
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0312AL381_4
# Molecule2: number of CA atoms  140 ( 1114),  selected   23 , name T0312.pdb
# PARAMETERS: T0312AL381_4.T0312.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:    23        47 - 69          3.00     3.00
  LCS_AVERAGE:     16.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        47 - 65          1.95     3.72
  LONGEST_CONTINUOUS_SEGMENT:    19        48 - 66          1.92     3.42
  LCS_AVERAGE:     12.92

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        50 - 63          0.96     4.82
  LONGEST_CONTINUOUS_SEGMENT:    14        51 - 64          0.95     4.86
  LCS_AVERAGE:      7.98

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:  140
LCS_GDT     R      47     R      47      6   19   23     3    4    6    8   13   15   16   19   20   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     S      48     S      48      6   19   23     3    4    6   11   13   18   19   20   20   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     A      49     A      49      7   19   23     4    9   14   15   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     V      50     V      50     14   19   23     4   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     I      51     I      51     14   19   23     7   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     G      52     G      52     14   19   23     5   11   13   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     Y      53     Y      53     14   19   23     7   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     Y      54     Y      54     14   19   23     7   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     D      55     D      55     14   19   23     5   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     Q      56     Q      56     14   19   23     4   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      57     E      57     14   19   23     4   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      58     K      58     14   19   23     4   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      59     K      59     14   19   23     4   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      60     E      60     14   19   23     7   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     Y      61     Y      61     14   19   23     7   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     V      62     V      62     14   19   23     7   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      63     K      63     14   19   23     7   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      64     K      64     14   19   23     4   11   14   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      65     E      65      7   19   23     4    6   10   16   17   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     L      66     L      66      6   19   23     4    6   10   11   16   18   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     M      67     M      67      6   14   23     3    6   10   11   11   14   19   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      68     E      68      6   11   23     3    6   10   11   11   13   16   20   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_GDT     P      69     P      69      3   11   23     1    3    6    8    9   12   15   17   21   21   22   23   23   23   23   23   23   23   23   23 
LCS_AVERAGE  LCS_A:  12.44  (   7.98   12.92   16.43 )

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     14     16     17     18     19     20     21     21     22     23     23     23     23     23     23     23     23     23 
GDT PERCENT_CA   5.00   7.86  10.00  11.43  12.14  12.86  13.57  14.29  15.00  15.00  15.71  16.43  16.43  16.43  16.43  16.43  16.43  16.43  16.43  16.43
GDT RMS_LOCAL    0.34   0.58   0.95   1.28   1.35   1.67   1.92   2.25   2.69   2.49   2.75   3.00   3.00   3.00   3.00   3.00   3.00   3.00   3.00   3.00
GDT RMS_ALL_CA   4.79   6.01   4.47   4.12   3.92   3.69   3.42   3.17   3.13   3.13   3.05   3.00   3.00   3.00   3.00   3.00   3.00   3.00   3.00   3.00

#      Molecule1      Molecule2       DISTANCE
LGA    R      47      R      47          5.399
LGA    S      48      S      48          3.341
LGA    A      49      A      49          1.721
LGA    V      50      V      50          2.247
LGA    I      51      I      51          2.213
LGA    G      52      G      52          2.781
LGA    Y      53      Y      53          1.845
LGA    Y      54      Y      54          1.094
LGA    D      55      D      55          1.879
LGA    Q      56      Q      56          3.470
LGA    E      57      E      57          3.725
LGA    K      58      K      58          1.842
LGA    K      59      K      59          1.841
LGA    E      60      E      60          1.908
LGA    Y      61      Y      61          1.171
LGA    V      62      V      62          2.025
LGA    K      63      K      63          2.410
LGA    K      64      K      64          2.331
LGA    E      65      E      65          1.699
LGA    L      66      L      66          2.683
LGA    M      67      M      67          3.752
LGA    E      68      E      68          5.184
LGA    P      69      P      69          5.781

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23  140    4.0     20    2.25    12.500    13.108     0.850

LGA_LOCAL      RMSD =  2.253  Number of atoms =   20  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.997  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  2.997  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.240228 * X  +  -0.578577 * Y  +   0.779448 * Z  +  50.460297
  Y_new =  -0.708211 * X  +  -0.444683 * Y  +  -0.548356 * Z  +  -4.078597
  Z_new =   0.663874 * X  +  -0.683744 * Y  +  -0.302929 * Z  +  16.755569 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.987851    1.153742  [ DEG:  -113.8955     66.1045 ]
  Theta =  -0.725987   -2.415606  [ DEG:   -41.5960   -138.4040 ]
  Phi   =  -1.897821    1.243772  [ DEG:  -108.7371     71.2629 ]
 
# 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: T0312AL381_4                                  
REMARK     2: T0312.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0312AL381_4.T0312.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23  140   4.0   20   2.25  13.108     3.00
REMARK  ---------------------------------------------------------- 
MOLECULE T0312AL381_4
REMARK Aligment from pdb entry: 1bf0
ATOM      1  N   ARG    47      44.703   5.331   0.972  1.00  0.00              
ATOM      2  CA  ARG    47      46.135   5.412   1.161  1.00  0.00              
ATOM      3  C   ARG    47      46.382   4.515   2.359  1.00  0.00              
ATOM      4  O   ARG    47      45.554   4.501   3.261  1.00  0.00              
ATOM      5  N   SER    48      47.474   3.713   2.438  1.00  0.00              
ATOM      6  CA  SER    48      47.792   2.853   3.573  1.00  0.00              
ATOM      7  C   SER    48      49.219   3.188   4.029  1.00  0.00              
ATOM      8  O   SER    48      50.124   3.293   3.207  1.00  0.00              
ATOM      9  N   ALA    49      49.462   3.351   5.353  1.00  0.00              
ATOM     10  CA  ALA    49      50.744   3.614   6.011  1.00  0.00              
ATOM     11  C   ALA    49      51.205   2.338   6.754  1.00  0.00              
ATOM     12  O   ALA    49      50.354   1.608   7.253  1.00  0.00              
ATOM     13  N   VAL    50      52.531   2.007   6.864  1.00  0.00              
ATOM     14  CA  VAL    50      53.031   0.752   7.485  1.00  0.00              
ATOM     15  C   VAL    50      52.896   0.600   9.011  1.00  0.00              
ATOM     16  O   VAL    50      53.124   1.528   9.786  1.00  0.00              
ATOM     17  N   ILE    51      52.469  -0.615   9.446  1.00  0.00              
ATOM     18  CA  ILE    51      52.205  -0.953  10.840  1.00  0.00              
ATOM     19  C   ILE    51      52.544  -2.385  11.196  1.00  0.00              
ATOM     20  O   ILE    51      52.574  -3.275  10.348  1.00  0.00              
ATOM     21  N   GLY    52      52.689  -2.620  12.510  1.00  0.00              
ATOM     22  CA  GLY    52      52.954  -3.914  13.128  1.00  0.00              
ATOM     23  C   GLY    52      51.986  -4.072  14.290  1.00  0.00              
ATOM     24  O   GLY    52      51.839  -3.123  15.055  1.00  0.00              
ATOM     25  N   TYR    53      51.318  -5.250  14.465  1.00  0.00              
ATOM     26  CA  TYR    53      50.425  -5.564  15.594  1.00  0.00              
ATOM     27  C   TYR    53      51.085  -6.701  16.375  1.00  0.00              
ATOM     28  O   TYR    53      51.668  -7.570  15.730  1.00  0.00              
ATOM     29  N   TYR    54      51.010  -6.791  17.744  1.00  0.00              
ATOM     30  CA  TYR    54      51.654  -7.878  18.498  1.00  0.00              
ATOM     31  C   TYR    54      50.625  -8.984  18.579  1.00  0.00              
ATOM     32  O   TYR    54      49.525  -8.760  19.083  1.00  0.00              
ATOM     33  N   ASP    55      50.966 -10.179  18.006  1.00  0.00              
ATOM     34  CA  ASP    55      50.115 -11.323  17.916  1.00  0.00              
ATOM     35  C   ASP    55      50.286 -12.183  19.156  1.00  0.00              
ATOM     36  O   ASP    55      51.360 -12.712  19.452  1.00  0.00              
ATOM     37  N   GLN    56      49.188 -12.302  19.921  1.00  0.00              
ATOM     38  CA  GLN    56      49.064 -12.928  21.227  1.00  0.00              
ATOM     39  C   GLN    56      49.298 -14.431  21.334  1.00  0.00              
ATOM     40  O   GLN    56      49.925 -14.893  22.285  1.00  0.00              
ATOM     41  N   GLU    57      48.830 -15.247  20.354  1.00  0.00              
ATOM     42  CA  GLU    57      49.071 -16.694  20.333  1.00  0.00              
ATOM     43  C   GLU    57      50.362 -17.037  19.580  1.00  0.00              
ATOM     44  O   GLU    57      50.765 -18.195  19.532  1.00  0.00              
ATOM     45  N   LYS    58      51.056 -16.016  19.000  1.00  0.00              
ATOM     46  CA  LYS    58      52.342 -16.151  18.318  1.00  0.00              
ATOM     47  C   LYS    58      53.557 -15.817  19.195  1.00  0.00              
ATOM     48  O   LYS    58      54.541 -16.556  19.190  1.00  0.00              
ATOM     49  N   LYS    59      53.515 -14.670  19.941  1.00  0.00              
ATOM     50  CA  LYS    59      54.576 -14.149  20.814  1.00  0.00              
ATOM     51  C   LYS    59      55.562 -13.221  20.086  1.00  0.00              
ATOM     52  O   LYS    59      56.672 -12.947  20.543  1.00  0.00              
ATOM     53  N   GLU    60      55.142 -12.681  18.919  1.00  0.00              
ATOM     54  CA  GLU    60      55.870 -11.730  18.097  1.00  0.00              
ATOM     55  C   GLU    60      54.857 -10.820  17.411  1.00  0.00              
ATOM     56  O   GLU    60      53.656 -11.098  17.425  1.00  0.00              
ATOM     57  N   TYR    61      55.304  -9.706  16.756  1.00  0.00              
ATOM     58  CA  TYR    61      54.468  -8.795  15.989  1.00  0.00              
ATOM     59  C   TYR    61      54.386  -9.201  14.537  1.00  0.00              
ATOM     60  O   TYR    61      55.369  -9.625  13.936  1.00  0.00              
ATOM     61  N   VAL    62      53.183  -9.047  13.952  1.00  0.00              
ATOM     62  CA  VAL    62      52.898  -9.355  12.561  1.00  0.00              
ATOM     63  C   VAL    62      52.646  -8.034  11.832  1.00  0.00              
ATOM     64  O   VAL    62      52.088  -7.124  12.451  1.00  0.00              
ATOM     65  N   LYS    63      53.010  -7.864  10.549  1.00  0.00              
ATOM     66  CA  LYS    63      52.802  -6.629   9.802  1.00  0.00              
ATOM     67  C   LYS    63      51.435  -6.559   9.154  1.00  0.00              
ATOM     68  O   LYS    63      50.855  -7.551   8.707  1.00  0.00              
ATOM     69  N   LYS    64      50.980  -5.303   9.049  1.00  0.00              
ATOM     70  CA  LYS    64      49.796  -4.898   8.329  1.00  0.00              
ATOM     71  C   LYS    64      50.139  -3.524   7.776  1.00  0.00              
ATOM     72  O   LYS    64      51.304  -3.129   7.733  1.00  0.00              
ATOM     73  N   GLU    65      49.127  -2.735   7.387  1.00  0.00              
ATOM     74  CA  GLU    65      49.210  -1.371   6.956  1.00  0.00              
ATOM     75  C   GLU    65      47.951  -0.793   7.575  1.00  0.00              
ATOM     76  O   GLU    65      46.972  -1.520   7.690  1.00  0.00              
ATOM     77  N   LEU    66      47.941   0.488   7.968  1.00  0.00              
ATOM     78  CA  LEU    66      46.820   1.239   8.522  1.00  0.00              
ATOM     79  C   LEU    66      46.404   2.256   7.448  1.00  0.00              
ATOM     80  O   LEU    66      47.273   2.867   6.831  1.00  0.00              
ATOM     81  N   MET    67      45.069   2.469   7.210  1.00  0.00              
ATOM     82  CA  MET    67      44.538   3.436   6.230  1.00  0.00              
ATOM     83  C   MET    67      44.576   4.867   6.763  1.00  0.00              
ATOM     84  O   MET    67      44.914   5.827   6.076  1.00  0.00              
ATOM     85  N   GLU    68      44.179   5.006   8.045  1.00  0.00              
ATOM     86  CA  GLU    68      44.033   6.258   8.757  1.00  0.00              
ATOM     87  C   GLU    68      42.648   6.361   9.323  1.00  0.00              
ATOM     88  O   GLU    68      42.474   6.591  10.518  1.00  0.00              
ATOM     89  N   PRO    69      41.584   6.163   8.504  1.00  0.00              
ATOM     90  CA  PRO    69      40.196   6.333   8.903  1.00  0.00              
ATOM     91  C   PRO    69      39.550   5.169   9.689  1.00  0.00              
ATOM     92  O   PRO    69      38.610   4.535   9.212  1.00  0.00              
END
