
#######################################################
#                                                     #
#                        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   54 (  439),  selected   54 , name one
# Molecule2: number of CA atoms  166 ( 1331),  selected   54 , 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:    54      91_A - 144_A       4.47     4.47
  LCS_AVERAGE:     32.53

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18     127_A - 144_A       1.21     7.91
  LCS_AVERAGE:      8.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17     128_A - 144_A       0.97     8.69
  LCS_AVERAGE:      5.93

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   54
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     H    91_A     H    91_A      7   11   54      3   14   20   23   29   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     S    92_A     S    92_A      7   11   54      3   14   20   23   29   35   38   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     F    93_A     F    93_A      7   11   54      4   14   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     E    94_A     E    94_A      7   11   54      3   14   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     V    95_A     V    95_A      7   11   54      4   14   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     N    96_A     N    96_A      7   11   54      5   13   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     L    97_A     L    97_A      7   11   54      3    8   19   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     D    98_A     D    98_A      7   11   54      3    8   11   23   29   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     N    99_A     N    99_A      3   12   54      3    3   17   22   25   29   35   42   46   49   49   49   51   51   52   52   53   53   53   53 
LCS_GDT     G   100_A     G   100_A      3   12   54      3    8   17   21   26   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     R   101_A     R   101_A      9   12   54      6    9    9   13   27   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     K   102_A     K   102_A      9   12   54      6    9    9   15   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     I   103_A     I   103_A      9   12   54      6    9    9   13   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     M   104_A     M   104_A      9   12   54      6    9    9   16   25   35   39   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     R   105_A     R   105_A      9   12   54      6    9    9   15   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     L   106_A     L   106_A      9   12   54      6    9    9   16   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     Q   107_A     Q   107_A      9   12   54      6    9    9   21   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     L   108_A     L   108_A      9   13   54      6    9   11   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     G   109_A     G   109_A      9   13   54      6    9    9   12   26   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     Q   110_A     Q   110_A      3   13   54      5   14   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     E   111_A     E   111_A      7   13   54      3    4   11   21   25   30   35   42   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     T   112_A     T   112_A      7   13   54      9   17   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     S   113_A     S   113_A      7   13   54      8   17   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     T   114_A     T   114_A      7   13   54      8   17   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     L   115_A     L   115_A      7   13   54      8   14   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     Q   116_A     Q   116_A      7   13   54      8   14   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     L   117_A     L   117_A      7   13   54      8   14   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     E   118_A     E   118_A      7   13   54      4   12   15   21   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     Q   119_A     Q   119_A      7   13   54      4    6   14   19   24   32   38   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     K   120_A     K   120_A      3   13   54      3    3    5   14   24   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     G   121_A     G   121_A      3   12   54      3    4    7   10   16   22   29   38   39   44   48   50   51   51   52   52   53   53   53   53 
LCS_GDT     R   122_A     R   122_A      4    5   54      3    3    4    4    5    7   11   15   20   30   38   43   47   50   52   52   53   53   53   53 
LCS_GDT     V   123_A     V   123_A      4    5   54      3    3    4    4    5    5    8   11   13   14   17   17   22   30   34   40   46   50   52   53 
LCS_GDT     L   124_A     L   124_A      5   10   54      3    3    5    7    9   10   11   13   15   21   23   37   41   45   49   50   53   53   53   53 
LCS_GDT     K   125_A     K   125_A      5   10   54      3    4    5    7   11   18   28   38   40   44   48   50   51   51   52   52   53   53   53   53 
LCS_GDT     M   126_A     M   126_A      5   10   54      3    4    7   11   20   32   35   40   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     D   127_A     D   127_A      5   18   54      8   14   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     E   128_A     E   128_A     17   18   54      8   14   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     A   129_A     A   129_A     17   18   54      6   17   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     F   130_A     F   130_A     17   18   54      4   12   17   23   29   35   38   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     S   131_A     S   131_A     17   18   54      8   17   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     I   132_A     I   132_A     17   18   54      9   17   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     S   133_A     S   133_A     17   18   54      9   17   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     L   134_A     L   134_A     17   18   54      9   17   20   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     E   135_A     E   135_A     17   18   54      9   17   19   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     Q   136_A     Q   136_A     17   18   54      9   17   19   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     T   137_A     T   137_A     17   18   54      9   17   19   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     E   138_A     E   138_A     17   18   54      9   17   19   23   30   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     E   139_A     E   139_A     17   18   54      9   17   19   22   27   35   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     L   140_A     L   140_A     17   18   54      9   17   19   22   25   29   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     T   141_A     T   141_A     17   18   54      9   17   19   22   25   32   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     E   142_A     E   142_A     17   18   54      9   17   19   22   25   32   40   44   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     M   143_A     M   143_A     17   18   54      9   17   19   22   25   28   34   38   46   49   49   50   51   51   52   52   53   53   53   53 
LCS_GDT     F   144_A     F   144_A     17   18   54      9   15   19   21   25   28   33   39   45   49   49   50   51   51   52   52   53   53   53   53 
LCS_AVERAGE  LCS_A:  15.58  (   5.93    8.27   32.53 )

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      9     17     20     23     30     35     40     44     46     49     49     50     51     51     52     52     53     53     53     53 
GDT PERCENT_AT   5.42  10.24  12.05  13.86  18.07  21.08  24.10  26.51  27.71  29.52  29.52  30.12  30.72  30.72  31.33  31.33  31.93  31.93  31.93  31.93
GDT RMS_LOCAL    0.18   0.59   0.96   1.18   1.78   1.92   2.34   2.51   2.68   2.95   2.95   3.25   3.32   3.32   3.66   3.66   4.05   4.05   4.05   4.05
GDT RMS_ALL_AT  11.48   8.77   5.86   5.92   5.29   5.54   5.13   5.09   5.12   4.97   4.97   4.67   4.70   4.70   4.58   4.58   4.50   4.50   4.50   4.50

# Checking swapping
#   possible swapping detected:  F    93_A      F    93_A
#   possible swapping detected:  E    94_A      E    94_A
#   possible swapping detected:  D    98_A      D    98_A
#   possible swapping detected:  E   118_A      E   118_A
#   possible swapping detected:  F   130_A      F   130_A
#   possible swapping detected:  E   138_A      E   138_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    H    91_A      H    91_A     2.611     0    0.607   0.865     7.758   55.595   42.333
LGA    S    92_A      S    92_A     3.396     0    0.095   0.496     4.551   43.452   41.429
LGA    F    93_A      F    93_A     2.619     0    0.156   1.288     7.010   60.952   43.290
LGA    E    94_A      E    94_A     2.876     0    0.058   0.704     4.087   55.357   49.524
LGA    V    95_A      V    95_A     2.248     0    0.044   0.061     2.695   66.905   66.054
LGA    N    96_A      N    96_A     1.058     0    0.118   0.445     2.881   90.714   78.810
LGA    L    97_A      L    97_A     0.818     0    0.041   0.107     1.933   84.048   83.988
LGA    D    98_A      D    98_A     2.844     0    0.405   1.145     8.081   57.262   37.321
LGA    N    99_A      N    99_A     5.953     0    0.442   0.694    10.147   26.548   14.226
LGA    G   100_A      G   100_A     3.628     0    0.214   0.214     4.179   52.500   52.500
LGA    R   101_A      R   101_A     2.809     0    0.588   1.439     7.576   52.619   28.225
LGA    K   102_A      K   102_A     3.268     0    0.034   0.766    11.507   52.262   26.772
LGA    I   103_A      I   103_A     2.370     0    0.090   1.051     8.546   57.500   40.357
LGA    M   104_A      M   104_A     3.636     0    0.053   1.010    12.373   46.905   26.488
LGA    R   105_A      R   105_A     2.163     0    0.120   1.197    15.958   59.405   26.320
LGA    L   106_A      L   106_A     2.866     0    0.047   0.273     8.793   59.524   36.131
LGA    Q   107_A      Q   107_A     2.292     0    0.086   1.388     9.572   63.452   33.333
LGA    L   108_A      L   108_A     2.302     0    0.041   0.120     9.245   66.905   40.833
LGA    G   109_A      G   109_A     3.806     0    0.672   0.672     4.234   45.119   45.119
LGA    Q   110_A      Q   110_A     1.067     0    0.449   1.264     3.256   75.000   73.175
LGA    E   111_A      E   111_A     4.836     0    0.028   0.292     8.607   34.524   20.847
LGA    T   112_A      T   112_A     2.095     0    0.122   1.098     3.708   60.952   60.680
LGA    S   113_A      S   113_A     1.714     0    0.069   0.185     2.240   72.857   71.508
LGA    T   114_A      T   114_A     1.717     0    0.112   0.997     3.778   72.857   66.395
LGA    L   115_A      L   115_A     1.610     0    0.038   0.151     3.037   75.000   67.083
LGA    Q   116_A      Q   116_A     1.065     0    0.041   0.803     3.075   81.429   72.593
LGA    L   117_A      L   117_A     1.326     0    0.049   1.268     5.627   81.429   61.071
LGA    E   118_A      E   118_A     2.044     0    0.046   0.292     2.832   62.976   67.566
LGA    Q   119_A      Q   119_A     4.388     0    0.097   0.394    12.089   38.810   19.259
LGA    K   120_A      K   120_A     3.484     0    0.538   0.834     9.691   38.690   32.751
LGA    G   121_A      G   121_A     9.045     0    0.731   0.731    11.038    3.690    3.690
LGA    R   122_A      R   122_A    13.660     0    0.569   1.680    19.293    0.000    0.000
LGA    V   123_A      V   123_A    17.987     0    0.092   1.367    22.407    0.000    0.000
LGA    L   124_A      L   124_A    16.308     0    0.605   1.454    19.710    0.000    0.000
LGA    K   125_A      K   125_A     9.342     0    0.096   0.324    11.725    3.929   19.418
LGA    M   126_A      M   126_A     6.178     0    0.138   1.157    10.270   24.167   13.869
LGA    D   127_A      D   127_A     1.460     0    0.603   1.010     5.134   75.000   60.536
LGA    E   128_A      E   128_A     1.657     0    0.101   0.627     3.256   72.857   67.619
LGA    A   129_A      A   129_A     2.531     0    0.052   0.070     3.218   57.262   58.762
LGA    F   130_A      F   130_A     3.382     0    0.122   1.242     4.176   55.476   48.485
LGA    S   131_A      S   131_A     1.535     0    0.097   0.258     2.609   75.119   71.746
LGA    I   132_A      I   132_A     0.776     0    0.103   0.974     3.310   88.214   79.881
LGA    S   133_A      S   133_A     1.551     0    0.031   0.067     2.343   81.548   75.952
LGA    L   134_A      L   134_A     1.352     0    0.065   1.417     5.677   83.810   64.524
LGA    E   135_A      E   135_A     1.391     0    0.038   1.192     6.506   81.429   53.122
LGA    Q   136_A      Q   136_A     1.701     0    0.045   0.198     2.439   77.143   71.164
LGA    T   137_A      T   137_A     1.381     0    0.032   0.112     2.134   77.262   76.667
LGA    E   138_A      E   138_A     0.853     0    0.033   0.521     1.802   83.810   85.556
LGA    E   139_A      E   139_A     2.547     0    0.051   0.282     3.916   55.833   50.370
LGA    L   140_A      L   140_A     3.862     0    0.050   1.365     7.766   43.452   33.452
LGA    T   141_A      T   141_A     3.723     0    0.036   0.096     4.469   43.452   45.306
LGA    E   142_A      E   142_A     3.904     0    0.040   0.931     7.045   37.738   34.868
LGA    M   143_A      M   143_A     5.903     0    0.074   0.705     7.180   18.690   17.083
LGA    F   144_A      F   144_A     6.696     0    0.551   0.569     9.414   13.452    9.394

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       54     216    216  100.00     439    439  100.00               166
SUMMARY(RMSD_GDC):     4.470          4.408                  5.764           17.740   14.864

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   54  166    4.0     44    2.51    20.482    18.680     1.686

LGA_LOCAL      RMSD:   2.510  Number of atoms:   44  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.090  Number of assigned atoms:   54 
Std_ASGN_ATOMS RMSD:   4.470  Standard rmsd on all 54 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.820260 * X  +   0.552690 * Y  +   0.147335 * Z  +  29.976259
  Y_new =  -0.331269 * X  +  -0.669010 * Y  +   0.665347 * Z  + -14.389812
  Z_new =   0.466300 * X  +   0.496950 * Y  +   0.731851 * Z  +  12.136304 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.757765 -0.485103  0.596514   [DEG: -158.0083  -27.7944   34.1777 ]
ZXZ:  2.923668  0.749762  0.753590   [DEG:  167.5138   42.9582   43.1775 ]
 
# END of job
