
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0349AL509_2-D1
# Molecule2: number of CA atoms   57 (  873),  selected   25 , name T0349_D1.pdb
# PARAMETERS: T0349AL509_2-D1.T0349_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:    23        28 - 67          4.71     5.50
  LCS_AVERAGE:     38.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        46 - 67          1.83     5.84
  LCS_AVERAGE:     29.19

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        49 - 65          0.95     5.60
  LCS_AVERAGE:     21.89

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:   57
LCS_GDT     G      26     G      26      4    4    7     4    4    5    5    5    5    5   14   16   17   18   21   22   22   23   23   23   23   23   24 
LCS_GDT     H      27     H      27      4    4    7     4    4    5    5    9   11   12   14   18   18   19   21   22   22   23   23   23   23   23   24 
LCS_GDT     L      28     L      28      4    4   23     4    4    5    6    7    7   10   16   18   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     V      29     V      29      4    4   23     4    4    5    6    7    7   10   11   18   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     P      45     P      45      0    0   23     0    0    1    3    3    4    4    4    5    7    7    7    8   14   18   18   21   21   21   21 
LCS_GDT     R      46     R      46      0   20   23     1    1    2    3    3   19   19   19   20   20   20   20   20   20   20   20   21   22   23   24 
LCS_GDT     L      49     L      49     17   20   23     4   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     V      50     V      50     17   20   23     4   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     H      51     H      51     17   20   23     4   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     E      52     E      52     17   20   23     4   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     D      53     D      53     17   20   23     5   13   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     D      54     D      54     17   20   23     3   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     L      55     L      55     17   20   23     5   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     A      56     A      56     17   20   23     8   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     G      57     G      57     17   20   23     8   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     A      58     A      58     17   20   23     8   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     R      59     R      59     17   20   23     8   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     R      60     R      60     17   20   23     8   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     L      61     L      61     17   20   23     8   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     L      62     L      62     17   20   23     8   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     T      63     T      63     17   20   23     8   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     D      64     D      64     17   20   23     7   15   16   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     A      65     A      65     17   20   23     4    9   14   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     G      66     G      66      4   20   23     3    4    5    8   15   17   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_GDT     L      67     L      67      3   20   23     3    3    8   18   18   19   19   19   20   20   21   21   22   22   23   23   23   23   23   24 
LCS_AVERAGE  LCS_A:  29.73  (  21.89   29.19   38.11 )

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      8     15     16     18     18     19     19     19     20     20     21     21     22     22     23     23     23     23     23     24 
GDT PERCENT_CA  14.04  26.32  28.07  31.58  31.58  33.33  33.33  33.33  35.09  35.09  36.84  36.84  38.60  38.60  40.35  40.35  40.35  40.35  40.35  42.11
GDT RMS_LOCAL    0.16   0.67   0.74   1.06   1.06   1.56   1.38   1.38   1.83   1.83   2.78   2.78   3.09   3.09   3.42   3.42   3.42   3.42   3.42   4.29
GDT RMS_ALL_CA   5.48   5.64   5.67   5.60   5.60   5.92   5.53   5.53   5.84   5.84   5.70   5.70   5.89   5.89   6.09   6.09   6.09   6.09   6.09   5.57

#      Molecule1      Molecule2       DISTANCE
LGA    G      26      G      26         11.473
LGA    H      27      H      27         10.832
LGA    L      28      L      28         10.797
LGA    V      29      V      29         10.658
LGA    P      45      P      45         14.161
LGA    R      46      R      46          6.935
LGA    L      49      L      49          1.252
LGA    V      50      V      50          0.864
LGA    H      51      H      51          0.785
LGA    E      52      E      52          1.336
LGA    D      53      D      53          1.915
LGA    D      54      D      54          0.985
LGA    L      55      L      55          0.585
LGA    A      56      A      56          0.519
LGA    G      57      G      57          0.587
LGA    A      58      A      58          0.369
LGA    R      59      R      59          0.750
LGA    R      60      R      60          0.877
LGA    L      61      L      61          0.724
LGA    L      62      L      62          0.677
LGA    T      63      T      63          0.796
LGA    D      64      D      64          1.230
LGA    A      65      A      65          1.700
LGA    G      66      G      66          3.700
LGA    L      67      L      67          2.148

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   25   57    4.0     19    1.38    32.895    32.298     1.285

LGA_LOCAL      RMSD =  1.378  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.528  Number of atoms =   25 
Std_ALL_ATOMS  RMSD =  5.391  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.710508 * X  +  -0.588267 * Y  +   0.386161 * Z  +   2.001516
  Y_new =   0.646503 * X  +   0.762393 * Y  +  -0.028109 * Z  + -65.749619
  Z_new =  -0.277871 * X  +   0.269626 * Y  +   0.922003 * Z  + -40.809986 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.284502   -2.857091  [ DEG:    16.3007   -163.6992 ]
  Theta =   0.281577    2.860015  [ DEG:    16.1332    163.8668 ]
  Phi   =   0.738267   -2.403325  [ DEG:    42.2996   -137.7004 ]
 
# 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: T0349AL509_2-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349AL509_2-D1.T0349_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   25   57   4.0   19   1.38  32.298     5.39
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL509_2-D1
REMARK Aligment from pdb entry: 1yj7A_
ATOM      1  N   GLY    26       3.535   4.730  -1.497  1.00  0.00              
ATOM      2  CA  GLY    26       4.293   4.578  -0.237  1.00  0.00              
ATOM      3  C   GLY    26       4.700   3.119  -0.054  1.00  0.00              
ATOM      4  O   GLY    26       5.881   2.779  -0.106  1.00  0.00              
ATOM      5  N   HIS    27       3.710   2.251   0.110  1.00  0.00              
ATOM      6  CA  HIS    27       3.924   0.842   0.389  1.00  0.00              
ATOM      7  C   HIS    27       2.920  -0.038  -0.364  1.00  0.00              
ATOM      8  O   HIS    27       1.756   0.319  -0.497  1.00  0.00              
ATOM      9  N   LEU    28       3.396  -1.181  -0.838  1.00  0.00              
ATOM     10  CA  LEU    28       2.554  -2.278  -1.326  1.00  0.00              
ATOM     11  C   LEU    28       2.675  -3.503  -0.416  1.00  0.00              
ATOM     12  O   LEU    28       3.498  -3.539   0.519  1.00  0.00              
ATOM     13  N   VAL    29       1.861  -4.520  -0.698  1.00  0.00              
ATOM     14  CA  VAL    29       1.938  -5.787   0.009  1.00  0.00              
ATOM     15  C   VAL    29       1.383  -5.760   1.417  1.00  0.00              
ATOM     16  O   VAL    29       1.693  -6.636   2.231  1.00  0.00              
ATOM     53  N   PRO    45      -4.552   7.652  -0.704  1.00  0.00              
ATOM     54  CA  PRO    45      -5.367   6.814  -1.546  1.00  0.00              
ATOM     55  C   PRO    45      -4.925   5.365  -1.391  1.00  0.00              
ATOM     56  O   PRO    45      -3.774   5.081  -1.082  1.00  0.00              
ATOM     57  N   ARG    46      -5.860   4.447  -1.598  1.00  0.00              
ATOM     58  CA  ARG    46      -5.634   3.039  -1.372  1.00  0.00              
ATOM     59  C   ARG    46      -6.157   2.230  -2.544  1.00  0.00              
ATOM     60  O   ARG    46      -7.192   2.574  -3.120  1.00  0.00              
ATOM     61  N   LEU    49      -0.856   5.177  -1.353  1.00  0.00              
ATOM     62  CA  LEU    49      -0.169   6.253  -2.071  1.00  0.00              
ATOM     63  C   LEU    49      -0.554   7.610  -1.504  1.00  0.00              
ATOM     64  O   LEU    49      -1.582   7.742  -0.844  1.00  0.00              
ATOM     65  N   VAL    50       0.257   8.620  -1.786  1.00  0.00              
ATOM     66  CA  VAL    50      -0.043   9.997  -1.427  1.00  0.00              
ATOM     67  C   VAL    50       0.234  10.906  -2.621  1.00  0.00              
ATOM     68  O   VAL    50       0.897  10.513  -3.577  1.00  0.00              
ATOM     69  N   HIS    51      -0.263  12.130  -2.553  1.00  0.00              
ATOM     70  CA  HIS    51       0.138  13.150  -3.516  1.00  0.00              
ATOM     71  C   HIS    51       1.634  13.330  -3.358  1.00  0.00              
ATOM     72  O   HIS    51       2.158  13.289  -2.232  1.00  0.00              
ATOM     73  N   GLU    52       2.357  13.491  -4.468  1.00  0.00              
ATOM     74  CA  GLU    52       3.819  13.519  -4.390  1.00  0.00              
ATOM     75  C   GLU    52       4.377  14.567  -3.442  1.00  0.00              
ATOM     76  O   GLU    52       5.392  14.324  -2.791  1.00  0.00              
ATOM     77  N   ASP    53       3.716  15.721  -3.344  1.00  0.00              
ATOM     78  CA  ASP    53       4.183  16.818  -2.526  1.00  0.00              
ATOM     79  C   ASP    53       4.127  16.470  -1.048  1.00  0.00              
ATOM     80  O   ASP    53       4.827  17.080  -0.247  1.00  0.00              
ATOM     81  N   ASP    54       3.307  15.481  -0.710  1.00  0.00              
ATOM     82  CA  ASP    54       3.098  15.069   0.673  1.00  0.00              
ATOM     83  C   ASP    54       4.002  13.909   1.105  1.00  0.00              
ATOM     84  O   ASP    54       3.891  13.417   2.246  1.00  0.00              
ATOM     85  N   LEU    55       4.893  13.461   0.219  1.00  0.00              
ATOM     86  CA  LEU    55       5.645  12.250   0.485  1.00  0.00              
ATOM     87  C   LEU    55       6.498  12.349   1.767  1.00  0.00              
ATOM     88  O   LEU    55       6.469  11.444   2.606  1.00  0.00              
ATOM     89  N   ALA    56       7.226  13.435   1.930  1.00  0.00              
ATOM     90  CA  ALA    56       8.108  13.558   3.108  1.00  0.00              
ATOM     91  C   ALA    56       7.294  13.600   4.410  1.00  0.00              
ATOM     92  O   ALA    56       7.605  12.887   5.355  1.00  0.00              
ATOM     93  N   GLY    57       6.235  14.399   4.449  1.00  0.00              
ATOM     94  CA  GLY    57       5.343  14.473   5.605  1.00  0.00              
ATOM     95  C   GLY    57       4.774  13.107   5.944  1.00  0.00              
ATOM     96  O   GLY    57       4.733  12.707   7.112  1.00  0.00              
ATOM     97  N   ALA    58       4.339  12.373   4.915  1.00  0.00              
ATOM     98  CA  ALA    58       3.770  11.041   5.103  1.00  0.00              
ATOM     99  C   ALA    58       4.751  10.028   5.675  1.00  0.00              
ATOM    100  O   ALA    58       4.429   9.320   6.634  1.00  0.00              
ATOM    101  N   ARG    59       5.947   9.950   5.099  1.00  0.00              
ATOM    102  CA  ARG    59       6.955   9.024   5.588  1.00  0.00              
ATOM    103  C   ARG    59       7.368   9.407   7.018  1.00  0.00              
ATOM    104  O   ARG    59       7.599   8.518   7.832  1.00  0.00              
ATOM    105  N   ARG    60       7.421  10.691   7.308  1.00  0.00              
ATOM    106  CA  ARG    60       7.742  11.172   8.660  1.00  0.00              
ATOM    107  C   ARG    60       6.745  10.648   9.690  1.00  0.00              
ATOM    108  O   ARG    60       7.138  10.052  10.703  1.00  0.00              
ATOM    109  N   LEU    61       5.450  10.821   9.403  1.00  0.00              
ATOM    110  CA  LEU    61       4.385  10.349  10.258  1.00  0.00              
ATOM    111  C   LEU    61       4.440   8.825  10.428  1.00  0.00              
ATOM    112  O   LEU    61       4.293   8.312  11.540  1.00  0.00              
ATOM    113  N   LEU    62       4.630   8.103   9.327  1.00  0.00              
ATOM    114  CA  LEU    62       4.681   6.656   9.392  1.00  0.00              
ATOM    115  C   LEU    62       5.893   6.197  10.220  1.00  0.00              
ATOM    116  O   LEU    62       5.731   5.330  11.101  1.00  0.00              
ATOM    117  N   THR    63       7.062   6.769   9.939  1.00  0.00              
ATOM    118  CA  THR    63       8.305   6.446  10.659  1.00  0.00              
ATOM    119  C   THR    63       8.123   6.689  12.160  1.00  0.00              
ATOM    120  O   THR    63       8.529   5.850  12.993  1.00  0.00              
ATOM    121  N   ASP    64       7.507   7.820  12.496  1.00  0.00              
ATOM    122  CA  ASP    64       7.279   8.210  13.896  1.00  0.00              
ATOM    123  C   ASP    64       6.318   7.309  14.630  1.00  0.00              
ATOM    124  O   ASP    64       6.240   7.370  15.863  1.00  0.00              
ATOM    125  N   ALA    65       5.549   6.496  13.900  1.00  0.00              
ATOM    126  CA  ALA    65       4.626   5.552  14.493  1.00  0.00              
ATOM    127  C   ALA    65       5.008   4.096  14.266  1.00  0.00              
ATOM    128  O   ALA    65       4.236   3.191  14.564  1.00  0.00              
ATOM    129  N   GLY    66       6.213   3.873  13.742  1.00  0.00              
ATOM    130  CA  GLY    66       6.741   2.538  13.541  1.00  0.00              
ATOM    131  C   GLY    66       6.121   1.721  12.420  1.00  0.00              
ATOM    132  O   GLY    66       6.111   0.504  12.489  1.00  0.00              
ATOM    133  N   LEU    67       5.568   2.394  11.407  1.00  0.00              
ATOM    134  CA  LEU    67       4.954   1.710  10.265  1.00  0.00              
ATOM    135  C   LEU    67       5.883   1.776   9.063  1.00  0.00              
ATOM    136  O   LEU    67       6.560   2.792   8.864  1.00  0.00              
END
