
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0283AL381_3-D1
# Molecule2: number of CA atoms   97 (  768),  selected   19 , name T0283_D1.pdb
# PARAMETERS: T0283AL381_3-D1.T0283_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:    19        75 - 93          3.46     3.46
  LCS_AVERAGE:     19.59

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        80 - 93          1.82     3.94
  LCS_AVERAGE:     12.81

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        81 - 92          0.69     4.70
  LCS_AVERAGE:     10.26

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:   97
LCS_GDT     V      75     V      75      7    8   19     5    6    7    7    8    9   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     T      76     T      76      7    8   19     5    5    7   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     D      77     D      77      7    8   19     5    6    7    7    8   12   12   15   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     L      78     L      78      7    8   19     5    6    7    7    8    8    8    8   10   11   14   19   19   19   19   19   19   19   19   19 
LCS_GDT     T      79     T      79      7    8   19     5    6    7    7    8    8    8    8   10   11   15   19   19   19   19   19   19   19   19   19 
LCS_GDT     G      80     G      80      7   14   19     4    6    7    7    8   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     E      81     E      81     12   14   19     5    9   12   12   13   14   14   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     D      82     D      82     12   14   19     6   11   12   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     V      83     V      83     12   14   19     8   11   12   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     A      84     A      84     12   14   19     8   11   12   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     A      85     A      85     12   14   19     8   11   12   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     F      86     F      86     12   14   19     8   11   12   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     C      87     C      87     12   14   19     8   11   12   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     D      88     D      88     12   14   19     8   11   12   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     E      89     E      89     12   14   19     8   11   12   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     L      90     L      90     12   14   19     8   11   12   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     M      91     M      91     12   14   19     8   11   12   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     K      92     K      92     12   14   19     8   11   12   12   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_GDT     D      93     D      93      3   14   19     3    3    4    9   13   14   15   16   16   17   17   19   19   19   19   19   19   19   19   19 
LCS_AVERAGE  LCS_A:  14.22  (  10.26   12.81   19.59 )

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     11     12     12     13     14     15     16     16     17     17     19     19     19     19     19     19     19     19     19 
GDT PERCENT_CA   8.25  11.34  12.37  12.37  13.40  14.43  15.46  16.49  16.49  17.53  17.53  19.59  19.59  19.59  19.59  19.59  19.59  19.59  19.59  19.59
GDT RMS_LOCAL    0.24   0.50   0.69   0.69   0.93   1.43   1.97   2.09   2.09   2.51   2.51   3.46   3.46   3.46   3.46   3.46   3.46   3.46   3.46   3.46
GDT RMS_ALL_CA   4.23   4.42   4.70   4.70   4.50   4.21   3.67   3.79   3.79   3.61   3.61   3.46   3.46   3.46   3.46   3.46   3.46   3.46   3.46   3.46

#      Molecule1      Molecule2       DISTANCE
LGA    V      75      V      75          3.942
LGA    T      76      T      76          2.227
LGA    D      77      D      77          6.947
LGA    L      78      L      78          9.653
LGA    T      79      T      79          7.708
LGA    G      80      G      80          3.807
LGA    E      81      E      81          3.338
LGA    D      82      D      82          1.903
LGA    V      83      V      83          1.100
LGA    A      84      A      84          0.825
LGA    A      85      A      85          0.759
LGA    F      86      F      86          1.089
LGA    C      87      C      87          0.966
LGA    D      88      D      88          1.154
LGA    E      89      E      89          1.189
LGA    L      90      L      90          1.405
LGA    M      91      M      91          1.420
LGA    K      92      K      92          0.949
LGA    D      93      D      93          3.133

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   97    4.0     16    2.09    14.948    14.754     0.731

LGA_LOCAL      RMSD =  2.089  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.788  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  3.458  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.854281 * X  +  -0.515180 * Y  +  -0.069235 * Z  +  -4.750912
  Y_new =  -0.517785 * X  +  -0.855119 * Y  +  -0.025901 * Z  +  41.281639
  Z_new =  -0.045861 * X  +   0.057976 * Y  +  -0.997264 * Z  +  17.842869 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.083523   -0.058070  [ DEG:   176.6729     -3.3272 ]
  Theta =   0.045877    3.095716  [ DEG:     2.6285    177.3715 ]
  Phi   =  -0.544897    2.596696  [ DEG:   -31.2203    148.7797 ]
 
# 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: T0283AL381_3-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0283AL381_3-D1.T0283_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19   97   4.0   16   2.09  14.754     3.46
REMARK  ---------------------------------------------------------- 
MOLECULE T0283AL381_3-D1
REMARK Aligment from pdb entry: 1qh8B
ATOM      1  N   VAL    75      18.640  32.913 -15.958  1.00  0.00              
ATOM      2  CA  VAL    75      17.185  33.150 -15.838  1.00  0.00              
ATOM      3  C   VAL    75      16.928  34.049 -14.633  1.00  0.00              
ATOM      4  O   VAL    75      16.143  35.018 -14.729  1.00  0.00              
ATOM      5  N   THR    76      17.477  33.684 -13.477  1.00  0.00              
ATOM      6  CA  THR    76      17.297  34.491 -12.267  1.00  0.00              
ATOM      7  C   THR    76      17.755  35.937 -12.479  1.00  0.00              
ATOM      8  O   THR    76      17.210  36.891 -11.871  1.00  0.00              
ATOM      9  N   ASP    77      18.894  36.135 -13.136  1.00  0.00              
ATOM     10  CA  ASP    77      19.414  37.466 -13.401  1.00  0.00              
ATOM     11  C   ASP    77      18.516  38.268 -14.320  1.00  0.00              
ATOM     12  O   ASP    77      18.254  39.454 -14.064  1.00  0.00              
ATOM     13  N   LEU    78      18.030  37.660 -15.407  1.00  0.00              
ATOM     14  CA  LEU    78      17.144  38.377 -16.319  1.00  0.00              
ATOM     15  C   LEU    78      15.875  38.824 -15.594  1.00  0.00              
ATOM     16  O   LEU    78      15.449  39.958 -15.834  1.00  0.00              
ATOM     17  N   THR    79      15.288  37.947 -14.804  1.00  0.00              
ATOM     18  CA  THR    79      14.051  38.297 -14.093  1.00  0.00              
ATOM     19  C   THR    79      14.282  39.196 -12.894  1.00  0.00              
ATOM     20  O   THR    79      13.328  39.800 -12.346  1.00  0.00              
ATOM     21  N   GLY    80      15.517  39.362 -12.438  1.00  0.00              
ATOM     22  CA  GLY    80      15.913  40.327 -11.435  1.00  0.00              
ATOM     23  C   GLY    80      15.564  39.969 -10.013  1.00  0.00              
ATOM     24  O   GLY    80      15.206  40.830  -9.179  1.00  0.00              
ATOM     25  N   GLU    81      15.608  38.676  -9.698  1.00  0.00              
ATOM     26  CA  GLU    81      15.348  38.240  -8.336  1.00  0.00              
ATOM     27  C   GLU    81      16.288  38.967  -7.375  1.00  0.00              
ATOM     28  O   GLU    81      17.520  38.924  -7.532  1.00  0.00              
ATOM     29  N   ASP    82      15.743  39.500  -6.281  1.00  0.00              
ATOM     30  CA  ASP    82      16.562  40.172  -5.269  1.00  0.00              
ATOM     31  C   ASP    82      17.106  39.198  -4.253  1.00  0.00              
ATOM     32  O   ASP    82      16.451  38.899  -3.250  1.00  0.00              
ATOM     33  N   VAL    83      18.268  38.597  -4.520  1.00  0.00              
ATOM     34  CA  VAL    83      18.852  37.582  -3.679  1.00  0.00              
ATOM     35  C   VAL    83      18.930  37.968  -2.215  1.00  0.00              
ATOM     36  O   VAL    83      18.563  37.193  -1.324  1.00  0.00              
ATOM     37  N   ALA    84      19.516  39.123  -1.920  1.00  0.00              
ATOM     38  CA  ALA    84      19.646  39.559  -0.539  1.00  0.00              
ATOM     39  C   ALA    84      18.322  39.533   0.230  1.00  0.00              
ATOM     40  O   ALA    84      18.229  38.947   1.317  1.00  0.00              
ATOM     41  N   ALA    85      17.303  40.123  -0.367  1.00  0.00              
ATOM     42  CA  ALA    85      15.954  40.183   0.204  1.00  0.00              
ATOM     43  C   ALA    85      15.322  38.814   0.328  1.00  0.00              
ATOM     44  O   ALA    85      14.856  38.423   1.402  1.00  0.00              
ATOM     45  N   PHE    86      15.517  37.929  -0.678  1.00  0.00              
ATOM     46  CA  PHE    86      14.955  36.588  -0.519  1.00  0.00              
ATOM     47  C   PHE    86      15.552  35.818   0.634  1.00  0.00              
ATOM     48  O   PHE    86      14.907  35.080   1.377  1.00  0.00              
ATOM     49  N   CYS    87      16.891  35.890   0.793  1.00  0.00              
ATOM     50  CA  CYS    87      17.611  35.201   1.839  1.00  0.00              
ATOM     51  C   CYS    87      17.243  35.751   3.228  1.00  0.00              
ATOM     52  O   CYS    87      16.913  34.916   4.068  1.00  0.00              
ATOM     53  N   ASP    88      17.056  37.066   3.298  1.00  0.00              
ATOM     54  CA  ASP    88      16.558  37.624   4.570  1.00  0.00              
ATOM     55  C   ASP    88      15.151  37.128   4.884  1.00  0.00              
ATOM     56  O   ASP    88      14.925  36.726   6.024  1.00  0.00              
ATOM     57  N   GLU    89      14.290  37.130   3.877  1.00  0.00              
ATOM     58  CA  GLU    89      12.928  36.637   4.040  1.00  0.00              
ATOM     59  C   GLU    89      12.878  35.166   4.414  1.00  0.00              
ATOM     60  O   GLU    89      12.194  34.755   5.365  1.00  0.00              
ATOM     61  N   LEU    90      13.736  34.299   3.829  1.00  0.00              
ATOM     62  CA  LEU    90      13.806  32.908   4.245  1.00  0.00              
ATOM     63  C   LEU    90      14.125  32.711   5.715  1.00  0.00              
ATOM     64  O   LEU    90      13.710  31.739   6.364  1.00  0.00              
ATOM     65  N   MET    91      15.076  33.469   6.267  1.00  0.00              
ATOM     66  CA  MET    91      15.505  33.334   7.650  1.00  0.00              
ATOM     67  C   MET    91      14.437  33.873   8.623  1.00  0.00              
ATOM     68  O   MET    91      14.098  33.242   9.615  1.00  0.00              
ATOM     69  N   LYS    92      13.830  34.971   8.206  1.00  0.00              
ATOM     70  CA  LYS    92      12.779  35.589   9.038  1.00  0.00              
ATOM     71  C   LYS    92      11.537  34.718   9.085  1.00  0.00              
ATOM     72  O   LYS    92      10.998  34.463  10.180  1.00  0.00              
ATOM     73  N   ASP    93      11.251  34.017   7.983  1.00  0.00              
ATOM     74  CA  ASP    93      10.071  33.156   7.912  1.00  0.00              
ATOM     75  C   ASP    93      10.335  31.757   8.412  1.00  0.00              
ATOM     76  O   ASP    93       9.414  30.952   8.476  1.00  0.00              
END
