
#######################################################
#                                                     #
#                        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 (  585),  selected   68 , name one
# Molecule2: number of CA atoms  192 ( 1575),  selected   68 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:D  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22     165_D - 186_D       4.86    36.07
  LONGEST_CONTINUOUS_SEGMENT:    22     166_D - 187_D       4.99    35.82
  LCS_AVERAGE:      8.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10     178_D - 187_D       1.37    48.77
  LCS_AVERAGE:      4.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8     146_D - 153_D       0.94    30.48
  LONGEST_CONTINUOUS_SEGMENT:     8     178_D - 185_D       0.97    48.80
  LONGEST_CONTINUOUS_SEGMENT:     8     179_D - 186_D       0.81    49.82
  LCS_AVERAGE:      2.86

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     E   120_D     E   120_D      3    8   13      1    4    5    6    7    9   11   12   12   13   13   14   15   16   17   18   20   21   23   26 
LCS_GDT     Y   121_D     Y   121_D      3    9   13      3    4    6    8    8    9   11   12   12   13   13   14   15   16   19   19   22   24   25   28 
LCS_GDT     D   122_D     D   122_D      5    9   13      3    5    5    6    7    9   11   12   12   13   13   14   15   17   19   19   22   24   26   28 
LCS_GDT     T   123_D     T   123_D      5    9   13      3    5    5    8    8    9   11   12   12   13   13   14   15   17   19   20   22   24   26   28 
LCS_GDT     F   124_D     F   124_D      5    9   13      3    5    6    8    8    9   11   12   12   13   14   14   15   17   19   20   22   24   26   28 
LCS_GDT     H   125_D     H   125_D      5    9   13      3    5    6    8    9   10   11   12   12   13   14   14   15   17   19   20   22   24   26   28 
LCS_GDT     G   126_D     G   126_D      5    9   13      3    5    7    8    9   10   11   12   12   14   15   16   16   17   19   20   22   24   26   28 
LCS_GDT     H   127_D     H   127_D      5    9   13      3    4    6    8    8    9   11   12   14   15   15   16   16   17   19   20   22   24   26   28 
LCS_GDT     V   128_D     V   128_D      5    9   13      3    4    6    8    8    9   11   12   12   13   13   15   16   17   19   19   22   24   26   28 
LCS_GDT     E   129_D     E   129_D      4    9   13      3    4    5    8    8    9   10   12   12   13   13   14   15   16   16   17   18   20   23   25 
LCS_GDT     G   130_D     G   130_D      4    6   13      3    4    4    5    7    9   11   12   12   13   13   14   15   16   16   17   18   20   23   25 
LCS_GDT     I   131_D     I   131_D      4    6   13      3    4    5    5    5    6    7    9   12   13   13   14   15   16   16   17   20   21   23   28 
LCS_GDT     S   132_D     S   132_D      4    6   13      3    4    4    5    5    6    8   10   10   11   12   13   14   16   16   17   18   20   23   25 
LCS_GDT     S   133_D     S   133_D      4    7   12      3    4    4    6    7    7    9   10   10   10   12   13   14   15   16   17   17   20   21   25 
LCS_GDT     R   134_D     R   134_D      4    7   12      3    4    5    5    7    7    9   10   10   11   12   14   15   16   16   18   22   24   26   28 
LCS_GDT     Q   135_D     Q   135_D      5    7   13      4    4    5    6    7    7    9   10   10   11   12   14   15   17   19   20   22   24   26   28 
LCS_GDT     Y   136_D     Y   136_D      5    7   13      4    4    5    6    7    7    9   10   10   11   14   14   15   17   19   20   22   24   26   28 
LCS_GDT     L   137_D     L   137_D      5    7   13      4    4    5    6    7    7    9   10   10   11   14   14   15   17   19   20   22   24   26   28 
LCS_GDT     K   138_D     K   138_D      5    7   13      4    4    5    6    7    7    9   10   10   10   11   12   12   13   16   17   18   21   23   26 
LCS_GDT     G   139_D     G   139_D      5    7   13      2    3    5    6    7    7    9   10   10   10   11   12   12   13   14   14   16   19   19   21 
LCS_GDT     F   140_D     F   140_D      4    7   13      2    3    4    4    6    7    9   10   10   10   11   12   12   13   14   15   16   19   19   20 
LCS_GDT     P   141_D     P   141_D      4    6   13      3    3    4    4    6    7    9   10   10   10   11   12   12   13   14   15   16   19   19   20 
LCS_GDT     F   142_D     F   142_D      4    4   13      3    4    5    5    5    5    6    8    9   10   10   12   12   13   14   15   16   19   19   20 
LCS_GDT     F   143_D     F   143_D      4    4   13      3    4    5    5    5    5    6    8    9   10   10   11   12   13   14   15   16   19   20   21 
LCS_GDT     P   144_D     P   144_D      4    4   13      3    4    5    5    5    5    6    8    9   10   12   13   14   16   17   19   20   21   23   25 
LCS_GDT     K   145_D     K   145_D      4    4   17      3    4    5    6    7    8    9   11   12   13   14   14   16   17   19   20   21   24   26   28 
LCS_GDT     T   146_D     T   146_D      8    9   17      3    4    8    8    9   10   10   11   14   15   15   16   16   17   19   20   22   24   26   28 
LCS_GDT     F   147_D     F   147_D      8    9   17      3    6    8    8    9   10   10   11   14   15   15   16   16   17   19   20   22   24   26   28 
LCS_GDT     Y   148_D     Y   148_D      8    9   17      3    6    8    8    9   10   10   11   14   15   15   16   16   17   19   20   22   24   26   28 
LCS_GDT     I   149_D     I   149_D      8    9   17      3    6    8    8    9   10   10   11   14   15   15   16   16   17   19   19   20   21   26   28 
LCS_GDT     N   150_D     N   150_D      8    9   17      3    6    8    8    9   10   10   11   14   15   15   16   16   17   19   19   20   21   21   25 
LCS_GDT     V   151_D     V   151_D      8    9   17      3    6    8    8    9   10   11   12   14   15   15   16   16   17   19   19   20   21   21   22 
LCS_GDT     Y   152_D     Y   152_D      8    9   17      3    6    8    8    9   10   10   11   14   15   15   16   16   17   19   19   20   21   21   22 
LCS_GDT     K   153_D     K   153_D      8    9   17      3    6    8    8    9   10   10   11   14   15   15   16   16   17   19   19   20   21   21   22 
LCS_GDT     D   154_D     D   154_D      6    9   17      3    5    7    8    9   10   10   11   14   15   15   16   16   17   19   19   20   21   21   22 
LCS_GDT     F   155_D     F   155_D      4    4   17      3    3    4    4    4    5    7    8   10   11   12   14   14   17   19   19   20   21   21   22 
LCS_GDT     E   156_D     E   156_D      4    6   17      3    3    4    5    5    7    7    8   10   11   12   13   14   17   19   19   20   21   21   22 
LCS_GDT     N   157_D     N   157_D      4    6   17      3    3    4    5    5    7    9    9   11   15   15   16   16   17   19   19   20   21   21   22 
LCS_GDT     K   158_D     K   158_D      4    6   17      3    3    4    5    5    7    9   10   14   15   15   16   16   17   19   19   20   21   23   25 
LCS_GDT     D   159_D     D   159_D      4    6   17      3    3    4    5    5    7    9   10   14   15   15   16   16   17   19   19   22   24   26   28 
LCS_GDT     E   160_D     E   160_D      4    6   17      3    3    4    5    6    8    9   11   14   15   15   16   16   17   19   19   22   24   26   28 
LCS_GDT     N   161_D     N   161_D      4    9   17      3    5    7    8    8    9    9   11   14   15   15   16   16   17   19   20   22   24   26   28 
LCS_GDT     N   162_D     N   162_D      4    9   17      3    4    6    7    8    9    9   10   10   11   14   14   15   17   19   20   22   24   26   28 
LCS_GDT     L   163_D     L   163_D      5    9   12      4    5    7    8    8    9    9   10   10   11   14   14   15   17   19   20   22   24   26   28 
LCS_GDT     C   164_D     C   164_D      6    9   12      4    5    7    8    8    9    9   10   10   11   14   14   15   17   19   20   22   24   26   28 
LCS_GDT     S   165_D     S   165_D      6    9   22      5    5    7    8    8    9    9   10   10   11   16   18   19   20   21   23   23   24   26   28 
LCS_GDT     G   166_D     G   166_D      6    9   22      5    5    7    8    8    9    9   10   10   11   14   14   19   20   21   23   23   24   26   28 
LCS_GDT     D   167_D     D   167_D      6    9   22      5    5    7    8    8    9    9   11   12   13   14   15   18   20   21   23   23   24   26   28 
LCS_GDT     D   168_D     D   168_D      6    9   22      5    5    7    8    8    9    9   14   15   16   17   18   19   20   21   23   23   23   25   27 
LCS_GDT     G   169_D     G   169_D      6    9   22      5    5    7    8    8    9   12   14   15   16   17   18   19   20   21   23   23   24   26   28 
LCS_GDT     E   170_D     E   170_D      5    8   22      3    4    6    8    8    9   12   14   15   16   17   18   19   20   21   23   23   23   23   26 
LCS_GDT     Y   171_D     Y   171_D      5    8   22      3    4    6    8    8   10   12   14   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     T   172_D     T   172_D      5    8   22      4    4    6    8    9   10   12   14   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     Y   173_D     Y   173_D      5    8   22      4    4    5    8    9   10   12   14   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     R   174_D     R   174_D      5    8   22      4    4    6    8    9   10   12   14   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     I   175_D     I   175_D      4    8   22      4    4    6    8    9   10   12   14   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     K   176_D     K   176_D      4    8   22      3    4    5    6    9   10   12   14   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     Y   177_D     Y   177_D      4    8   22      3    4    5    6    9   10   12   14   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     P   178_D     P   178_D      8   10   22      4    4    8    9    9   10   10   13   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     E   179_D     E   179_D      8   10   22      4    7    8    9    9   10   12   14   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     Q   180_D     Q   180_D      8   10   22      4    4    8    9    9   10   10   13   15   16   17   17   18   20   21   23   23   23   23   23 
LCS_GDT     L   181_D     L   181_D      8   10   22      6    7    8    9    9   10   12   14   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     E   182_D     E   182_D      8   10   22      6    7    8    9    9   10   12   14   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     E   183_D     E   183_D      8   10   22      6    7    8    9    9   10   11   12   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     V   184_D     V   184_D      8   10   22      6    7    8    9    9   10   12   14   15   16   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     F   185_D     F   185_D      8   10   22      6    7    8    9    9   10   10   10   14   15   17   18   19   20   21   23   23   23   23   23 
LCS_GDT     N   186_D     N   186_D      8   10   22      6    7    8    9    9   10   10   10   10   13   15   15   16   20   21   23   23   23   23   23 
LCS_GDT     Y   187_D     Y   187_D      7   10   22      3    3    3    7    9   10   10   10   10   13   15   15   16   17   21   23   23   23   23   23 
LCS_AVERAGE  LCS_A:   5.30  (   2.86    4.17    8.88 )

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      6      7      8      9      9     10     12     14     15     16     17     18     19     20     21     23     23     24     26     28 
GDT PERCENT_AT   3.12   3.65   4.17   4.69   4.69   5.21   6.25   7.29   7.81   8.33   8.85   9.37   9.90  10.42  10.94  11.98  11.98  12.50  13.54  14.58
GDT RMS_LOCAL    0.25   0.50   0.81   1.00   1.00   1.37   2.60   2.95   3.00   3.17   3.42   3.85   4.19   4.35   4.59   5.04   5.04   6.59   6.98   7.30
GDT RMS_ALL_AT  50.04  50.25  49.82  49.21  49.21  48.77  37.78  37.78  37.65  37.51  37.44  36.62  36.28  36.55  36.54  35.67  35.67  29.27  29.31  29.28

# Checking swapping
#   possible swapping detected:  Y   121_D      Y   121_D
#   possible swapping detected:  Y   136_D      Y   136_D
#   possible swapping detected:  F   143_D      F   143_D
#   possible swapping detected:  E   156_D      E   156_D
#   possible swapping detected:  D   159_D      D   159_D
#   possible swapping detected:  E   160_D      E   160_D
#   possible swapping detected:  D   168_D      D   168_D
#   possible swapping detected:  Y   177_D      Y   177_D
#   possible swapping detected:  E   182_D      E   182_D
#   possible swapping detected:  E   183_D      E   183_D
#   possible swapping detected:  Y   187_D      Y   187_D

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E   120_D      E   120_D    40.893     0    0.135   0.745    42.226    0.000    0.000
LGA    Y   121_D      Y   121_D    38.278     0    0.700   1.179    48.363    0.000    0.000
LGA    D   122_D      D   122_D    33.507     0    0.467   0.703    35.709    0.000    0.000
LGA    T   123_D      T   123_D    34.141     0    0.122   1.092    35.941    0.000    0.000
LGA    F   124_D      F   124_D    34.913     0    0.092   1.280    36.163    0.000    0.000
LGA    H   125_D      H   125_D    35.836     0    0.101   1.041    41.366    0.000    0.000
LGA    G   126_D      G   126_D    36.955     0    0.229   0.229    38.842    0.000    0.000
LGA    H   127_D      H   127_D    40.462     0    0.084   0.464    41.193    0.000    0.000
LGA    V   128_D      V   128_D    43.840     0    0.002   0.022    47.733    0.000    0.000
LGA    E   129_D      E   129_D    48.467     0    0.430   0.509    52.317    0.000    0.000
LGA    G   130_D      G   130_D    50.072     0    0.599   0.599    50.206    0.000    0.000
LGA    I   131_D      I   131_D    50.936     0    0.128   0.727    51.725    0.000    0.000
LGA    S   132_D      S   132_D    50.849     0    0.145   0.609    53.131    0.000    0.000
LGA    S   133_D      S   133_D    49.950     0    0.505   0.576    50.213    0.000    0.000
LGA    R   134_D      R   134_D    46.233     0    0.596   1.729    47.250    0.000    0.000
LGA    Q   135_D      Q   135_D    49.797     0    0.110   0.233    51.929    0.000    0.000
LGA    Y   136_D      Y   136_D    51.471     0    0.060   1.093    52.986    0.000    0.000
LGA    L   137_D      L   137_D    56.123     0    0.095   0.848    60.038    0.000    0.000
LGA    K   138_D      K   138_D    57.371     0    0.659   1.043    58.784    0.000    0.000
LGA    G   139_D      G   139_D    59.904     0    0.224   0.224    59.904    0.000    0.000
LGA    F   140_D      F   140_D    59.742     0    0.050   0.129    63.896    0.000    0.000
LGA    P   141_D      P   141_D    62.796     0    0.660   0.563    63.438    0.000    0.000
LGA    F   142_D      F   142_D    58.832     0    0.625   1.121    60.761    0.000    0.000
LGA    F   143_D      F   143_D    61.277     0    0.653   1.403    67.324    0.000    0.000
LGA    P   144_D      P   144_D    59.984     0    0.349   0.783    61.172    0.000    0.000
LGA    K   145_D      K   145_D    62.461     0    0.655   0.649    71.767    0.000    0.000
LGA    T   146_D      T   146_D    59.369     0    0.656   0.999    60.568    0.000    0.000
LGA    F   147_D      F   147_D    56.433     0    0.285   1.482    56.956    0.000    0.000
LGA    Y   148_D      Y   148_D    55.145     0    0.161   1.262    62.456    0.000    0.000
LGA    I   149_D      I   149_D    52.433     0    0.131   1.037    52.883    0.000    0.000
LGA    N   150_D      N   150_D    53.430     0    0.058   1.052    58.014    0.000    0.000
LGA    V   151_D      V   151_D    47.863     0    0.135   1.161    49.911    0.000    0.000
LGA    Y   152_D      Y   152_D    46.889     0    0.099   1.385    53.702    0.000    0.000
LGA    K   153_D      K   153_D    41.818     0    0.653   1.043    44.076    0.000    0.000
LGA    D   154_D      D   154_D    40.516     0    0.616   0.895    44.588    0.000    0.000
LGA    F   155_D      F   155_D    37.646     0    0.262   1.228    39.767    0.000    0.000
LGA    E   156_D      E   156_D    38.865     0    0.533   1.316    44.571    0.000    0.000
LGA    N   157_D      N   157_D    36.246     0    0.467   1.248    37.388    0.000    0.000
LGA    K   158_D      K   158_D    32.369     0    0.052   0.708    33.671    0.000    0.000
LGA    D   159_D      D   159_D    28.916     0    0.069   1.392    31.074    0.000    0.000
LGA    E   160_D      E   160_D    22.251     0    0.600   1.316    24.608    0.000    0.000
LGA    N   161_D      N   161_D    24.494     0    0.090   0.133    30.472    0.000    0.000
LGA    N   162_D      N   162_D    20.237     0    0.172   1.289    22.344    0.000    0.000
LGA    L   163_D      L   163_D    17.238     0    0.059   0.276    19.999    0.000    0.000
LGA    C   164_D      C   164_D    13.914     0    0.057   0.748    18.404    0.000    0.000
LGA    S   165_D      S   165_D     8.467     0    0.066   0.533    12.387    1.310    5.317
LGA    G   166_D      G   166_D    10.209     0    0.050   0.050    10.209    3.571    3.571
LGA    D   167_D      D   167_D    10.288     0    0.148   0.239    16.575    2.976    1.488
LGA    D   168_D      D   168_D     4.724     0    0.013   1.253     7.633   34.524   25.179
LGA    G   169_D      G   169_D     3.274     0    0.520   0.520     3.449   53.571   53.571
LGA    E   170_D      E   170_D     1.966     0    0.074   0.160     3.537   68.810   60.053
LGA    Y   171_D      Y   171_D     2.157     0    0.153   1.276     7.398   68.810   51.865
LGA    T   172_D      T   172_D     2.243     0    0.016   1.309     3.288   62.976   59.456
LGA    Y   173_D      Y   173_D     3.523     0    0.090   1.087     9.285   48.333   26.548
LGA    R   174_D      R   174_D     2.304     0    0.100   1.413     8.519   55.595   42.857
LGA    I   175_D      I   175_D     3.394     0    0.153   0.588     6.827   65.833   43.452
LGA    K   176_D      K   176_D     2.742     0    0.618   0.983     9.286   60.952   36.825
LGA    Y   177_D      Y   177_D     2.476     0    0.318   1.195    10.287   66.786   30.476
LGA    P   178_D      P   178_D     4.645     0    0.671   0.829     8.237   43.690   29.524
LGA    E   179_D      E   179_D     2.921     0    0.010   1.201     4.621   50.238   43.704
LGA    Q   180_D      Q   180_D     5.566     0    0.029   1.371    12.341   28.929   15.132
LGA    L   181_D      L   181_D     3.284     0    0.090   0.192     9.007   64.048   37.619
LGA    E   182_D      E   182_D     2.922     0    0.045   1.125     6.465   51.548   40.159
LGA    E   183_D      E   183_D     6.041     0    0.041   0.212    11.809   22.976   11.481
LGA    V   184_D      V   184_D     2.121     0    0.034   0.036     4.300   50.476   57.075
LGA    F   185_D      F   185_D     6.340     0    0.010   0.347    10.135   14.762   12.165
LGA    N   186_D      N   186_D    10.553     0    0.099   0.090    13.879    1.190    0.595
LGA    Y   187_D      Y   187_D    11.334     0    0.613   1.397    16.902    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     585    585  100.00               192
SUMMARY(RMSD_GDC):    22.666         22.642                 23.387            4.802    3.584

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68  192    4.0     14    2.95     6.901     6.115     0.459

LGA_LOCAL      RMSD:   2.950  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  37.776  Number of assigned atoms:   68 
Std_ASGN_ATOMS RMSD:  22.666  Standard rmsd on all 68 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.622840 * X  +   0.780049 * Y  +   0.059947 * Z  + -37.226444
  Y_new =  -0.292908 * X  +  -0.161452 * Y  +  -0.942411 * Z  + -18.418106
  Z_new =  -0.725448 * X  +  -0.604530 * Y  +   0.329042 * Z  + -144.022415 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.702004  0.811685 -1.072345   [DEG: -154.8134   46.5061  -61.4409 ]
ZXZ:  0.063524  1.235508 -2.265527   [DEG:    3.6397   70.7894 -129.8051 ]
 
# END of job
