
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0347AL333_2-D1
# Molecule2: number of CA atoms   89 (  730),  selected   32 , name T0347_D1.pdb
# PARAMETERS: T0347AL333_2-D1.T0347_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:    13        51 - 63          4.27    27.85
  LCS_AVERAGE:     13.13

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        27 - 31          0.25    30.11
  LONGEST_CONTINUOUS_SEGMENT:     5        51 - 55          1.99    26.88
  LONGEST_CONTINUOUS_SEGMENT:     5        59 - 63          1.96    20.24
  LCS_AVERAGE:      4.78

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        27 - 31          0.25    30.11
  LCS_AVERAGE:      4.00

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:   89
LCS_GDT     R      27     R      27      5    5   11     5    5    5    5    5    6    8    8    9    9   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     E      28     E      28      5    5   11     5    5    5    5    5    6    8    8    9   10   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     V      29     V      29      5    5   11     5    5    5    5    5    6    8    8    9   10   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     E      30     E      30      5    5   11     5    5    5    5    5    6    8    8    9   10   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     L      31     L      31      5    5   11     5    5    5    5    5    6    8    8    9    9   10   10   11   13   15   16   18   18   18   19 
LCS_GDT     K      32     K      32      3    4   11     3    3    3    4    4    6    8    8    9    9    9   10   11   11   11   12   14   14   15   18 
LCS_GDT     R      33     R      33      3    4   11     3    3    3    4    4    4    8    8    9    9    9   10   11   11   11   12   14   14   16   18 
LCS_GDT     K      34     K      34      3    4   11     3    3    3    4    4    6    8    8    9    9    9   10   11   11   11   12   14   14   15   15 
LCS_GDT     E      35     E      35      3    4   11     3    3    3    4    4    4    5    6    9    9    9   10   11   11   11   12   12   14   15   15 
LCS_GDT     W      36     W      36      3    3   11     3    3    3    3    3    4    5    6    6    7    8   10   11   11   11   12   14   14   15   15 
LCS_GDT     R      37     R      37      3    3   11     3    3    3    3    3    4    5    6    6    7    8    9   11   11   11   12   12   13   13   15 
LCS_GDT     H      51     H      51      4    5   13     4    4    5    5    6    7    8   10   10   11   12   12   12   12   13   13   14   14   14   15 
LCS_GDT     I      52     I      52      4    5   13     4    4    5    5    6    7    8   10   10   11   12   12   12   12   13   13   14   14   14   15 
LCS_GDT     V      53     V      53      4    5   13     4    4    5    5    6    7    8   10   10   11   12   12   12   12   13   13   14   14   14   15 
LCS_GDT     P      54     P      54      4    5   13     4    4    5    5    6    7    8   10   10   11   12   12   12   12   13   13   14   14   14   15 
LCS_GDT     V      55     V      55      3    5   13     0    3    3    3    3    5    6    8   10   11   12   12   12   12   13   13   14   14   15   15 
LCS_GDT     V      56     V      56      3    3   13     3    3    4    5    6    6    8   10   10   11   12   12   12   12   13   13   14   14   15   15 
LCS_GDT     A      57     A      57      3    4   13     3    3    4    5    5    6    8   10   10   11   12   12   13   13   16   17   18   18   18   19 
LCS_GDT     G      58     G      58      4    4   13     3    4    4    5    5    5    8   10   10   11   12   12   13   15   16   17   18   18   18   19 
LCS_GDT     P      59     P      59      4    5   13     3    4    4    4    6    7    8   10   10   11   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     K      60     K      60      4    5   13     3    4    4    4    5    7    8   10   10   11   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     D      61     D      61      4    5   13     3    4    5    5    6    7    8   10   10   11   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     R      62     R      62      3    5   13     3    4    4    5    5    6    6    8   10   11   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     A      63     A      63      3    5   13     1    4    4    4    4    5    5    8    8   10   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     Y      64     Y      64      3    3   11     1    4    4    4    5    6    7    8    8   10   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     L      65     L      65      3    3   11     3    3    4    4    5    6    7    8    8   10   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     I      66     I      66      3    3   11     3    3    3    3    5    6    7    8    8   10   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     D      67     D      67      3    3   11     3    3    3    3    3    4    5    7    7    8   10   11   13   14   16   17   18   18   18   19 
LCS_GDT     E      87     E      87      3    4   11     3    3    3    4    4    6    7    7    8   10   12   13   14   15   16   17   18   18   18   19 
LCS_GDT     V      88     V      88      3    4   11     3    3    3    4    5    6    7    7    8    9   10   12   14   15   16   17   18   18   18   19 
LCS_GDT     A      89     A      89      3    4    9     3    4    4    4    5    6    7    7    8    8    8   11   11   14   15   15   16   17   18   19 
LCS_GDT     K      90     K      90      3    4    9     0    3    3    4    4    6    7    7    8    8    8    8    9   10   13   14   16   16   17   17 
LCS_AVERAGE  LCS_A:   7.30  (   4.00    4.78   13.13 )

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      5      5      5      5      6      7      8     10     10     11     12     13     14     15     16     17     18     18     18     19 
GDT PERCENT_CA   5.62   5.62   5.62   5.62   6.74   7.87   8.99  11.24  11.24  12.36  13.48  14.61  15.73  16.85  17.98  19.10  20.22  20.22  20.22  21.35
GDT RMS_LOCAL    0.25   0.25   0.25   0.25   1.38   1.79   2.13   2.61   2.61   2.97   3.42   4.56   4.73   5.03   5.26   5.50   5.77   5.77   5.77   6.10
GDT RMS_ALL_CA  30.11  30.11  30.11  30.11  28.57  29.08  29.18  28.99  28.99  28.60  28.30  15.86  15.81  15.96  15.80  15.62  15.35  15.35  15.35  15.53

#      Molecule1      Molecule2       DISTANCE
LGA    R      27      R      27         55.327
LGA    E      28      E      28         51.293
LGA    V      29      V      29         48.675
LGA    E      30      E      30         51.188
LGA    L      31      L      31         50.396
LGA    K      32      K      32         40.119
LGA    R      33      R      33         39.824
LGA    K      34      K      34         42.135
LGA    E      35      E      35         37.217
LGA    W      36      W      36         32.369
LGA    R      37      R      37         34.186
LGA    H      51      H      51          1.723
LGA    I      52      I      52          0.337
LGA    V      53      V      53          0.985
LGA    P      54      P      54          1.475
LGA    V      55      V      55          5.094
LGA    V      56      V      56          3.682
LGA    A      57      A      57          3.453
LGA    G      58      G      58          3.969
LGA    P      59      P      59          3.103
LGA    K      60      K      60          3.692
LGA    D      61      D      61          0.790
LGA    R      62      R      62          7.162
LGA    A      63      A      63         10.856
LGA    Y      64      Y      64         13.774
LGA    L      65      L      65         19.497
LGA    I      66      I      66         23.047
LGA    D      67      D      67         27.764
LGA    E      87      E      87         22.161
LGA    V      88      V      88         25.232
LGA    A      89      A      89         24.285
LGA    K      90      K      90         23.104

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32   89    4.0     10    2.61    10.393     8.798     0.369

LGA_LOCAL      RMSD =  2.611  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 28.605  Number of atoms =   32 
Std_ALL_ATOMS  RMSD = 11.995  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.452505 * X  +  -0.600772 * Y  +   0.659023 * Z  +  -1.507989
  Y_new =  -0.708581 * X  +   0.690922 * Y  +   0.143318 * Z  +  37.260044
  Z_new =  -0.541435 * X  +  -0.402120 * Y  +  -0.738341 * Z  +  30.711628 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.642885    0.498708  [ DEG:  -151.4262     28.5738 ]
  Theta =   0.572143    2.569450  [ DEG:    32.7814    147.2186 ]
  Phi   =  -2.139121    1.002472  [ DEG:  -122.5626     57.4374 ]
 
# 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: T0347AL333_2-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347AL333_2-D1.T0347_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32   89   4.0   10   2.61   8.798    12.00
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL333_2-D1
REMARK Aligment from pdb entry: 1bh9_B
ATOM     13  N   ARG    27      -5.245   6.594  13.462  1.00  0.00              
ATOM     14  CA  ARG    27      -5.645   7.291  12.235  1.00  0.00              
ATOM     15  C   ARG    27      -5.887   8.787  12.366  1.00  0.00              
ATOM     16  O   ARG    27      -5.523   9.552  11.473  1.00  0.00              
ATOM     17  N   GLU    28      -6.537   9.206  13.445  1.00  0.00              
ATOM     18  CA  GLU    28      -6.768  10.627  13.620  1.00  0.00              
ATOM     19  C   GLU    28      -5.390  11.260  13.651  1.00  0.00              
ATOM     20  O   GLU    28      -5.115  12.211  12.911  1.00  0.00              
ATOM     21  N   VAL    29      -4.529  10.701  14.503  1.00  0.00              
ATOM     22  CA  VAL    29      -3.159  11.161  14.668  1.00  0.00              
ATOM     23  C   VAL    29      -2.428  11.190  13.339  1.00  0.00              
ATOM     24  O   VAL    29      -1.818  12.200  12.990  1.00  0.00              
ATOM     25  N   GLU    30      -2.480  10.089  12.593  1.00  0.00              
ATOM     26  CA  GLU    30      -1.794  10.072  11.310  1.00  0.00              
ATOM     27  C   GLU    30      -2.445  10.936  10.256  1.00  0.00              
ATOM     28  O   GLU    30      -1.763  11.419   9.360  1.00  0.00              
ATOM     29  N   LEU    31      -3.750  11.153  10.355  1.00  0.00              
ATOM     30  CA  LEU    31      -4.391  11.997   9.375  1.00  0.00              
ATOM     31  C   LEU    31      -3.910  13.420   9.676  1.00  0.00              
ATOM     32  O   LEU    31      -3.624  14.193   8.758  1.00  0.00              
ATOM     33  N   LYS    32      -0.672  18.339   8.718  1.00  0.00              
ATOM     34  CA  LYS    32       0.318  19.265   9.244  1.00  0.00              
ATOM     35  C   LYS    32       1.509  19.466   8.320  1.00  0.00              
ATOM     36  O   LYS    32       1.893  20.604   8.054  1.00  0.00              
ATOM     37  N   ARG    33       2.098  18.388   7.812  1.00  0.00              
ATOM     38  CA  ARG    33       3.247  18.583   6.942  1.00  0.00              
ATOM     39  C   ARG    33       3.130  18.408   5.435  1.00  0.00              
ATOM     40  O   ARG    33       4.113  18.611   4.715  1.00  0.00              
ATOM     41  N   LYS    34       1.960  18.045   4.934  1.00  0.00              
ATOM     42  CA  LYS    34       1.829  17.913   3.495  1.00  0.00              
ATOM     43  C   LYS    34       2.239  19.258   2.890  1.00  0.00              
ATOM     44  O   LYS    34       1.976  20.321   3.461  1.00  0.00              
ATOM     45  N   GLU    35       2.885  19.213   1.737  1.00  0.00              
ATOM     46  CA  GLU    35       3.325  20.434   1.097  1.00  0.00              
ATOM     47  C   GLU    35       3.950  20.126  -0.238  1.00  0.00              
ATOM     48  O   GLU    35       4.643  19.123  -0.394  1.00  0.00              
ATOM     49  N   TRP    36       3.710  21.012  -1.192  1.00  0.00              
ATOM     50  CA  TRP    36       4.241  20.871  -2.527  1.00  0.00              
ATOM     51  C   TRP    36       5.744  21.113  -2.576  1.00  0.00              
ATOM     52  O   TRP    36       6.278  21.923  -1.830  1.00  0.00              
ATOM     53  N   ARG    37       6.445  20.417  -3.479  1.00  0.00              
ATOM     54  CA  ARG    37       7.891  20.601  -3.604  1.00  0.00              
ATOM     55  C   ARG    37       8.099  22.012  -4.155  1.00  0.00              
ATOM     56  O   ARG    37       7.417  22.406  -5.104  1.00  0.00              
ATOM    109  N   HIS    51      10.825  35.806 -16.168  1.00  0.00              
ATOM    110  CA  HIS    51      11.784  36.216 -15.135  1.00  0.00              
ATOM    111  C   HIS    51      11.821  35.121 -14.072  1.00  0.00              
ATOM    112  O   HIS    51      10.925  34.270 -14.026  1.00  0.00              
ATOM    113  N   ILE    52      12.844  35.146 -13.217  1.00  0.00              
ATOM    114  CA  ILE    52      12.934  34.170 -12.138  1.00  0.00              
ATOM    115  C   ILE    52      12.034  34.762 -11.056  1.00  0.00              
ATOM    116  O   ILE    52      11.484  35.855 -11.234  1.00  0.00              
ATOM    117  N   VAL    53      11.921  34.060  -9.930  1.00  0.00              
ATOM    118  CA  VAL    53      11.079  34.500  -8.826  1.00  0.00              
ATOM    119  C   VAL    53      11.716  34.225  -7.460  1.00  0.00              
ATOM    120  O   VAL    53      12.655  33.450  -7.342  1.00  0.00              
ATOM    121  N   PRO    54      11.202  34.875  -6.428  1.00  0.00              
ATOM    122  CA  PRO    54      11.761  34.740  -5.093  1.00  0.00              
ATOM    123  C   PRO    54      11.293  33.566  -4.251  1.00  0.00              
ATOM    124  O   PRO    54      10.271  32.937  -4.515  1.00  0.00              
ATOM    125  N   VAL    55       6.830  30.098  -1.619  1.00  0.00              
ATOM    126  CA  VAL    55       6.227  29.642  -0.369  1.00  0.00              
ATOM    127  C   VAL    55       4.793  30.135  -0.249  1.00  0.00              
ATOM    128  O   VAL    55       3.909  29.397   0.177  1.00  0.00              
ATOM    129  N   VAL    56       4.577  31.384  -0.636  1.00  0.00              
ATOM    130  CA  VAL    56       3.256  31.985  -0.592  1.00  0.00              
ATOM    131  C   VAL    56       2.320  31.254  -1.553  1.00  0.00              
ATOM    132  O   VAL    56       1.178  30.959  -1.222  1.00  0.00              
ATOM    133  N   ALA    57       2.821  30.962  -2.748  1.00  0.00              
ATOM    134  CA  ALA    57       2.061  30.254  -3.765  1.00  0.00              
ATOM    135  C   ALA    57       1.734  28.839  -3.270  1.00  0.00              
ATOM    136  O   ALA    57       0.665  28.323  -3.561  1.00  0.00              
ATOM    137  N   GLY    58       2.647  28.217  -2.526  1.00  0.00              
ATOM    138  CA  GLY    58       2.414  26.874  -1.993  1.00  0.00              
ATOM    139  C   GLY    58       1.367  26.888  -0.894  1.00  0.00              
ATOM    140  O   GLY    58       0.585  25.962  -0.767  1.00  0.00              
ATOM    141  N   PRO    59       1.374  27.933  -0.081  1.00  0.00              
ATOM    142  CA  PRO    59       0.399  28.042   0.987  1.00  0.00              
ATOM    143  C   PRO    59      -1.002  28.239   0.438  1.00  0.00              
ATOM    144  O   PRO    59      -1.948  27.627   0.929  1.00  0.00              
ATOM    145  N   LYS    60      -1.131  29.091  -0.578  1.00  0.00              
ATOM    146  CA  LYS    60      -2.416  29.377  -1.212  1.00  0.00              
ATOM    147  C   LYS    60      -2.958  28.167  -1.976  1.00  0.00              
ATOM    148  O   LYS    60      -4.165  27.928  -2.015  1.00  0.00              
ATOM    149  N   ASP    61      -2.062  27.390  -2.568  1.00  0.00              
ATOM    150  CA  ASP    61      -2.467  26.222  -3.327  1.00  0.00              
ATOM    151  C   ASP    61      -2.882  25.111  -2.389  1.00  0.00              
ATOM    152  O   ASP    61      -3.740  24.301  -2.721  1.00  0.00              
ATOM    153  N   ARG    62      -2.283  25.068  -1.209  1.00  0.00              
ATOM    154  CA  ARG    62      -2.662  24.041  -0.259  1.00  0.00              
ATOM    155  C   ARG    62      -4.100  24.332   0.170  1.00  0.00              
ATOM    156  O   ARG    62      -4.923  23.431   0.218  1.00  0.00              
ATOM    157  N   ALA    63      -4.404  25.591   0.456  1.00  0.00              
ATOM    158  CA  ALA    63      -5.756  25.978   0.844  1.00  0.00              
ATOM    159  C   ALA    63      -6.776  25.626  -0.247  1.00  0.00              
ATOM    160  O   ALA    63      -7.875  25.154   0.049  1.00  0.00              
ATOM    161  N   TYR    64      -6.406  25.868  -1.502  1.00  0.00              
ATOM    162  CA  TYR    64      -7.243  25.539  -2.654  1.00  0.00              
ATOM    163  C   TYR    64      -7.529  24.041  -2.618  1.00  0.00              
ATOM    164  O   TYR    64      -8.689  23.619  -2.672  1.00  0.00              
ATOM    165  N   LEU    65      -6.462  23.246  -2.541  1.00  0.00              
ATOM    166  CA  LEU    65      -6.596  21.801  -2.480  1.00  0.00              
ATOM    167  C   LEU    65      -7.556  21.474  -1.356  1.00  0.00              
ATOM    168  O   LEU    65      -8.471  20.681  -1.531  1.00  0.00              
ATOM    169  N   ILE    66      -7.352  22.116  -0.211  1.00  0.00              
ATOM    170  CA  ILE    66      -8.197  21.888   0.946  1.00  0.00              
ATOM    171  C   ILE    66      -9.667  22.135   0.716  1.00  0.00              
ATOM    172  O   ILE    66     -10.508  21.382   1.184  1.00  0.00              
ATOM    173  N   ASP    67      -9.975  23.201  -0.008  1.00  0.00              
ATOM    174  CA  ASP    67     -11.351  23.543  -0.298  1.00  0.00              
ATOM    175  C   ASP    67     -11.983  22.586  -1.303  1.00  0.00              
ATOM    176  O   ASP    67     -13.174  22.310  -1.222  1.00  0.00              
ATOM    177  N   GLU    87     -11.197  22.058  -2.234  1.00  0.00              
ATOM    178  CA  GLU    87     -11.736  21.129  -3.216  1.00  0.00              
ATOM    179  C   GLU    87     -12.024  19.764  -2.580  1.00  0.00              
ATOM    180  O   GLU    87     -13.090  19.198  -2.789  1.00  0.00              
ATOM    181  N   VAL    88     -11.078  19.238  -1.804  1.00  0.00              
ATOM    182  CA  VAL    88     -11.276  17.947  -1.146  1.00  0.00              
ATOM    183  C   VAL    88     -12.423  18.050  -0.146  1.00  0.00              
ATOM    184  O   VAL    88     -13.279  17.179  -0.083  1.00  0.00              
ATOM    185  N   ALA    89     -12.450  19.126   0.628  1.00  0.00              
ATOM    186  CA  ALA    89     -13.518  19.320   1.604  1.00  0.00              
ATOM    187  C   ALA    89     -14.884  19.443   0.933  1.00  0.00              
ATOM    188  O   ALA    89     -15.887  18.978   1.478  1.00  0.00              
ATOM    189  N   LYS    90     -14.925  20.049  -0.252  1.00  0.00              
ATOM    190  CA  LYS    90     -16.179  20.194  -0.981  1.00  0.00              
ATOM    191  C   LYS    90     -16.589  18.881  -1.658  1.00  0.00              
ATOM    192  O   LYS    90     -17.767  18.537  -1.690  1.00  0.00              
END
