
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0363AL242_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   26 , name T0363_D1.pdb
# PARAMETERS: T0363AL242_5-D1.T0363_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:    26        11 - 56          4.53     4.53
  LCS_AVERAGE:     56.52

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        12 - 48          1.93     5.95
  LONGEST_CONTINUOUS_SEGMENT:    17        33 - 49          1.81     5.91
  LCS_AVERAGE:     30.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        33 - 45          0.98     6.35
  LCS_AVERAGE:     20.15

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:   46
LCS_GDT     N      11     N      11      3    5   26     2    4    4    4    4    4    5    5    6    8    8   12   21   21   21   21   22   24   24   24 
LCS_GDT     Q      12     Q      12      3   17   26     1    4    4    4    7   11   16   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     D      33     D      33     13   17   26     4    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     E      34     E      34     13   17   26     3    4    8   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     G      35     G      35     13   17   26     6    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     I      36     I      36     13   17   26     6    8   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     T      37     T      37     13   17   26     6    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     V      38     V      38     13   17   26     7    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     Q      39     Q      39     13   17   26     7    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     T      40     T      40     13   17   26     7    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     A      41     A      41     13   17   26     7    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     I      42     I      42     13   17   26     7    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     T      43     T      43     13   17   26     7    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     Q      44     Q      44     13   17   26     7    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     S      45     S      45     13   17   26     6    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     G      46     G      46     12   17   26     5    9   12   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     I      47     I      47     11   17   26     5    5   11   14   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     L      48     L      48      7   17   26     5    5    8   11   14   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     S      49     S      49      6   17   26     4    4    8   11   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     Q      50     Q      50      6   16   26     4    4    8   11   13   15   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     F      51     F      51      4   14   26     3    3    4   11   15   18   19   20   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     P      52     P      52      4    5   26     3    3    4    6    6   11   13   16   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     E      53     E      53      4    5   26     4    4    4    6    8   11   13   15   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     I      54     I      54      4    5   26     4    4    4    6    8   11   13   15   20   23   23   23   24   25   25   25   25   25   25   25 
LCS_GDT     D      55     D      55      4    5   26     4    4    4    4    6   10   12   15   17   17   20   23   24   25   25   25   25   25   25   25 
LCS_GDT     L      56     L      56      4    5   26     4    4    4    4    5    7   11   15   17   17   17   23   24   25   25   25   25   25   25   25 
LCS_AVERAGE  LCS_A:  35.76  (  20.15   30.60   56.52 )

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      9     12     14     15     18     19     20     20     23     23     23     24     25     25     25     25     25     25     25 
GDT PERCENT_CA  15.22  19.57  26.09  30.43  32.61  39.13  41.30  43.48  43.48  50.00  50.00  50.00  52.17  54.35  54.35  54.35  54.35  54.35  54.35  54.35
GDT RMS_LOCAL    0.29   0.43   0.81   1.09   1.29   1.99   2.13   2.32   2.32   3.38   3.38   3.38   3.80   4.05   4.05   4.05   4.05   4.05   4.05   4.05
GDT RMS_ALL_CA   7.50   7.48   6.57   6.22   6.19   5.79   5.79   5.62   5.62   4.74   4.74   4.74   4.58   4.59   4.59   4.59   4.59   4.59   4.59   4.59

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          8.589
LGA    Q      12      Q      12          3.870
LGA    D      33      D      33          1.169
LGA    E      34      E      34          2.045
LGA    G      35      G      35          0.794
LGA    I      36      I      36          1.577
LGA    T      37      T      37          1.707
LGA    V      38      V      38          1.816
LGA    Q      39      Q      39          2.223
LGA    T      40      T      40          1.679
LGA    A      41      A      41          1.228
LGA    I      42      I      42          2.201
LGA    T      43      T      43          3.564
LGA    Q      44      Q      44          3.862
LGA    S      45      S      45          2.685
LGA    G      46      G      46          1.871
LGA    I      47      I      47          1.307
LGA    L      48      L      48          2.843
LGA    S      49      S      49          1.824
LGA    Q      50      Q      50          3.130
LGA    F      51      F      51          2.663
LGA    P      52      P      52          7.929
LGA    E      53      E      53          9.352
LGA    I      54      I      54          9.221
LGA    D      55      D      55         13.579
LGA    L      56      L      56         13.541

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26   46    4.0     20    2.32    36.957    37.094     0.826

LGA_LOCAL      RMSD =  2.320  Number of atoms =   20  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.509  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  4.535  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.417496 * X  +   0.805333 * Y  +   0.420875 * Z  +  37.012924
  Y_new =   0.200732 * X  +   0.369992 * Y  +  -0.907090 * Z  +  59.726189
  Z_new =  -0.886230 * X  +   0.463190 * Y  +  -0.007186 * Z  + -30.816479 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.586309   -1.555283  [ DEG:    90.8888    -89.1112 ]
  Theta =   1.089142    2.052450  [ DEG:    62.4033    117.5967 ]
  Phi   =   0.448169   -2.693423  [ DEG:    25.6782   -154.3218 ]
 
# 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: T0363AL242_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL242_5-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26   46   4.0   20   2.32  37.094     4.53
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL242_5-D1
REMARK Aligment from pdb entry: 1tyg_B
ATOM     41  N   ASN    11      18.248   6.922   6.777  1.00  0.00              
ATOM     42  CA  ASN    11      19.641   6.661   7.224  1.00  0.00              
ATOM     43  C   ASN    11      19.938   5.250   7.762  1.00  0.00              
ATOM     44  O   ASN    11      19.423   4.867   8.803  1.00  0.00              
ATOM     45  N   GLN    12      20.833   4.515   7.110  1.00  0.00              
ATOM     46  CA  GLN    12      20.882   3.059   7.279  1.00  0.00              
ATOM     47  C   GLN    12      20.536   2.473   8.657  1.00  0.00              
ATOM     48  O   GLN    12      19.658   1.594   8.736  1.00  0.00              
ATOM     49  N   ASP    33      21.204   2.935   9.722  1.00  0.00              
ATOM     50  CA  ASP    33      21.123   2.253  11.031  1.00  0.00              
ATOM     51  C   ASP    33      20.595   3.075  12.233  1.00  0.00              
ATOM     52  O   ASP    33      20.333   4.266  12.121  1.00  0.00              
ATOM     53  N   GLU    34      20.466   2.393  13.368  1.00  0.00              
ATOM     54  CA  GLU    34      19.989   2.904  14.660  1.00  0.00              
ATOM     55  C   GLU    34      20.717   4.134  15.226  1.00  0.00              
ATOM     56  O   GLU    34      20.077   5.081  15.701  1.00  0.00              
ATOM     57  N   GLY    35      22.048   4.084  15.239  1.00  0.00              
ATOM     58  CA  GLY    35      22.862   5.193  15.741  1.00  0.00              
ATOM     59  C   GLY    35      23.870   5.669  14.700  1.00  0.00              
ATOM     60  O   GLY    35      24.109   4.994  13.693  1.00  0.00              
ATOM     61  N   ILE    36      24.468   6.831  14.949  1.00  0.00              
ATOM     62  CA  ILE    36      25.478   7.345  14.040  1.00  0.00              
ATOM     63  C   ILE    36      26.067   8.685  14.407  1.00  0.00              
ATOM     64  O   ILE    36      25.553   9.358  15.297  1.00  0.00              
ATOM     65  N   THR    37      27.155   9.040  13.716  1.00  0.00              
ATOM     66  CA  THR    37      27.894  10.301  13.911  1.00  0.00              
ATOM     67  C   THR    37      28.142  11.033  12.590  1.00  0.00              
ATOM     68  O   THR    37      28.308  10.400  11.548  1.00  0.00              
ATOM     69  N   VAL    38      28.196  12.360  12.627  1.00  0.00              
ATOM     70  CA  VAL    38      28.480  13.119  11.408  1.00  0.00              
ATOM     71  C   VAL    38      29.561  12.464  10.526  1.00  0.00              
ATOM     72  O   VAL    38      29.483  12.506   9.287  1.00  0.00              
ATOM     73  N   GLN    39      30.561  11.854  11.153  1.00  0.00              
ATOM     74  CA  GLN    39      31.571  11.174  10.374  1.00  0.00              
ATOM     75  C   GLN    39      30.974   9.963   9.636  1.00  0.00              
ATOM     76  O   GLN    39      31.046   9.922   8.402  1.00  0.00              
ATOM     77  N   THR    40      30.326   9.041  10.361  1.00  0.00              
ATOM     78  CA  THR    40      29.666   7.844   9.762  1.00  0.00              
ATOM     79  C   THR    40      28.899   8.188   8.493  1.00  0.00              
ATOM     80  O   THR    40      28.881   7.411   7.516  1.00  0.00              
ATOM     81  N   ALA    41      28.254   9.359   8.557  1.00  0.00              
ATOM     82  CA  ALA    41      27.376   9.858   7.519  1.00  0.00              
ATOM     83  C   ALA    41      28.181  10.255   6.284  1.00  0.00              
ATOM     84  O   ALA    41      27.869   9.783   5.194  1.00  0.00              
ATOM     85  N   ILE    42      29.214  11.086   6.453  1.00  0.00              
ATOM     86  CA  ILE    42      30.097  11.471   5.344  1.00  0.00              
ATOM     87  C   ILE    42      30.742  10.257   4.675  1.00  0.00              
ATOM     88  O   ILE    42      30.817  10.166   3.452  1.00  0.00              
ATOM     89  N   THR    43      31.201   9.324   5.495  1.00  0.00              
ATOM     90  CA  THR    43      31.644   8.032   5.008  1.00  0.00              
ATOM     91  C   THR    43      30.646   7.352   4.035  1.00  0.00              
ATOM     92  O   THR    43      30.943   7.176   2.850  1.00  0.00              
ATOM     93  N   GLN    44      29.465   6.981   4.518  1.00  0.00              
ATOM     94  CA  GLN    44      28.469   6.338   3.662  1.00  0.00              
ATOM     95  C   GLN    44      28.183   7.029   2.313  1.00  0.00              
ATOM     96  O   GLN    44      27.732   6.378   1.375  1.00  0.00              
ATOM     97  N   SER    45      28.429   8.338   2.226  1.00  0.00              
ATOM     98  CA  SER    45      28.182   9.119   1.003  1.00  0.00              
ATOM     99  C   SER    45      29.469   9.490   0.284  1.00  0.00              
ATOM    100  O   SER    45      29.427  10.233  -0.707  1.00  0.00              
ATOM    101  N   GLY    46      30.590   8.989   0.818  1.00  0.00              
ATOM    102  CA  GLY    46      31.941   9.054   0.222  1.00  0.00              
ATOM    103  C   GLY    46      32.626  10.405   0.262  1.00  0.00              
ATOM    104  O   GLY    46      33.391  10.725  -0.635  1.00  0.00              
ATOM    105  N   ILE    47      32.355  11.173   1.313  1.00  0.00              
ATOM    106  CA  ILE    47      32.806  12.573   1.439  1.00  0.00              
ATOM    107  C   ILE    47      33.895  12.771   2.499  1.00  0.00              
ATOM    108  O   ILE    47      34.206  13.894   2.900  1.00  0.00              
ATOM    109  N   LEU    48      34.463  11.653   2.936  1.00  0.00              
ATOM    110  CA  LEU    48      35.467  11.629   3.979  1.00  0.00              
ATOM    111  C   LEU    48      36.733  12.308   3.479  1.00  0.00              
ATOM    112  O   LEU    48      37.393  13.013   4.245  1.00  0.00              
ATOM    113  N   SER    49      37.048  12.139   2.192  1.00  0.00              
ATOM    114  CA  SER    49      38.249  12.749   1.608  1.00  0.00              
ATOM    115  C   SER    49      37.999  14.013   0.739  1.00  0.00              
ATOM    116  O   SER    49      38.690  14.270  -0.259  1.00  0.00              
ATOM    117  N   GLN    50      37.022  14.812   1.160  1.00  0.00              
ATOM    118  CA  GLN    50      36.555  15.963   0.401  1.00  0.00              
ATOM    119  C   GLN    50      36.319  17.084   1.377  1.00  0.00              
ATOM    120  O   GLN    50      35.799  16.853   2.471  1.00  0.00              
ATOM    121  N   PHE    51      36.679  18.301   0.988  1.00  0.00              
ATOM    122  CA  PHE    51      36.462  19.454   1.835  1.00  0.00              
ATOM    123  C   PHE    51      35.011  19.673   1.709  1.00  0.00              
ATOM    124  O   PHE    51      34.541  19.783   0.589  1.00  0.00              
ATOM    125  N   PRO    52      34.291  19.677   2.831  1.00  0.00              
ATOM    126  CA  PRO    52      32.859  20.059   2.874  1.00  0.00              
ATOM    127  C   PRO    52      32.621  20.733   4.195  1.00  0.00              
ATOM    128  O   PRO    52      33.380  20.536   5.121  1.00  0.00              
ATOM    129  N   GLU    53      31.586  21.538   4.306  1.00  0.00              
ATOM    130  CA  GLU    53      31.228  22.110   5.620  1.00  0.00              
ATOM    131  C   GLU    53      29.901  21.465   6.000  1.00  0.00              
ATOM    132  O   GLU    53      29.044  21.311   5.128  1.00  0.00              
ATOM    133  N   ILE    54      29.705  21.074   7.260  1.00  0.00              
ATOM    134  CA  ILE    54      28.419  20.420   7.636  1.00  0.00              
ATOM    135  C   ILE    54      27.613  21.173   8.676  1.00  0.00              
ATOM    136  O   ILE    54      28.127  21.478   9.753  1.00  0.00              
ATOM    137  N   ASP    55      26.352  21.478   8.385  1.00  0.00              
ATOM    138  CA  ASP    55      25.513  22.035   9.458  1.00  0.00              
ATOM    139  C   ASP    55      24.379  21.096   9.856  1.00  0.00              
ATOM    140  O   ASP    55      23.855  20.370   9.005  1.00  0.00              
ATOM    141  N   LEU    56      24.031  21.090  11.145  1.00  0.00              
ATOM    142  CA  LEU    56      23.090  20.119  11.715  1.00  0.00              
ATOM    143  C   LEU    56      22.149  20.892  12.600  1.00  0.00              
ATOM    144  O   LEU    56      22.574  21.436  13.625  1.00  0.00              
END
