
#######################################################
#                                                     #
#                        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   34 (  136),  selected   33 , name T0351AL381_5
# Molecule2: number of CA atoms   56 (  935),  selected   33 , name T0351.pdb
# PARAMETERS: T0351AL381_5.T0351.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:    16        24 - 39          4.77    19.09
  LCS_AVERAGE:     26.24

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        43 - 55          1.47    15.62
  LCS_AVERAGE:     16.34

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        43 - 54          0.64    14.62
  LCS_AVERAGE:     12.39

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:   56
LCS_GDT     N      24     N      24      3    8   16     3    3    5    5    7    8   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     D      25     D      25      4    8   16     3    3    5    5    6    9   10   12   13   15   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     G      26     G      26      4    8   16     3    3    5    5    7    8    8   11   12   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     N      27     N      27      4    8   16     3    3    5    5    7    8    8   11   12   12   13   14   19   19   21   21   22   22   23   24 
LCS_GDT     G      28     G      28      5    8   16     3    5    5    5    7    8    8   11   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     S      29     S      29      5    8   16     3    5    8   10   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     Y      30     Y      30      5    8   16     3    5    5   10   11   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     I      31     I      31      5    8   16     3    5    5    5    7    8    8   11   15   16   17   19   19   20   21   21   22   22   23   24 
LCS_GDT     E      32     E      32      5    6   16     3    5    5    5    6    8    9   11   12   12   13   14   15   15   16   21   22   22   23   24 
LCS_GDT     K      33     K      33      4    6   16     3    4    4    5    6    8    9   11   12   12   13   14   15   15   16   19   21   22   23   24 
LCS_GDT     W      34     W      34      4    6   16     3    4    4    4    5    8    9   11   12   12   13   14   15   15   16   16   19   20   22   24 
LCS_GDT     N      35     N      35      4    6   16     3    4    4    5    6    8    9   10   12   12   13   14   15   15   16   16   17   17   21   22 
LCS_GDT     L      36     L      36      3    6   16     3    3    3    5    6    8    9    9   12   12   13   15   17   17   18   18   20   21   21   23 
LCS_GDT     R      37     R      37      4    6   16     3    4    4    5    6    8    9    9   10   12   13   15   17   17   18   18   20   21   21   23 
LCS_GDT     A      38     A      38      4    6   16     3    4    4    5    5    8    9    9   10   12   13   15   17   17   18   18   20   21   21   23 
LCS_GDT     P      39     P      39      4    6   16     3    4    4    5    5    6    7    9   10   12   13   15   17   17   18   18   20   21   21   23 
LCS_GDT     L      40     L      40      4    6   15     3    4    4    4    5    6    7    8    8    8    8   10   13   15   16   17   20   21   21   23 
LCS_GDT     P      41     P      41      4    6    9     3    3    4    4    4    6    7    8    8    8    8    8    8    8    9   10   10   10   16   17 
LCS_GDT     T      42     T      42      4    6    9     3    3    4    5    5    6    7    8    8    8    8    8    8    8    9   10   10   10   10   11 
LCS_GDT     Q      43     Q      43     12   13   14     9   11   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     A      44     A      44     12   13   14     7   11   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     E      45     E      45     12   13   14     9   11   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     L      46     L      46     12   13   14     9   11   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     E      47     E      47     12   13   14     9   11   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     T      48     T      48     12   13   14     9   11   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     W      49     W      49     12   13   14     9   11   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     W      50     W      50     12   13   14     9   11   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     E      51     E      51     12   13   14     9   11   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     E      52     E      52     12   13   14     9   11   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     L      53     L      53     12   13   14     8   11   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     Q      54     Q      54     12   13   14     4    9   12   12   13   13   14   15   15   16   18   19   19   20   21   21   22   22   23   24 
LCS_GDT     K      55     K      55      3   13   14     3    3    4    4    5   12   12   13   13   13   16   17   19   20   21   21   22   22   23   24 
LCS_GDT     N      56     N      56      3    3   14     3    3    4    4    4    4    6    6    9    9   13   14   14   14   14   17   20   22   23   23 
LCS_AVERAGE  LCS_A:  18.33  (  12.39   16.34   26.24 )

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     11     12     12     13     13     14     15     15     16     18     19     19     20     21     21     22     22     23     24 
GDT PERCENT_CA  16.07  19.64  21.43  21.43  23.21  23.21  25.00  26.79  26.79  28.57  32.14  33.93  33.93  35.71  37.50  37.50  39.29  39.29  41.07  42.86
GDT RMS_LOCAL    0.38   0.44   0.64   0.64   1.25   1.25   1.64   2.09   2.09   2.43   3.30   3.45   3.45   3.73   4.07   4.07   4.42   4.42   4.79   5.56
GDT RMS_ALL_CA  14.95  14.95  14.62  14.62  13.59  13.59  13.41  13.13  13.13  13.42  13.10  13.36  13.36  13.40  13.58  13.58  13.48  13.48  13.82  12.21

#      Molecule1      Molecule2       DISTANCE
LGA    N      24      N      24          3.746
LGA    D      25      D      25          7.532
LGA    G      26      G      26          8.452
LGA    N      27      N      27         11.194
LGA    G      28      G      28          6.765
LGA    S      29      S      29          3.459
LGA    Y      30      Y      30          1.634
LGA    I      31      I      31          4.990
LGA    E      32      E      32          8.176
LGA    K      33      K      33         11.296
LGA    W      34      W      34         14.080
LGA    N      35      N      35         20.195
LGA    L      36      L      36         21.268
LGA    R      37      R      37         26.280
LGA    A      38      A      38         26.265
LGA    P      39      P      39         26.958
LGA    L      40      L      40         24.993
LGA    P      41      P      41         27.414
LGA    T      42      T      42         24.466
LGA    Q      43      Q      43          2.594
LGA    A      44      A      44          1.608
LGA    E      45      E      45          2.719
LGA    L      46      L      46          2.621
LGA    E      47      E      47          1.428
LGA    T      48      T      48          0.846
LGA    W      49      W      49          0.984
LGA    W      50      W      50          1.630
LGA    E      51      E      51          1.958
LGA    E      52      E      52          1.387
LGA    L      53      L      53          1.428
LGA    Q      54      Q      54          1.769
LGA    K      55      K      55          8.332
LGA    N      56      N      56         12.016

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34   56    4.0     15    2.09    26.339    24.034     0.686

LGA_LOCAL      RMSD =  2.088  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.419  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  9.154  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.996719 * X  +  -0.080138 * Y  +  -0.011355 * Z  +  -9.440813
  Y_new =  -0.069327 * X  +   0.772883 * Y  +   0.630750 * Z  +  -6.261343
  Z_new =  -0.041771 * X  +   0.629467 * Y  +  -0.775903 * Z  +  -1.597329 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.460017   -0.681575  [ DEG:   140.9486    -39.0514 ]
  Theta =   0.041783    3.099810  [ DEG:     2.3940    177.6060 ]
  Phi   =  -3.072149    0.069444  [ DEG:  -176.0212      3.9788 ]
 
# 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: T0351AL381_5                                  
REMARK     2: T0351.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0351AL381_5.T0351.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34   56   4.0   15   2.09  24.034     9.15
REMARK  ---------------------------------------------------------- 
MOLECULE T0351AL381_5
REMARK Aligment from pdb entry: 1emwA
ATOM      1  N   ASN    24     -12.430   1.433  11.548  1.00  0.00              
ATOM      2  CA  ASN    24     -12.554   2.898  11.298  1.00  0.00              
ATOM      3  C   ASN    24     -12.589   3.654  12.630  1.00  0.00              
ATOM      4  O   ASN    24     -12.714   3.066  13.686  1.00  0.00              
ATOM      5  N   ASP    25     -12.479   4.953  12.589  1.00  0.00              
ATOM      6  CA  ASP    25     -12.505   5.742  13.853  1.00  0.00              
ATOM      7  C   ASP    25     -13.553   6.856  13.756  1.00  0.00              
ATOM      8  O   ASP    25     -14.439   6.962  14.582  1.00  0.00              
ATOM      9  N   GLY    26     -13.461   7.683  12.751  1.00  0.00              
ATOM     10  CA  GLY    26     -14.453   8.784  12.601  1.00  0.00              
ATOM     11  C   GLY    26     -15.186   8.650  11.263  1.00  0.00              
ATOM     12  O   GLY    26     -16.396   8.732  11.195  1.00  0.00              
ATOM     13  N   ASN    27     -14.458   8.441  10.200  1.00  0.00              
ATOM     14  CA  ASN    27     -15.111   8.300   8.866  1.00  0.00              
ATOM     15  C   ASN    27     -14.732   6.960   8.225  1.00  0.00              
ATOM     16  O   ASN    27     -15.490   6.387   7.469  1.00  0.00              
ATOM     17  N   GLY    28     -13.564   6.455   8.521  1.00  0.00              
ATOM     18  CA  GLY    28     -13.139   5.155   7.927  1.00  0.00              
ATOM     19  C   GLY    28     -12.259   5.425   6.707  1.00  0.00              
ATOM     20  O   GLY    28     -12.727   5.872   5.679  1.00  0.00              
ATOM     21  N   SER    29     -10.985   5.158   6.812  1.00  0.00              
ATOM     22  CA  SER    29     -10.079   5.405   5.653  1.00  0.00              
ATOM     23  C   SER    29      -9.068   4.262   5.510  1.00  0.00              
ATOM     24  O   SER    29      -8.668   3.647   6.477  1.00  0.00              
ATOM     25  N   TYR    30      -8.659   3.975   4.304  1.00  0.00              
ATOM     26  CA  TYR    30      -7.676   2.872   4.084  1.00  0.00              
ATOM     27  C   TYR    30      -6.404   3.411   3.428  1.00  0.00              
ATOM     28  O   TYR    30      -6.377   4.507   2.905  1.00  0.00              
ATOM     29  N   ILE    31      -5.353   2.639   3.448  1.00  0.00              
ATOM     30  CA  ILE    31      -4.080   3.092   2.819  1.00  0.00              
ATOM     31  C   ILE    31      -4.178   2.947   1.297  1.00  0.00              
ATOM     32  O   ILE    31      -3.489   3.617   0.554  1.00  0.00              
ATOM     33  N   GLU    32      -5.031   2.078   0.831  1.00  0.00              
ATOM     34  CA  GLU    32      -5.177   1.887  -0.641  1.00  0.00              
ATOM     35  C   GLU    32      -6.309   0.899  -0.931  1.00  0.00              
ATOM     36  O   GLU    32      -6.753   0.178  -0.061  1.00  0.00              
ATOM     37  N   LYS    33      -6.775   0.855  -2.149  1.00  0.00              
ATOM     38  CA  LYS    33      -7.874  -0.095  -2.492  1.00  0.00              
ATOM     39  C   LYS    33      -7.323  -1.223  -3.369  1.00  0.00              
ATOM     40  O   LYS    33      -6.863  -0.997  -4.470  1.00  0.00              
ATOM     41  N   TRP    34      -7.352  -2.435  -2.885  1.00  0.00              
ATOM     42  CA  TRP    34      -6.812  -3.571  -3.693  1.00  0.00              
ATOM     43  C   TRP    34      -7.929  -4.443  -4.236  1.00  0.00              
ATOM     44  O   TRP    34      -7.845  -4.965  -5.331  1.00  0.00              
ATOM     45  N   ASN    35      -8.954  -4.641  -3.472  1.00  0.00              
ATOM     46  CA  ASN    35     -10.039  -5.519  -3.944  1.00  0.00              
ATOM     47  C   ASN    35     -11.370  -4.789  -3.986  1.00  0.00              
ATOM     48  O   ASN    35     -11.530  -3.698  -3.477  1.00  0.00              
ATOM     49  N   LEU    36     -12.336  -5.434  -4.559  1.00  0.00              
ATOM     50  CA  LEU    36     -13.712  -4.865  -4.627  1.00  0.00              
ATOM     51  C   LEU    36     -14.701  -5.999  -4.370  1.00  0.00              
ATOM     52  O   LEU    36     -14.494  -7.113  -4.810  1.00  0.00              
ATOM     53  N   ARG    37     -15.769  -5.747  -3.664  1.00  0.00              
ATOM     54  CA  ARG    37     -16.731  -6.853  -3.404  1.00  0.00              
ATOM     55  C   ARG    37     -18.175  -6.379  -3.620  1.00  0.00              
ATOM     56  O   ARG    37     -18.532  -5.268  -3.281  1.00  0.00              
ATOM     57  N   ALA    38     -19.010  -7.224  -4.159  1.00  0.00              
ATOM     58  CA  ALA    38     -20.434  -6.837  -4.371  1.00  0.00              
ATOM     59  C   ALA    38     -21.343  -8.033  -4.054  1.00  0.00              
ATOM     60  O   ALA    38     -21.417  -8.970  -4.818  1.00  0.00              
ATOM     61  N   PRO    39     -22.005  -7.978  -2.931  1.00  0.00              
ATOM     62  CA  PRO    39     -22.893  -9.097  -2.542  1.00  0.00              
ATOM     63  C   PRO    39     -24.148  -9.124  -3.420  1.00  0.00              
ATOM     64  O   PRO    39     -25.238  -8.826  -2.973  1.00  0.00              
ATOM     65  N   LEU    40     -24.006  -9.482  -4.668  1.00  0.00              
ATOM     66  CA  LEU    40     -25.188  -9.531  -5.569  1.00  0.00              
ATOM     67  C   LEU    40     -25.675 -10.974  -5.721  1.00  0.00              
ATOM     68  O   LEU    40     -24.903 -11.874  -5.988  1.00  0.00              
ATOM     69  N   PRO    41     -26.948 -11.202  -5.550  1.00  0.00              
ATOM     70  CA  PRO    41     -27.480 -12.588  -5.683  1.00  0.00              
ATOM     71  C   PRO    41     -28.058 -12.807  -7.084  1.00  0.00              
ATOM     72  O   PRO    41     -29.104 -13.403  -7.247  1.00  0.00              
ATOM     73  N   THR    42     -27.386 -12.333  -8.098  1.00  0.00              
ATOM     74  CA  THR    42     -27.901 -12.518  -9.486  1.00  0.00              
ATOM     75  C   THR    42     -26.980 -13.460 -10.266  1.00  0.00              
ATOM     76  O   THR    42     -27.358 -14.558 -10.625  1.00  0.00              
ATOM     77  N   GLN    43      -7.498  -6.918  -7.432  1.00  0.00              
ATOM     78  CA  GLN    43      -6.215  -6.804  -8.154  1.00  0.00              
ATOM     79  C   GLN    43      -5.197  -7.589  -7.335  1.00  0.00              
ATOM     80  O   GLN    43      -4.359  -7.014  -6.670  1.00  0.00              
ATOM     81  N   ALA    44      -5.316  -8.903  -7.335  1.00  0.00              
ATOM     82  CA  ALA    44      -4.403  -9.777  -6.516  1.00  0.00              
ATOM     83  C   ALA    44      -2.980  -9.200  -6.448  1.00  0.00              
ATOM     84  O   ALA    44      -2.301  -9.363  -5.460  1.00  0.00              
ATOM     85  N   GLU    45      -2.532  -8.506  -7.458  1.00  0.00              
ATOM     86  CA  GLU    45      -1.169  -7.918  -7.375  1.00  0.00              
ATOM     87  C   GLU    45      -1.124  -6.947  -6.197  1.00  0.00              
ATOM     88  O   GLU    45      -0.308  -7.070  -5.306  1.00  0.00              
ATOM     89  N   LEU    46      -2.017  -5.998  -6.174  1.00  0.00              
ATOM     90  CA  LEU    46      -2.057  -5.036  -5.044  1.00  0.00              
ATOM     91  C   LEU    46      -2.562  -5.761  -3.797  1.00  0.00              
ATOM     92  O   LEU    46      -2.068  -5.571  -2.704  1.00  0.00              
ATOM     93  N   GLU    47      -3.528  -6.621  -3.960  1.00  0.00              
ATOM     94  CA  GLU    47      -4.042  -7.379  -2.800  1.00  0.00              
ATOM     95  C   GLU    47      -2.924  -8.306  -2.298  1.00  0.00              
ATOM     96  O   GLU    47      -2.945  -8.770  -1.172  1.00  0.00              
ATOM     97  N   THR    48      -1.922  -8.545  -3.119  1.00  0.00              
ATOM     98  CA  THR    48      -0.792  -9.399  -2.683  1.00  0.00              
ATOM     99  C   THR    48       0.261  -8.533  -1.976  1.00  0.00              
ATOM    100  O   THR    48       1.014  -8.999  -1.145  1.00  0.00              
ATOM    101  N   TRP    49       0.297  -7.263  -2.295  1.00  0.00              
ATOM    102  CA  TRP    49       1.267  -6.340  -1.647  1.00  0.00              
ATOM    103  C   TRP    49       0.992  -6.344  -0.161  1.00  0.00              
ATOM    104  O   TRP    49       1.870  -6.386   0.679  1.00  0.00              
ATOM    105  N   TRP    50      -0.253  -6.266   0.137  1.00  0.00              
ATOM    106  CA  TRP    50      -0.696  -6.224   1.542  1.00  0.00              
ATOM    107  C   TRP    50      -0.465  -7.565   2.201  1.00  0.00              
ATOM    108  O   TRP    50       0.235  -7.668   3.189  1.00  0.00              
ATOM    109  N   GLU    51      -0.998  -8.603   1.646  1.00  0.00              
ATOM    110  CA  GLU    51      -0.751  -9.949   2.230  1.00  0.00              
ATOM    111  C   GLU    51       0.766 -10.149   2.362  1.00  0.00              
ATOM    112  O   GLU    51       1.234 -10.939   3.159  1.00  0.00              
ATOM    113  N   GLU    52       1.537  -9.422   1.584  1.00  0.00              
ATOM    114  CA  GLU    52       3.016  -9.550   1.666  1.00  0.00              
ATOM    115  C   GLU    52       3.565  -8.705   2.825  1.00  0.00              
ATOM    116  O   GLU    52       4.636  -8.968   3.334  1.00  0.00              
ATOM    117  N   LEU    53       2.844  -7.696   3.257  1.00  0.00              
ATOM    118  CA  LEU    53       3.346  -6.865   4.381  1.00  0.00              
ATOM    119  C   LEU    53       2.681  -7.310   5.685  1.00  0.00              
ATOM    120  O   LEU    53       2.438  -6.523   6.578  1.00  0.00              
ATOM    121  N   GLN    54       2.392  -8.572   5.788  1.00  0.00              
ATOM    122  CA  GLN    54       1.744  -9.095   7.023  1.00  0.00              
ATOM    123  C   GLN    54       0.315  -8.557   7.127  1.00  0.00              
ATOM    124  O   GLN    54      -0.217  -8.397   8.207  1.00  0.00              
ATOM    125  N   LYS    55      -0.317  -8.282   6.015  1.00  0.00              
ATOM    126  CA  LYS    55      -1.711  -7.762   6.068  1.00  0.00              
ATOM    127  C   LYS    55      -2.664  -8.880   6.495  1.00  0.00              
ATOM    128  O   LYS    55      -2.678  -9.948   5.916  1.00  0.00              
ATOM    129  N   ASN    56      -3.460  -8.645   7.499  1.00  0.00              
ATOM    130  CA  ASN    56      -4.405  -9.702   7.952  1.00  0.00              
ATOM    131  C   ASN    56      -5.798  -9.465   7.348  1.00  0.00              
ATOM    132  O   ASN    56      -6.469  -8.517   7.706  1.00  0.00              
ATOM    133  N   PRO    57      -6.191 -10.333   6.446  1.00  0.00              
ATOM    134  CA  PRO    57      -7.515 -10.203   5.805  1.00  0.00              
ATOM    135  C   PRO    57      -8.589 -10.876   6.665  1.00  0.00              
ATOM    136  O   PRO    57      -8.449 -12.016   7.064  1.00  0.00              
END
