
#######################################################
#                                                     #
#                        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   16 (   64),  selected   16 , name T0283AL381_4-D1
# Molecule2: number of CA atoms   97 (  768),  selected   16 , name T0283_D1.pdb
# PARAMETERS: T0283AL381_4-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:    16        81 - 96          3.73     3.73
  LCS_AVERAGE:     16.49

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        81 - 91          1.78     4.94
  LONGEST_CONTINUOUS_SEGMENT:    11        82 - 92          1.75     4.31
  LCS_AVERAGE:      9.86

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        82 - 90          0.28     4.30
  LCS_AVERAGE:      6.83

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     E      81     E      81      3   11   16     3    3    3    3    4    4   10   11   12   12   12   12   16   16   16   16   16   16   16   16 
LCS_GDT     D      82     D      82      9   11   16     9    9    9    9   10   10   11   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     V      83     V      83      9   11   16     9    9    9    9   10   10   11   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     A      84     A      84      9   11   16     9    9    9    9   10   10   11   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     A      85     A      85      9   11   16     9    9    9    9   10   10   11   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     F      86     F      86      9   11   16     9    9    9    9   10   10   11   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     C      87     C      87      9   11   16     9    9    9    9   10   10   11   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     D      88     D      88      9   11   16     9    9    9    9   10   10   11   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     E      89     E      89      9   11   16     9    9    9    9   10   10   11   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     L      90     L      90      9   11   16     9    9    9    9   10   10   11   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     M      91     M      91      3   11   16     3    3    4    8   10   10   11   11   12   12   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     K      92     K      92      4   11   16     3    4    4    4    5   10   11   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     D      93     D      93      4    6   16     3    4    4    4    5    6    6    9   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     T      94     T      94      4    6   16     3    4    4    4    5    6    6    7   11   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     K      95     K      95      4    6   16     1    4    4    4    6    7    9   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     T      96     T      96      3    3   16     0    3    3    3    6    7   10   11   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_AVERAGE  LCS_A:  11.06  (   6.83    9.86   16.49 )

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      9      9      9     10     10     11     11     13     14     15     15     16     16     16     16     16     16     16     16 
GDT PERCENT_CA   9.28   9.28   9.28   9.28  10.31  10.31  11.34  11.34  13.40  14.43  15.46  15.46  16.49  16.49  16.49  16.49  16.49  16.49  16.49  16.49
GDT RMS_LOCAL    0.28   0.28   0.28   0.28   1.04   1.04   1.75   1.75   2.76   3.03   3.29   3.29   3.73   3.73   3.73   3.73   3.73   3.73   3.73   3.73
GDT RMS_ALL_CA   4.30   4.30   4.30   4.30   4.60   4.60   4.31   4.31   3.87   3.90   3.86   3.86   3.73   3.73   3.73   3.73   3.73   3.73   3.73   3.73

#      Molecule1      Molecule2       DISTANCE
LGA    E      81      E      81          5.758
LGA    D      82      D      82          1.134
LGA    V      83      V      83          0.827
LGA    A      84      A      84          0.930
LGA    A      85      A      85          1.034
LGA    F      86      F      86          0.552
LGA    C      87      C      87          0.865
LGA    D      88      D      88          1.336
LGA    E      89      E      89          0.767
LGA    L      90      L      90          0.859
LGA    M      91      M      91          3.203
LGA    K      92      K      92          3.918
LGA    D      93      D      93          7.195
LGA    T      94      T      94          7.994
LGA    K      95      K      95          8.080
LGA    T      96      T      96          7.024

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16   97    4.0     11    1.75    11.598    11.553     0.595

LGA_LOCAL      RMSD =  1.750  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.309  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  3.727  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.462019 * X  +   0.548451 * Y  +  -0.696951 * Z  +  -3.995048
  Y_new =   0.049072 * X  +  -0.800460 * Y  +  -0.597374 * Z  +  59.134857
  Z_new =  -0.885511 * X  +   0.241798 * Y  +  -0.396741 * Z  +  16.491095 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.594247   -0.547346  [ DEG:   148.6394    -31.3606 ]
  Theta =   1.087593    2.053999  [ DEG:    62.3145    117.6855 ]
  Phi   =   0.105815   -3.035777  [ DEG:     6.0628   -173.9372 ]
 
# 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_4-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0283AL381_4-D1.T0283_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16   97   4.0   11   1.75  11.553     3.73
REMARK  ---------------------------------------------------------- 
MOLECULE T0283AL381_4-D1
REMARK Aligment from pdb entry: 1kw4A
ATOM      1  N   GLU    81      21.627  42.602  -5.921  1.00  0.00              
ATOM      2  CA  GLU    81      20.543  43.198  -5.136  1.00  0.00              
ATOM      3  C   GLU    81      19.302  42.301  -5.125  1.00  0.00              
ATOM      4  O   GLU    81      18.627  42.186  -4.098  1.00  0.00              
ATOM      5  N   ASP    82      19.001  41.672  -6.260  1.00  0.00              
ATOM      6  CA  ASP    82      17.847  40.774  -6.351  1.00  0.00              
ATOM      7  C   ASP    82      18.026  39.594  -5.386  1.00  0.00              
ATOM      8  O   ASP    82      17.093  39.201  -4.687  1.00  0.00              
ATOM      9  N   VAL    83      19.225  39.018  -5.369  1.00  0.00              
ATOM     10  CA  VAL    83      19.508  37.895  -4.477  1.00  0.00              
ATOM     11  C   VAL    83      19.379  38.321  -3.010  1.00  0.00              
ATOM     12  O   VAL    83      18.857  37.569  -2.189  1.00  0.00              
ATOM     13  N   ALA    84      19.834  39.529  -2.679  1.00  0.00              
ATOM     14  CA  ALA    84      19.753  39.999  -1.294  1.00  0.00              
ATOM     15  C   ALA    84      18.298  40.123  -0.830  1.00  0.00              
ATOM     16  O   ALA    84      17.984  39.882   0.338  1.00  0.00              
ATOM     17  N   ALA    85      17.408  40.495  -1.742  1.00  0.00              
ATOM     18  CA  ALA    85      15.994  40.613  -1.395  1.00  0.00              
ATOM     19  C   ALA    85      15.368  39.226  -1.216  1.00  0.00              
ATOM     20  O   ALA    85      14.495  39.029  -0.365  1.00  0.00              
ATOM     21  N   PHE    86      15.827  38.271  -2.019  1.00  0.00              
ATOM     22  CA  PHE    86      15.361  36.887  -1.944  1.00  0.00              
ATOM     23  C   PHE    86      15.728  36.308  -0.569  1.00  0.00              
ATOM     24  O   PHE    86      14.898  35.683   0.100  1.00  0.00              
ATOM     25  N   CYS    87      16.969  36.534  -0.141  1.00  0.00              
ATOM     26  CA  CYS    87      17.441  36.042   1.155  1.00  0.00              
ATOM     27  C   CYS    87      16.689  36.733   2.304  1.00  0.00              
ATOM     28  O   CYS    87      16.297  36.087   3.281  1.00  0.00              
ATOM     29  N   ASP    88      16.472  38.040   2.178  1.00  0.00              
ATOM     30  CA  ASP    88      15.768  38.809   3.203  1.00  0.00              
ATOM     31  C   ASP    88      14.380  38.252   3.513  1.00  0.00              
ATOM     32  O   ASP    88      13.931  38.290   4.664  1.00  0.00              
ATOM     33  N   GLU    89      13.711  37.727   2.492  1.00  0.00              
ATOM     34  CA  GLU    89      12.361  37.195   2.645  1.00  0.00              
ATOM     35  C   GLU    89      12.250  35.716   3.013  1.00  0.00              
ATOM     36  O   GLU    89      11.146  35.219   3.246  1.00  0.00              
ATOM     37  N   LEU    90      13.377  35.010   3.063  1.00  0.00              
ATOM     38  CA  LEU    90      13.369  33.595   3.438  1.00  0.00              
ATOM     39  C   LEU    90      13.356  33.480   4.957  1.00  0.00              
ATOM     40  O   LEU    90      14.237  34.004   5.635  1.00  0.00              
ATOM     41  N   MET    91      12.361  32.775   5.514  1.00  0.00              
ATOM     42  CA  MET    91      12.265  32.618   6.968  1.00  0.00              
ATOM     43  C   MET    91      13.550  32.180   7.670  1.00  0.00              
ATOM     44  O   MET    91      14.131  31.145   7.343  1.00  0.00              
ATOM     45  N   LYS    92      13.990  32.990   8.628  1.00  0.00              
ATOM     46  CA  LYS    92      15.191  32.684   9.388  1.00  0.00              
ATOM     47  C   LYS    92      16.532  32.971   8.734  1.00  0.00              
ATOM     48  O   LYS    92      17.574  32.607   9.283  1.00  0.00              
ATOM     49  N   ASP    93      16.528  33.639   7.583  1.00  0.00              
ATOM     50  CA  ASP    93      17.781  33.924   6.884  1.00  0.00              
ATOM     51  C   ASP    93      18.149  35.407   6.815  1.00  0.00              
ATOM     52  O   ASP    93      19.190  35.762   6.260  1.00  0.00              
ATOM     53  N   THR    94      17.321  36.268   7.397  1.00  0.00              
ATOM     54  CA  THR    94      17.577  37.705   7.337  1.00  0.00              
ATOM     55  C   THR    94      18.925  38.184   7.879  1.00  0.00              
ATOM     56  O   THR    94      19.426  39.222   7.445  1.00  0.00              
ATOM     57  N   LYS    95      19.525  37.442   8.804  1.00  0.00              
ATOM     58  CA  LYS    95      20.813  37.848   9.363  1.00  0.00              
ATOM     59  C   LYS    95      21.978  37.677   8.391  1.00  0.00              
ATOM     60  O   LYS    95      23.091  38.121   8.673  1.00  0.00              
ATOM     61  N   THR    96      21.724  37.047   7.249  1.00  0.00              
ATOM     62  CA  THR    96      22.781  36.804   6.269  1.00  0.00              
ATOM     63  C   THR    96      22.731  37.691   5.020  1.00  0.00              
ATOM     64  O   THR    96      23.546  37.536   4.108  1.00  0.00              
END
