
#######################################################
#                                                     #
#                        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   68 (  529),  selected   68 , name one
# Molecule2: number of CA atoms  198 ( 1543),  selected   68 , 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:    21     115_A - 135_A       4.57    25.02
  LCS_AVERAGE:      8.08

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9     115_A - 123_A       1.90    23.85
  LCS_AVERAGE:      3.57

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7     148_A - 154_A       0.72    26.64
  LCS_AVERAGE:      2.44

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   68
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     G   115_A     G   115_A      6    9   21      1    5    7    7    8   11   11   15   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     E   116_A     E   116_A      6    9   21      3    5    7    7    8   11   11   14   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     L   117_A     L   117_A      6    9   21      3    5    7    7    8   11   11   15   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     K   118_A     K   118_A      6    9   21      3    5    7    7    8   11   11   15   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     A   119_A     A   119_A      6    9   21      4    5    7    7    8   11   11   15   16   17   19   23   24   27   29   33   33   36   39   40 
LCS_GDT     T   120_A     T   120_A      6    9   21      4    5    7    7    8    9   11   15   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     V   121_A     V   121_A      4    9   21      4    4    5    6    8    9   11   15   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     G   122_A     G   122_A      4    9   21      4    4    5    6    8    9   11   15   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     E   123_A     E   123_A      4    9   21      3    4    4    5    8    9   11   15   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     N   124_A     N   124_A      4    7   21      3    4    4    5    8    9   11   15   15   17   19   23   25   27   29   33   33   36   39   40 
LCS_GDT     S   125_A     S   125_A      4    7   21      3    4    4    5    8    9   11   12   15   17   19   19   23   26   28   33   33   36   38   39 
LCS_GDT     N   126_A     N   126_A      4    7   21      3    3    4    5    8    9   11   12   14   16   18   19   20   21   26   31   33   36   38   39 
LCS_GDT     I   127_A     I   127_A      4    7   21      3    4    4    5    8    9   11   15   15   17   19   23   25   27   29   33   33   36   39   40 
LCS_GDT     T   128_A     T   128_A      4    7   21      3    4    4    5    8    9   11   15   15   17   19   20   25   27   29   33   33   36   39   40 
LCS_GDT     L   129_A     L   129_A      6    7   21      3    5    6    6    8   11   11   14   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     F   130_A     F   130_A      6    7   21      3    5    6    6    8   11   11   15   15   17   20   21   25   27   29   33   33   36   39   40 
LCS_GDT     D   131_A     D   131_A      6    7   21      3    5    6    6    8   11   11   15   15   17   20   21   25   27   29   33   33   36   39   40 
LCS_GDT     V   132_A     V   132_A      6    7   21      3    4    6    6    8   11   11   15   15   17   20   21   24   26   29   33   33   36   39   40 
LCS_GDT     Q   133_A     Q   133_A      6    7   21      3    5    6    6    8   11   11   15   15   17   19   20   24   26   29   33   33   36   39   40 
LCS_GDT     E   134_A     E   134_A      6    7   21      3    5    6    6    8   11   11   13   15   16   19   19   20   25   27   33   33   35   39   40 
LCS_GDT     Y   135_A     Y   135_A      4    7   21      3    4    5    6    7    8   11   13   13   14   15   16   20   22   26   29   32   35   39   40 
LCS_GDT     S   136_A     S   136_A      4    7   14      3    4    5    5    6    6    7    8    9   10   11   11   16   19   20   22   26   27   29   36 
LCS_GDT     V   137_A     V   137_A      4    7   14      3    4    5    5    6    6    7    8    9   10   11   11   12   16   17   19   22   26   30   37 
LCS_GDT     S   138_A     S   138_A      4    7   14      3    3    5    5    6    6    8   11   12   12   12   12   12   13   13   14   16   18   21   21 
LCS_GDT     D   139_A     D   139_A      3    7   14      3    3    3    5    6    9   10   11   12   12   12   12   12   13   13   14   14   15   16   17 
LCS_GDT     N   140_A     N   140_A      6    8   14      4    6    6    7    8    9   10   11   12   12   12   12   12   13   13   14   14   16   19   19 
LCS_GDT     T   141_A     T   141_A      6    8   14      4    6    6    7    8    9   10   11   12   12   12   12   12   13   13   14   16   18   20   21 
LCS_GDT     I   142_A     I   142_A      6    8   14      4    6    6    7    8    9   10   11   12   12   12   12   12   13   13   14   16   17   20   21 
LCS_GDT     T   143_A     T   143_A      6    8   14      4    6    6    7    8    9   10   11   12   12   12   12   12   13   13   14   15   17   19   20 
LCS_GDT     V   144_A     V   144_A      6    8   14      4    6    6    7    8    9   10   11   12   12   12   12   12   13   14   15   16   18   19   20 
LCS_GDT     T   145_A     T   145_A      6    8   14      4    6    6    7    8    8   10   11   12   12   12   12   15   15   16   16   17   18   19   21 
LCS_GDT     P   146_A     P   146_A      4    8   14      3    3    6    7    8    9   10   11   12   12   12   12   15   15   16   16   17   18   19   20 
LCS_GDT     K   147_A     K   147_A      4    8   14      3    4    6    7    8    9   10   11   12   12   12   12   15   15   16   16   17   18   19   20 
LCS_GDT     I   148_A     I   148_A      7    8   14      3    7    7    7    7    9   10   11   12   12   12   12   15   15   16   16   17   18   19   20 
LCS_GDT     P   149_A     P   149_A      7    8   14      3    7    7    7    8    8   10   11   12   12   12   12   15   15   16   16   17   18   19   20 
LCS_GDT     P   150_A     P   150_A      7    8   14      3    7    7    7    8    8    9    9   10   11   11   12   15   15   19   19   21   24   25   25 
LCS_GDT     C   151_A     C   151_A      7    8   12      3    7    7    7    8    8    9    9   10   11   12   14   15   18   20   21   24   26   26   28 
LCS_GDT     T   152_A     T   152_A      7    8   12      3    7    7    7    8    8    9    9   10   11   13   16   18   19   20   21   24   26   26   28 
LCS_GDT     T   153_A     T   153_A      7    8   12      3    7    7    7    8    8    9   10   11   12   13   16   18   19   20   21   24   26   26   28 
LCS_GDT     G   154_A     G   154_A      7    8   12      3    7    7    7    8    8    9   10   11   12   13   16   18   19   20   21   24   26   26   28 
LCS_GDT     T   155_A     T   155_A      4    8   12      4    4    5    6    8    8    9   10   11   12   13   16   18   19   20   21   22   26   27   36 
LCS_GDT     W   156_A     W   156_A      4    8   13      4    4    5    6    8    8    9   10   11   12   13   16   18   22   27   33   33   36   39   40 
LCS_GDT     K   157_A     K   157_A      5    8   14      4    5    5    6    8    8    9   11   14   17   20   21   25   27   29   33   33   36   39   40 
LCS_GDT     P   158_A     P   158_A      5    8   14      4    5    7    7    8    8    9   10   11   12   15   18   24   26   29   33   33   36   38   39 
LCS_GDT     W   159_A     W   159_A      5    8   14      3    5    5    6    8    8    9   10   11   12   15   19   19   26   28   31   33   36   38   39 
LCS_GDT     H   160_A     H   160_A      5    8   14      3    5    5    6    8    8    9   10   12   14   16   19   20   25   27   31   33   36   39   40 
LCS_GDT     N   161_A     N   161_A      5    8   14      3    5    5    6    8    8    9   13   13   14   15   17   19   22   25   29   29   31   35   37 
LCS_GDT     D   162_A     D   162_A      4    4   15      3    3    4    5    6    8    9   13   13   14   15   17   19   22   24   29   29   31   34   36 
LCS_GDT     L   163_A     L   163_A      4    4   15      0    3    4    5    6    8   10   13   14   17   17   21   24   27   29   33   33   36   39   40 
LCS_GDT     T   164_A     T   164_A      3    3   15      1    3    4    5    6    8   11   14   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     S   165_A     S   165_A      3    4   15      1    3    3    4    6    8   11   14   16   17   20   21   25   27   29   33   33   36   39   40 
LCS_GDT     K   166_A     K   166_A      3    6   15      1    3    3    4    6    7   10   11   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     L   167_A     L   167_A      3    6   15      0    3    3    4    6    7   11   14   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     G   168_A     G   168_A      5    6   15      4    4    5    5    5    6   10   14   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     S   169_A     S   169_A      5    6   15      4    4    5    5    6    8   11   13   15   17   19   23   25   27   29   33   33   36   39   40 
LCS_GDT     L   170_A     L   170_A      5    6   15      4    4    5    5    6    8   11   13   15   17   19   23   25   27   29   31   33   36   39   40 
LCS_GDT     K   171_A     K   171_A      5    6   15      4    4    5    5    6    6    7    9   10   12   14   16   19   22   28   29   32   34   37   38 
LCS_GDT     S   172_A     S   172_A      5    5   15      3    4    5    5    6    6    7   13   14   14   16   23   23   24   28   31   32   36   38   40 
LCS_GDT     V   173_A     V   173_A      3    4   15      3    3    4    5    5    5    6   13   14   14   19   23   23   24   28   31   33   36   38   40 
LCS_GDT     F   174_A     F   174_A      3    5   15      1    3    4    5    6    8   11   13   15   17   19   23   25   27   29   33   33   36   39   40 
LCS_GDT     F   175_A     F   175_A      3    5   15      3    3    4    5    7    8   11   13   15   17   19   23   25   27   29   33   33   36   39   40 
LCS_GDT     E   176_A     E   176_A      3    5   15      3    4    4    6    8    8   11   14   16   17   20   23   25   27   29   33   33   36   39   40 
LCS_GDT     S   177_A     S   177_A      3    6   12      3    4    5    6    8    8    9   10   13   16   20   21   24   26   29   33   33   36   39   40 
LCS_GDT     Y   178_A     Y   178_A      3    6   12      2    4    4    5    6    7    7    9    9   11   13   14   16   19   21   27   32   34   39   40 
LCS_GDT     T   179_A     T   179_A      4    6   12      3    4    4    5    5    7    7    9   10   11   13   14   18   24   26   29   32   35   39   40 
LCS_GDT     C   180_A     C   180_A      4    6   11      3    4    4    5    5    7    7    9   10   11   13   14   16   22   25   29   32   35   39   40 
LCS_GDT     N   181_A     N   181_A      4    6   11      3    4    4    5    5    7    7    9   10   11   13   14   16   19   20   26   31   33   39   40 
LCS_GDT     N   182_A     N   182_A      4    6   11      3    4    4    5    5    7    7    9   10   11   13   14   16   19   20   22   30   33   39   40 
LCS_AVERAGE  LCS_A:   4.69  (   2.44    3.57    8.08 )

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      4      7      7      7      8     11     11     15     16     17     20     23     25     27     29     33     33     36     39     40 
GDT PERCENT_AT   2.02   3.54   3.54   3.54   4.04   5.56   5.56   7.58   8.08   8.59  10.10  11.62  12.63  13.64  14.65  16.67  16.67  18.18  19.70  20.20
GDT RMS_LOCAL    0.00   0.72   0.72   0.72   1.34   2.09   2.09   3.25   3.24   3.36   4.19   4.57   4.94   5.07   5.26   5.94   5.78   6.12   6.81   7.00
GDT RMS_ALL_AT  23.85  26.64  26.64  26.64  26.80  22.01  22.01  25.39  15.31  15.45  14.88  15.26  14.64  14.81  14.57  14.74  14.93  14.78  14.26  13.97

# Checking swapping
#   possible swapping detected:  D   131_A      D   131_A
#   possible swapping detected:  Y   135_A      Y   135_A
#   possible swapping detected:  D   139_A      D   139_A
#   possible swapping detected:  E   176_A      E   176_A
#   possible swapping detected:  Y   178_A      Y   178_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G   115_A      G   115_A     3.418     0    0.000   0.000     4.906   43.690   43.690
LGA    E   116_A      E   116_A     4.794     0    0.079   0.883    12.535   42.143   20.159
LGA    L   117_A      L   117_A     2.396     0    0.088   1.042     7.735   52.262   35.298
LGA    K   118_A      K   118_A     2.785     0    0.000   1.193    11.098   55.952   30.529
LGA    A   119_A      A   119_A     2.766     0    0.148   0.216     4.646   60.952   55.048
LGA    T   120_A      T   120_A     3.122     0    0.079   0.851     6.924   47.143   34.354
LGA    V   121_A      V   121_A     3.280     0    0.067   0.087     7.150   57.381   39.864
LGA    G   122_A      G   122_A     2.421     0    0.168   0.168     2.847   73.452   73.452
LGA    E   123_A      E   123_A     3.475     0    0.135   0.939     8.435   47.381   28.783
LGA    N   124_A      N   124_A     4.627     0    0.106   0.958     5.874   37.381   32.500
LGA    S   125_A      S   125_A     6.078     0    0.698   0.845     9.403   22.857   17.698
LGA    N   126_A      N   126_A     7.300     0    0.407   0.418    11.762   13.690    7.440
LGA    I   127_A      I   127_A     3.391     0    0.084   1.186     8.200   39.167   33.214
LGA    T   128_A      T   128_A     3.807     0    0.163   1.009     7.305   45.000   34.082
LGA    L   129_A      L   129_A     5.080     0    0.597   1.528    11.307   28.214   15.714
LGA    F   130_A      F   130_A     3.538     0    0.125   0.545     7.013   52.143   35.238
LGA    D   131_A      D   131_A     3.025     0    0.056   0.155     6.826   55.476   41.250
LGA    V   132_A      V   132_A     1.372     0    0.146   0.835     6.203   74.048   58.095
LGA    Q   133_A      Q   133_A     4.026     0    0.122   1.186     7.525   32.619   34.127
LGA    E   134_A      E   134_A     7.859     0    0.641   1.130     8.819    8.571   10.423
LGA    Y   135_A      Y   135_A    11.765     0    0.057   1.457    17.682    0.000    0.000
LGA    S   136_A      S   136_A    17.271     0    0.218   0.746    19.381    0.000    0.000
LGA    V   137_A      V   137_A    22.135     0    0.060   1.189    24.189    0.000    0.000
LGA    S   138_A      S   138_A    27.688     0    0.403   0.931    29.803    0.000    0.000
LGA    D   139_A      D   139_A    30.447     0    0.571   1.445    32.223    0.000    0.000
LGA    N   140_A      N   140_A    30.517     0    0.594   1.202    34.543    0.000    0.000
LGA    T   141_A      T   141_A    30.114     0    0.000   0.955    33.741    0.000    0.000
LGA    I   142_A      I   142_A    28.279     0    0.044   0.129    28.593    0.000    0.000
LGA    T   143_A      T   143_A    30.666     0    0.167   0.940    34.232    0.000    0.000
LGA    V   144_A      V   144_A    30.605     0    0.139   1.089    32.239    0.000    0.000
LGA    T   145_A      T   145_A    34.823     0    0.198   1.077    38.570    0.000    0.000
LGA    P   146_A      P   146_A    32.905     0    0.641   0.638    36.468    0.000    0.000
LGA    K   147_A      K   147_A    36.750     0    0.402   1.082    42.437    0.000    0.000
LGA    I   148_A      I   148_A    35.451     0    0.378   0.749    36.134    0.000    0.000
LGA    P   149_A      P   149_A    38.200     0    0.057   0.354    40.388    0.000    0.000
LGA    P   150_A      P   150_A    36.195     0    0.076   0.117    38.758    0.000    0.000
LGA    C   151_A      C   151_A    33.626     0    0.176   0.645    35.183    0.000    0.000
LGA    T   152_A      T   152_A    37.658     0    0.396   1.073    41.491    0.000    0.000
LGA    T   153_A      T   153_A    36.028     0    0.486   0.847    37.510    0.000    0.000
LGA    G   154_A      G   154_A    33.674     0    0.567   0.567    33.777    0.000    0.000
LGA    T   155_A      T   155_A    31.205     0    0.094   0.144    33.304    0.000    0.000
LGA    W   156_A      W   156_A    28.137     0    0.101   0.977    29.027    0.000    0.000
LGA    K   157_A      K   157_A    28.171     0    0.197   0.861    32.378    0.000    0.000
LGA    P   158_A      P   158_A    27.837     0    0.078   0.378    30.447    0.000    0.000
LGA    W   159_A      W   159_A    25.086     0    0.126   1.134    34.125    0.000    0.000
LGA    H   160_A      H   160_A    19.731     0    0.683   1.237    21.502    0.000    0.000
LGA    N   161_A      N   161_A    21.479     0    0.055   1.216    23.570    0.000    0.000
LGA    D   162_A      D   162_A    18.444     0    0.583   0.616    19.370    0.000    0.000
LGA    L   163_A      L   163_A    17.029     0    0.618   0.805    19.993    0.000    0.000
LGA    T   164_A      T   164_A    22.018     0    0.604   1.363    26.468    0.000    0.000
LGA    S   165_A      S   165_A    19.555     0    0.626   0.574    21.137    0.000    0.000
LGA    K   166_A      K   166_A    17.908     0    0.551   1.505    21.423    0.000    0.000
LGA    L   167_A      L   167_A    19.909     0    0.572   1.450    23.553    0.000    0.000
LGA    G   168_A      G   168_A    21.475     0    0.668   0.668    22.504    0.000    0.000
LGA    S   169_A      S   169_A    25.538     0    0.019   0.536    29.726    0.000    0.000
LGA    L   170_A      L   170_A    28.352     0    0.121   0.107    32.588    0.000    0.000
LGA    K   171_A      K   171_A    34.245     0    0.468   0.388    35.925    0.000    0.000
LGA    S   172_A      S   172_A    35.163     0    0.517   0.480    35.894    0.000    0.000
LGA    V   173_A      V   173_A    36.321     0    0.589   0.545    38.736    0.000    0.000
LGA    F   174_A      F   174_A    36.363     0    0.605   1.384    40.313    0.000    0.000
LGA    F   175_A      F   175_A    32.846     0    0.631   1.477    34.735    0.000    0.000
LGA    E   176_A      E   176_A    33.671     0    0.103   1.028    34.190    0.000    0.000
LGA    S   177_A      S   177_A    36.194     0    0.224   0.637    39.143    0.000    0.000
LGA    Y   178_A      Y   178_A    35.881     0    0.329   0.344    36.739    0.000    0.000
LGA    T   179_A      T   179_A    36.591     0    0.106   1.049    38.999    0.000    0.000
LGA    C   180_A      C   180_A    32.343     0    0.395   0.923    34.387    0.000    0.000
LGA    N   181_A      N   181_A    36.215     0    0.541   1.060    39.877    0.000    0.000
LGA    N   182_A      N   182_A    34.435     0    0.474   1.297    41.174    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       68     272    272  100.00     529    529  100.00               198
SUMMARY(RMSD_GDC):    12.754         12.672                 13.331            4.493    3.439

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68  198    4.0     15    3.25     7.828     6.403     0.448

LGA_LOCAL      RMSD:   3.250  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  25.390  Number of assigned atoms:   68 
Std_ASGN_ATOMS RMSD:  12.754  Standard rmsd on all 68 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.492745 * X  +   0.384495 * Y  +   0.780619 * Z  + -121.236572
  Y_new =  -0.856877 * X  +  -0.370625 * Y  +  -0.358329 * Z  + 375.926788
  Z_new =   0.151541 * X  +  -0.845459 * Y  +   0.512088 * Z  +  68.631157 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.092667 -0.152127 -1.026201   [DEG: -119.9010   -8.7162  -58.7970 ]
ZXZ:  1.140457  1.033182  2.964235   [DEG:   65.3433   59.1970  169.8382 ]
 
# END of job
