  N   ASP    49     -75.743   1.592 -23.207  1.00  0.00              
ATOM     58  CA  ASP    49     -77.056   2.189 -22.940  1.00  0.00              
ATOM     59  C   ASP    49     -78.169   1.863 -23.939  1.00  0.00              
ATOM     60  O   ASP    49     -79.316   1.764 -23.530  1.00  0.00              
ATOM     61  N   GLN    50     -77.884   1.744 -25.232  1.00  0.00              
ATOM     62  CA  GLN    50     -78.892   1.253 -26.158  1.00  0.00              
ATOM     63  C   GLN    50     -79.332  -0.153 -25.691  1.00  0.00              
ATOM     64  O   GLN    50     -80.525  -0.479 -25.678  1.00  0.00              
ATOM     65  N   ASP    51     -78.360  -0.982 -25.331  1.00  0.00              
ATOM     66  CA  ASP    51     -78.698  -2.368 -24.908  1.00  0.00              
ATOM     67  C   ASP    51     -79.496  -2.320 -23.599  1.00  0.00              
ATOM     68  O   ASP    51     -80.492  -3.037 -23.427  1.00  0.00              
ATOM     69  N   LEU    52     -79.080  -1.433 -22.693  1.00  0.00              
ATOM     70  CA  LEU    52     -79.741  -1.284 -21.403  1.00  0.00              
ATOM     71  C   LEU    52     -81.216  -0.910 -21.556  1.00  0.00              
ATOM     72  O   LEU    52     -82.082  -1.491 -20.909  1.00  0.00              
ATOM     73  N   ILE    53     -81.485   0.093 -22.397  1.00  0.00              
ATOM     74  CA  ILE    53     -82.838   0.587 -22.553  1.00  0.00              
ATOM     75  C   ILE    53     -83.717  -0.377 -23.334  1.00  0.00              
ATOM     76  O   ILE    53     -84.897  -0.413 -23.107  1.00  0.00              
ATOM     77  N   ALA    54     -83.150  -1.159 -24.246  1.00  0.00              
ATOM     78  CA  ALA    54     -83.890  -2.295 -24.877  1.00  0.00              
ATOM     79  C   ALA    54     -84.316  -3.387 -23.866  1.00  0.00              
ATOM     80  O   ALA    54     -85.478  -3.873 -23.914  1.00  0.00              
ATOM     81  N   ALA    55     -83.401  -3.779 -22.976  1.00  0.00              
ATOM     82  CA  ALA    55     -83.678  -4.806 -21.925  1.00  0.00              
ATOM     83  C   ALA    55     -84.564  -4.306 -20.790  1.00  0.00              
ATOM     84  O   ALA    55     -85.291  -5.090 -20.155  1.00  0.00              
ATOM     85  N   LEU    56     -84.519  -2.995 -20.543  1.00  0.00              
ATOM     86  CA  LEU    56     -85.472  -2.336 -19.649  1.00  0.00              
ATOM     87  C   LEU    56     -86.931  -2.730 -19.944  1.00  0.00              
ATOM     88  O   LEU    56     -87.712  -2.991 -19.024  1.00  0.00              
ATOM     89  N   PRO    57     -87.293  -2.764 -21.220  1.00  0.00              
ATOM     90  CA  PRO    57     -88.646  -3.119 -21.636  1.00  0.00              
ATOM     91  C   PRO    57     -89.110  -4.442 -21.024  1.00  0.00              
ATOM     92  O   PRO    57     -90.275  -4.592 -20.705  1.00  0.00              
ATOM     93  N   GLN    58     -88.182  -5.383 -20.858  1.00  0.00              
ATOM     94  CA  GLN    58     -88.445  -6.697 -20.258  1.00  0.00              
ATOM     95  C   GLN    58     -89.025  -6.646 -18.852  1.00  0.00              
ATOM     96  O   GLN    58     -89.744  -7.563 -18.452  1.00  0.00              
ATOM     97  N   TYR    59     -90.604  -3.840 -17.498  1.00  0.00              
ATOM     98  CA  TYR    59     -91.517  -2.702 -17.476  1.00  0.00              
ATOM     99  C   TYR    59     -92.936  -3.138 -17.894  1.00  0.00              
ATOM    100  O   TYR    59     -93.108  -4.073 -18.689  1.00  0.00              
ATOM    101  N   ASP    60     -93.941  -2.517 -17.282  1.00  0.00              
ATOM    102  CA  ASP    60     -95.264  -2.418 -17.885  1.00  0.00              
ATOM    103  C   ASP    60     -95.699  -0.934 -17.809  1.00  0.00              
ATOM    104  O   ASP    60     -94.940  -0.089 -17.283  1.00  0.00              
ATOM    105  N   ALA    61     -96.882  -0.607 -18.342  1.00  0.00              
ATOM    106  CA  ALA    61     -97.395   0.773 -18.347  1.00  0.00              
ATOM    107  C   ALA    61     -97.424   1.406 -16.950  1.00  0.00              
ATOM    108  O   ALA    61     -97.463   2.628 -16.823  1.00  0.00              
ATOM    109  N   ALA    62     -97.399   0.554 -15.920  1.00  0.00              
ATOM    110  CA  ALA    62     -97.560   0.949 -14.510  1.00  0.00              
ATOM    111  C   ALA    62     -96.251   1.185 -13.736  1.00  0.00              
ATOM    112  O   ALA    62     -96.260   1.778 -12.653  1.00  0.00              
ATOM    113  N   LEU    63     -95.133   0.676 -14.245  1.00  0.00              
ATOM    114  CA  LEU    63     -93.899   0.700 -13.440  1.00  0.00              
ATOM    115  C   LEU    63     -92.891  -0.357 -13.818  1.00  0.00              
ATOM    116  O   LEU    63     -92.990  -0.952 -14.881  1.00  0.00              
ATOM    117  N   ILE    64     -91.897  -0.573 -12.962  1.00  0.00              
ATOM    118  CA  ILE    64     -90.808  -1.479 -13.320  1.00  0.00              
ATOM    119  C   ILE    64     -90.323  -2.317 -12.155  1.00  0.00              
ATOM    120  O   ILE    64     -90.277  -1.835 -11.026  1.00  0.00              
ATOM    121  N   ALA    65     -89.969  -3.568 -12.433  1.00  0.00              
ATOM    122  CA  ALA    65     -89.326  -4.428 -11.428  1.00  0.00              
ATOM    123  C   ALA    65     -87.922  -3.965 -11.064  1.00  0.00              
ATOM    124  O   ALA    65     -87.127  -3.651 -11.951  1.00  0.00              
ATOM    125  N   ARG    66     -87.610  -3.959  -9.769  1.00  0.00              
ATOM    126  CA  ARG    66     -86.268  -3.656  -9.288  1.00  0.00              
ATOM    127  C   ARG    66     -85.735  -4.792  -8.402  1.00  0.00              
ATOM    128  O   ARG    66     -86.499  -5.691  -7.996  1.00  0.00              
ATOM    129  N   VAL    67     -84.429  -4.762  -8.141  1.00  0.00              
ATOM    130  CA  VAL    67     -83.751  -5.750  -7.287  1.00  0.00              
ATOM    131  C   VAL    67     -84.178  -7.200  -7.512  1.00  0.00              
ATOM    132  O   VAL    67     -84.700  -7.860  -6.613  1.00  0.00              
END
