
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0378AL243_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   11 , name T0378_D1.pdb
# PARAMETERS: T0378AL243_5-D1.T0378_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:    10        79 - 88          4.82     5.22
  LONGEST_CONTINUOUS_SEGMENT:    10        80 - 89          4.89     5.39
  LCS_AVERAGE:     11.24

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        82 - 85          1.17     8.14
  LCS_AVERAGE:      3.78

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        79 - 81          0.42    14.18
  LONGEST_CONTINUOUS_SEGMENT:     3        81 - 83          0.46    14.85
  LONGEST_CONTINUOUS_SEGMENT:     3        82 - 84          0.19     8.73
  LONGEST_CONTINUOUS_SEGMENT:     3        83 - 85          0.80     7.74
  LONGEST_CONTINUOUS_SEGMENT:     3        84 - 86          0.74    10.03
  LONGEST_CONTINUOUS_SEGMENT:     3        85 - 87          0.76     8.13
  LONGEST_CONTINUOUS_SEGMENT:     3        86 - 88          0.54    13.40
  LONGEST_CONTINUOUS_SEGMENT:     3        87 - 89          0.78     9.04
  LCS_AVERAGE:      3.37

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:   89
LCS_GDT     T      79     T      79      3    3   10     3    3    3    3    3    3    6    6    7    8    8   10   11   11   11   11   11   11   11   11 
LCS_GDT     T      80     T      80      3    3   10     3    3    3    3    3    4    6    6    7    8    8   10   11   11   11   11   11   11   11   11 
LCS_GDT     P      81     P      81      3    3   10     3    3    3    3    4    4    6    6    7    8    8   10   11   11   11   11   11   11   11   11 
LCS_GDT     Q      82     Q      82      3    4   10     3    3    3    4    4    4    5    5    7    8    8   10   11   11   11   11   11   11   11   11 
LCS_GDT     P      83     P      83      3    4   10     3    3    3    4    4    4    6    6    7    8    8   10   11   11   11   11   11   11   11   11 
LCS_GDT     L      84     L      84      3    4   10     3    3    3    4    4    4    6    6    7    8    8   10   11   11   11   11   11   11   11   11 
LCS_GDT     M      85     M      85      3    4   10     0    3    3    4    4    4    6    6    7    8    8   10   11   11   11   11   11   11   11   11 
LCS_GDT     A      86     A      86      3    3   10     0    3    3    3    3    4    5    5    6    8    8   10   11   11   11   11   11   11   11   11 
LCS_GDT     V      87     V      87      3    3   10     1    3    3    3    3    3    4    5    6    8    8   10   11   11   11   11   11   11   11   11 
LCS_GDT     F      88     F      88      3    3   10     0    3    3    3    3    3    4    5    6    8    8   10   11   11   11   11   11   11   11   11 
LCS_GDT     D      89     D      89      3    3   10     0    3    3    3    3    3    4    4    6    6    7    8   11   11   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   6.13  (   3.37    3.78   11.24 )

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      3      3      3      4      4      4      6      6      7      8      8     10     11     11     11     11     11     11     11     11 
GDT PERCENT_CA   3.37   3.37   3.37   4.49   4.49   4.49   6.74   6.74   7.87   8.99   8.99  11.24  12.36  12.36  12.36  12.36  12.36  12.36  12.36  12.36
GDT RMS_LOCAL    0.19   0.19   0.19   1.17   1.17   1.17   2.92   2.92   3.27   3.71   3.71   4.82   5.06   5.06   5.06   5.06   5.06   5.06   5.06   5.06
GDT RMS_ALL_CA   8.73   8.73   8.73   8.14   8.14   8.14   7.51   7.51   7.77   6.55   6.55   5.22   5.06   5.06   5.06   5.06   5.06   5.06   5.06   5.06

#      Molecule1      Molecule2       DISTANCE
LGA    T      79      T      79          3.751
LGA    T      80      T      80          3.216
LGA    P      81      P      81          3.108
LGA    Q      82      Q      82          4.487
LGA    P      83      P      83          2.291
LGA    L      84      L      84          3.194
LGA    M      85      M      85          2.274
LGA    A      86      A      86          8.060
LGA    V      87      V      87         12.476
LGA    F      88      F      88         11.756
LGA    D      89      D      89         15.163

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11   89    4.0      6    2.92     6.742     6.129     0.199

LGA_LOCAL      RMSD =  2.918  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.767  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  5.058  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.128329 * X  +  -0.543728 * Y  +   0.829392 * Z  + -69.129387
  Y_new =  -0.552754 * X  +  -0.655145 * Y  +  -0.515022 * Z  + 107.114212
  Z_new =   0.823405 * X  +  -0.524542 * Y  +  -0.216473 * Z  +  75.609528 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.962195    1.179398  [ DEG:  -112.4255     67.5745 ]
  Theta =  -0.967385   -2.174208  [ DEG:   -55.4271   -124.5729 ]
  Phi   =  -1.798919    1.342674  [ DEG:  -103.0704     76.9296 ]
 
# 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: T0378AL243_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378AL243_5-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11   89   4.0    6   2.92   6.129     5.06
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL243_5-D1
REMARK Aligment from pdb entry: 1zjrA
ATOM      1  N   THR    79       8.572  27.327  35.559  1.00  0.00              
ATOM      2  CA  THR    79       7.374  28.092  35.884  1.00  0.00              
ATOM      3  C   THR    79       6.226  27.167  36.269  1.00  0.00              
ATOM      4  O   THR    79       5.528  27.403  37.255  1.00  0.00              
ATOM      5  N   THR    80       6.038  26.110  35.486  1.00  0.00              
ATOM      6  CA  THR    80       4.971  25.153  35.741  1.00  0.00              
ATOM      7  C   THR    80       5.149  24.502  37.111  1.00  0.00              
ATOM      8  O   THR    80       4.175  24.077  37.735  1.00  0.00              
ATOM      9  N   PRO    81       6.394  24.428  37.572  1.00  0.00              
ATOM     10  CA  PRO    81       6.698  23.840  38.873  1.00  0.00              
ATOM     11  C   PRO    81       6.128  24.736  39.965  1.00  0.00              
ATOM     12  O   PRO    81       5.647  24.257  40.993  1.00  0.00              
ATOM     13  N   GLN    82       6.190  26.043  39.729  1.00  0.00              
ATOM     14  CA  GLN    82       5.693  27.028  40.680  1.00  0.00              
ATOM     15  C   GLN    82       4.189  26.905  40.889  1.00  0.00              
ATOM     16  O   GLN    82       3.707  26.943  42.021  1.00  0.00              
ATOM     17  N   PRO    83       3.448  26.757  39.795  1.00  0.00              
ATOM     18  CA  PRO    83       1.997  26.636  39.877  1.00  0.00              
ATOM     19  C   PRO    83       1.622  25.362  40.631  1.00  0.00              
ATOM     20  O   PRO    83       0.709  25.366  41.456  1.00  0.00              
ATOM     21  N   LEU    84       2.335  24.275  40.350  1.00  0.00              
ATOM     22  CA  LEU    84       2.081  23.002  41.019  1.00  0.00              
ATOM     23  C   LEU    84       2.428  23.120  42.496  1.00  0.00              
ATOM     24  O   LEU    84       1.761  22.536  43.353  1.00  0.00              
ATOM     25  N   MET    85       3.478  23.881  42.784  1.00  0.00              
ATOM     26  CA  MET    85       3.919  24.101  44.153  1.00  0.00              
ATOM     27  C   MET    85       2.795  24.834  44.876  1.00  0.00              
ATOM     28  O   MET    85       2.419  24.491  45.997  1.00  0.00              
ATOM     29  N   ALA    86       2.258  25.847  44.208  1.00  0.00              
ATOM     30  CA  ALA    86       1.181  26.647  44.765  1.00  0.00              
ATOM     31  C   ALA    86      -0.087  25.811  44.894  1.00  0.00              
ATOM     32  O   ALA    86      -0.841  25.953  45.856  1.00  0.00              
ATOM     33  N   VAL    87      -0.309  24.932  43.923  1.00  0.00              
ATOM     34  CA  VAL    87      -1.482  24.068  43.923  1.00  0.00              
ATOM     35  C   VAL    87      -1.413  23.167  45.154  1.00  0.00              
ATOM     36  O   VAL    87      -2.414  22.917  45.818  1.00  0.00              
ATOM     37  N   PHE    88      -0.213  22.684  45.454  1.00  0.00              
ATOM     38  CA  PHE    88      -0.013  21.815  46.602  1.00  0.00              
ATOM     39  C   PHE    88      -0.377  22.534  47.900  1.00  0.00              
ATOM     40  O   PHE    88      -1.068  21.984  48.753  1.00  0.00              
ATOM     41  N   ASP    89       0.096  23.767  48.046  1.00  0.00              
ATOM     42  CA  ASP    89      -0.200  24.560  49.237  1.00  0.00              
ATOM     43  C   ASP    89      -1.710  24.749  49.359  1.00  0.00              
ATOM     44  O   ASP    89      -2.277  24.679  50.451  1.00  0.00              
END
