
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   51 (  445),  selected   51 , name one
# Molecule2: number of CA atoms  207 ( 1714),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40     147_A - 186_A       4.72     8.46
  LCS_AVERAGE:     17.55

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32     147_A - 178_A       1.67    11.87
  LONGEST_CONTINUOUS_SEGMENT:    32     148_A - 179_A       2.00    11.31
  LCS_AVERAGE:     10.98

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30     147_A - 176_A       0.77    12.30
  LCS_AVERAGE:      9.41

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     A   147_A     A   147_A     30   32   40      6   21   28   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     Y   148_A     Y   148_A     30   32   40      6   20   29   30   30   30   30   32   34   34   35   36   36   37   40   42   43   44   44   46 
LCS_GDT     I   149_A     I   149_A     30   32   40      7   25   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     C   150_A     C   150_A     30   32   40     10   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     R   151_A     R   151_A     30   32   40     12   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     D   152_A     D   152_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     L   153_A     L   153_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     R   154_A     R   154_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     D   155_A     D   155_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     M   156_A     M   156_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     Y   157_A     Y   157_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     K   158_A     K   158_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     Y   159_A     Y   159_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     L   160_A     L   160_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     G   161_A     G   161_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     D   162_A     D   162_A     30   32   40     14   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     K   163_A     K   163_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     E   164_A     E   164_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     K   165_A     K   165_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     T   166_A     T   166_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     K   167_A     K   167_A     30   32   40     10   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     E   168_A     E   168_A     30   32   40     12   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     Y   169_A     Y   169_A     30   32   40     12   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     N   170_A     N   170_A     30   32   40     12   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     D   171_A     D   171_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     K   172_A     K   172_A     30   32   40     13   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     M   173_A     M   173_A     30   32   40     12   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     K   174_A     K   174_A     30   32   40     16   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     N   175_A     N   175_A     30   32   40     12   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     G   176_A     G   176_A     30   32   40     12   27   29   30   30   30   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     D   177_A     D   177_A      6   32   40      3    5    6    7    9   11   16   30   33   34   35   35   35   35   38   38   42   44   44   46 
LCS_GDT     E   178_A     E   178_A      6   32   40      4    5    6    7   20   24   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     K   179_A     K   179_A      6   32   40      4    5    6    7    9   11   11   31   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     W   180_A     W   180_A      6    7   40      4    5    9   20   27   28   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     N   181_A     N   181_A      6    7   40      4    5    6    7   16   26   30   32   34   34   35   36   36   37   41   42   43   44   44   46 
LCS_GDT     S   182_A     S   182_A      6    7   40      3    3    6    7    9   11   14   20   26   31   34   36   36   37   41   42   43   44   44   46 
LCS_GDT     V   183_A     V   183_A      3    7   40      3    3    4    4    5    8   10   12   13   16   18   20   24   33   41   42   43   44   44   46 
LCS_GDT     L   184_A     L   184_A      3    6   40      3    3    4    5    9   11   13   20   25   30   34   36   36   37   41   42   43   44   44   46 
LCS_GDT     Y   185_A     Y   185_A      3    6   40      3    3    4    5    9   11   11   13   16   19   28   32   35   37   41   42   43   44   44   46 
LCS_GDT     D   186_A     D   186_A      4    6   40      3    4    4    6    9   11   11   12   13   16   18   20   23   26   27   32   36   40   43   46 
LCS_GDT     Y   187_A     Y   187_A      4    6   23      3    4    4    5    7    9   10   12   13   16   18   20   21   22   25   27   29   32   34   38 
LCS_GDT     K   188_A     K   188_A      4    6   23      3    4    5    7    9   11   11   12   13   16   18   20   23   24   27   31   32   36   40   43 
LCS_GDT     H   189_A     H   189_A      4    6   23      3    4    5    6    7    9   10   13   14   18   19   25   29   33   39   42   43   44   44   46 
LCS_GDT     M   190_A     M   190_A      4    6   23      3    4    4    5    6    7    8    9   11   14   20   25   31   36   41   42   43   44   44   46 
LCS_GDT     R   191_A     R   191_A      4    6   23      3    4    4    5    6    8   12   14   17   23   25   29   34   37   41   42   43   44   44   46 
LCS_GDT     Y   192_A     Y   192_A      4    5   23      3    3    4    5    5    6   10   10   13   19   22   26   31   37   41   42   43   44   44   46 
LCS_GDT     I   193_A     I   193_A      4    5   23      3    3    4    5    5    7    9   13   16   18   23   29   34   37   41   42   43   44   44   46 
LCS_GDT     H   194_A     H   194_A      4    5   23      3    3    4    5    5    6    9   11   12   15   18   20   22   24   27   31   34   39   42   46 
LCS_GDT     G   195_A     G   195_A      4    4   23      3    3    4    4    4    6    7    9   12   15   18   20   23   24   27   31   32   35   40   43 
LCS_GDT     G   196_A     G   196_A      4    4   23      3    3    4    5    9   11   11   12   14   16   18   20   23   26   27   32   34   37   41   44 
LCS_GDT     Y   197_A     Y   197_A      4    4   23      3    3    4    4    5    5    8   12   13   14   16   20   23   26   27   32   34   37   41   44 
LCS_AVERAGE  LCS_A:  12.65  (   9.41   10.98   17.55 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
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_AT     16     27     29     30     30     30     30     32     34     34     35     36     36     37     41     42     43     44     44     46 
GDT PERCENT_AT   7.73  13.04  14.01  14.49  14.49  14.49  14.49  15.46  16.43  16.43  16.91  17.39  17.39  17.87  19.81  20.29  20.77  21.26  21.26  22.22
GDT RMS_LOCAL    0.37   0.60   0.72   0.77   0.77   0.77   0.77   1.67   2.15   2.09   2.30   3.14   3.14   3.59   4.79   4.83   5.03   5.16   5.16   5.81
GDT RMS_ALL_AT  12.38  12.04  12.23  12.30  12.30  12.30  12.30  11.38  10.68  11.10  10.81   9.50   9.50   9.11   7.87   7.93   7.78   7.83   7.83   7.49

# Checking swapping
#   possible swapping detected:  Y   148_A      Y   148_A
#   possible swapping detected:  Y   157_A      Y   157_A
#   possible swapping detected:  Y   169_A      Y   169_A
#   possible swapping detected:  D   177_A      D   177_A
#   possible swapping detected:  D   186_A      D   186_A
#   possible swapping detected:  Y   187_A      Y   187_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A   147_A      A   147_A     2.757     0    0.023   0.025     3.266   59.167   57.333
LGA    Y   148_A      Y   148_A     2.603     0    0.049   0.120     4.886   62.976   47.897
LGA    I   149_A      I   149_A     2.101     0    0.031   0.630     3.460   68.810   63.095
LGA    C   150_A      C   150_A     1.348     0    0.069   0.093     2.550   86.190   79.127
LGA    R   151_A      R   151_A     0.359     0    0.049   0.996     4.497   95.238   76.147
LGA    D   152_A      D   152_A     1.012     0    0.038   0.163     2.355   85.952   78.393
LGA    L   153_A      L   153_A     0.846     0    0.014   0.083     1.407   90.476   85.952
LGA    R   154_A      R   154_A     0.228     0    0.086   1.353     5.298   97.619   78.052
LGA    D   155_A      D   155_A     0.469     0    0.043   0.066     0.812   95.238   92.857
LGA    M   156_A      M   156_A     0.971     0    0.068   1.558     7.602   90.476   68.333
LGA    Y   157_A      Y   157_A     0.470     0    0.078   0.267     1.326   95.238   88.294
LGA    K   158_A      K   158_A     0.838     0    0.074   0.680     3.690   90.476   80.370
LGA    Y   159_A      Y   159_A     0.508     0    0.100   1.363     8.693   88.214   55.913
LGA    L   160_A      L   160_A     0.774     0    0.098   0.118     1.539   90.476   87.143
LGA    G   161_A      G   161_A     0.942     0    0.097   0.097     1.071   88.214   88.214
LGA    D   162_A      D   162_A     0.605     0    0.064   0.955     3.255   97.619   81.607
LGA    K   163_A      K   163_A     0.382     0    0.010   0.624     2.397  100.000   93.968
LGA    E   164_A      E   164_A     0.571     0    0.020   0.675     2.478   92.857   87.725
LGA    K   165_A      K   165_A     0.560     0    0.046   1.017     4.427   90.476   78.836
LGA    T   166_A      T   166_A     0.464     0    0.059   0.076     0.801   92.857   95.918
LGA    K   167_A      K   167_A     1.254     0    0.112   1.220     5.419   88.214   65.026
LGA    E   168_A      E   168_A     0.875     0    0.020   0.157     2.172   90.476   83.651
LGA    Y   169_A      Y   169_A     0.679     0    0.022   0.299     1.301   90.476   89.762
LGA    N   170_A      N   170_A     1.128     0    0.017   1.115     3.104   83.690   77.560
LGA    D   171_A      D   171_A     1.089     0    0.020   0.043     1.751   85.952   80.476
LGA    K   172_A      K   172_A     0.475     0    0.032   0.084     0.647   92.857   96.825
LGA    M   173_A      M   173_A     1.159     0    0.046   1.104     3.855   83.690   74.643
LGA    K   174_A      K   174_A     1.171     0    0.121   0.243     1.437   83.690   84.444
LGA    N   175_A      N   175_A     0.345     0    0.350   1.158     2.730   90.833   85.476
LGA    G   176_A      G   176_A     0.317     0    0.613   0.613     2.045   82.024   82.024
LGA    D   177_A      D   177_A     5.440     0    0.620   1.058    11.330   33.095   17.143
LGA    E   178_A      E   178_A     5.320     0    0.087   1.451    10.637   22.738   12.804
LGA    K   179_A      K   179_A     6.916     0    0.023   0.823    12.286   14.405    7.672
LGA    W   180_A      W   180_A     4.941     0    0.225   1.137     7.717   23.571   26.224
LGA    N   181_A      N   181_A     5.940     0    0.413   0.817     7.706   16.190   31.012
LGA    S   182_A      S   182_A    11.920     0    0.608   0.807    14.680    0.119    0.079
LGA    V   183_A      V   183_A    15.828     0    0.131   1.107    18.148    0.000    0.000
LGA    L   184_A      L   184_A    13.155     0    0.641   0.616    15.656    0.000    0.357
LGA    Y   185_A      Y   185_A    13.980     0    0.485   1.182    17.701    0.000    0.000
LGA    D   186_A      D   186_A    19.570     0    0.051   1.095    24.306    0.000    0.000
LGA    Y   187_A      Y   187_A    24.504     0    0.259   1.412    34.440    0.000    0.000
LGA    K   188_A      K   188_A    23.363     0    0.048   0.800    29.701    0.000    0.000
LGA    H   189_A      H   189_A    17.963     0    0.161   1.276    19.864    0.000    0.000
LGA    M   190_A      M   190_A    18.011     0    0.667   0.940    18.011    0.000    0.000
LGA    R   191_A      R   191_A    15.607     0    0.086   1.516    16.373    0.000    0.000
LGA    Y   192_A      Y   192_A    15.005     0    0.120   1.244    16.303    0.000    0.000
LGA    I   193_A      I   193_A    16.689     0    0.595   0.581    19.099    0.000    0.000
LGA    H   194_A      H   194_A    22.254     0    0.633   1.122    29.117    0.000    0.000
LGA    G   195_A      G   195_A    26.397     0    0.545   0.545    26.625    0.000    0.000
LGA    G   196_A      G   196_A    27.742     0    0.063   0.063    28.138    0.000    0.000
LGA    Y   197_A      Y   197_A    27.420     0    0.108   1.086    29.081    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     445    445  100.00               207
SUMMARY(RMSD_GDC):     7.130          6.990                  8.295           13.240   11.982

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   51  207    4.0     32    1.67    15.821    14.457     1.812

LGA_LOCAL      RMSD:   1.666  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.376  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   7.130  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.923632 * X  +   0.021118 * Y  +  -0.382698 * Z  + -17.414968
  Y_new =  -0.379979 * X  +   0.181219 * Y  +  -0.907070 * Z  + -37.175488
  Z_new =   0.050197 * X  +   0.983216 * Y  +   0.175404 * Z  +  68.838661 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.390292 -0.050218  1.394255   [DEG:  -22.3621   -2.8773   79.8849 ]
ZXZ: -0.399247  1.394480  0.051010   [DEG:  -22.8752   79.8978    2.9226 ]
 
# END of job
