
#######################################################
#                                                     #
#                        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   63 (  472),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  472),  selected   63 , 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:    63       1_A - 63_A        1.92     1.92
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.92     1.92
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       4_A - 36_A        0.96     3.24
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.94     3.18
  LCS_AVERAGE:     40.24

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     1_A     G     1_A      3   63   63      0    3    5    7    8   20   57   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     11   63   63      4    9   14   34   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   63   63      4   12   29   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     33   63   63      4   14   33   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     33   63   63      7   21   33   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     33   63   63      6   25   33   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     33   63   63      5   25   33   42   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     33   63   63     10   25   33   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     33   63   63     12   25   33   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     33   63   63     12   25   33   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     33   63   63     12   21   33   39   50   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     33   63   63     12   21   33   40   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     33   63   63      6   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     33   63   63     10   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     33   63   63      5   16   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     33   63   63      4   21   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     33   63   63      8   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     33   63   63     10   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     33   63   63      5   20   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     33   63   63     12   25   33   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     33   63   63     12   25   33   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     33   63   63     12   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     33   63   63     12   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     33   63   63     12   25   33   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     33   63   63     12   25   33   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     33   63   63     12   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     33   63   63     12   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     33   63   63     10   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     33   63   63     10   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     33   63   63     10   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     33   63   63      8   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     33   63   63      8   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     33   63   63      8   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     33   63   63      8   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     33   63   63      7   22   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     33   63   63      7   25   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     33   63   63      8   20   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     28   63   63      4   16   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     28   63   63      4   20   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     28   63   63      4   25   33   43   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     13   63   63      4   11   20   30   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     10   63   63      3    7   11   18   35   54   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     11   63   63      3   12   23   42   52   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     11   63   63      3    9   28   44   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     15   63   63      3    8   21   40   52   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     16   63   63      3   16   32   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     17   63   63      6   22   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     17   63   63      6   17   27   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     17   63   63      6   16   32   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     17   63   63      5   17   33   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     17   63   63      7   22   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     17   63   63      8   22   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     17   63   63      5   22   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     17   63   63      7   22   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     17   63   63      7   22   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     17   63   63      5   22   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     17   63   63      7   22   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     17   63   63      8   22   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     17   63   63      8   22   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     17   63   63      6   20   34   45   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     17   63   63      4    7   21   42   54   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     17   63   63      4   21   28   38   46   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     17   63   63      4   21   31   38   46   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  80.08  (  40.24  100.00  100.00 )

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     12     25     34     45     54     59     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  19.05  39.68  53.97  71.43  85.71  93.65  96.83 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.61   1.08   1.33   1.57   1.73   1.81   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92
GDT RMS_ALL_AT   4.31   3.39   2.02   1.98   1.93   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92

# Checking swapping
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  Y    50_A      Y    50_A
#   possible swapping detected:  D    52_A      D    52_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     4.050     0    0.183   0.183     5.206   40.952   40.952
LGA    S     2_A      S     2_A     2.437     0    0.667   0.901     4.631   56.548   55.556
LGA    S     3_A      S     3_A     1.831     0    0.177   0.327     3.772   75.000   66.746
LGA    F     4_A      F     4_A     1.386     0    0.083   0.215     3.621   75.119   63.247
LGA    C     5_A      C     5_A     1.786     0    0.044   0.783     2.683   72.976   70.317
LGA    D     6_A      D     6_A     1.870     0    0.082   1.096     5.938   70.833   54.048
LGA    S     7_A      S     7_A     2.612     0    0.095   0.563     4.772   57.262   52.937
LGA    K     8_A      K     8_A     2.030     0    0.119   0.783     6.708   68.810   57.196
LGA    C     9_A      C     9_A     1.660     0    0.048   0.063     1.983   72.857   75.714
LGA    G    10_A      G    10_A     2.071     0    0.059   0.059     2.329   66.786   66.786
LGA    V    11_A      V    11_A     2.985     0    0.051   0.057     3.680   55.357   52.109
LGA    R    12_A      R    12_A     2.671     0    0.084   1.253     7.158   59.048   48.874
LGA    C    13_A      C    13_A     1.087     0    0.638   0.717     2.717   73.214   77.460
LGA    S    14_A      S    14_A     1.287     0    0.072   0.603     1.851   83.810   83.095
LGA    K    15_A      K    15_A     1.293     0    0.103   0.666     4.921   81.429   65.450
LGA    A    16_A      A    16_A     1.363     0    0.082   0.101     1.576   79.286   79.714
LGA    G    17_A      G    17_A     1.292     0    0.204   0.204     1.367   81.429   81.429
LGA    Y    18_A      Y    18_A     1.593     0    0.249   1.275     8.044   77.143   53.254
LGA    Q    19_A      Q    19_A     1.173     0    0.061   0.932     2.605   88.214   76.138
LGA    E    20_A      E    20_A     1.705     0    0.021   0.748     6.373   72.976   52.063
LGA    R    21_A      R    21_A     2.308     0    0.069   1.215     9.072   66.786   39.481
LGA    C    22_A      C    22_A     1.546     0    0.084   0.132     1.798   75.000   75.714
LGA    L    23_A      L    23_A     1.211     0    0.022   0.270     1.899   81.429   80.357
LGA    K    24_A      K    24_A     1.879     0    0.087   0.957     7.129   70.833   53.968
LGA    Y    25_A      Y    25_A     2.087     0    0.126   0.647     3.941   68.810   64.048
LGA    C    26_A      C    26_A     1.162     0    0.013   0.082     1.383   83.690   82.937
LGA    G    27_A      G    27_A     0.780     0    0.054   0.054     1.111   85.952   85.952
LGA    I    28_A      I    28_A     1.371     0    0.028   0.744     4.163   81.429   70.714
LGA    C    29_A      C    29_A     1.131     0    0.076   0.761     4.012   85.952   77.063
LGA    C    30_A      C    30_A     0.649     0    0.144   0.147     0.946   90.476   93.651
LGA    E    31_A      E    31_A     0.610     0    0.018   0.743     3.528   90.476   80.317
LGA    K    32_A      K    32_A     0.772     0    0.054   1.191     5.648   92.857   70.476
LGA    C    33_A      C    33_A     0.804     0    0.181   0.224     1.398   88.214   87.460
LGA    H    34_A      H    34_A     1.265     0    0.139   1.227     3.115   81.548   72.714
LGA    C    35_A      C    35_A     1.297     0    0.014   0.602     2.554   79.286   74.524
LGA    V    36_A      V    36_A     1.507     0    0.071   0.260     2.868   79.286   71.973
LGA    P    37_A      P    37_A     0.798     0    0.029   0.255     1.420   83.690   84.014
LGA    S    38_A      S    38_A     1.559     0    0.541   0.794     4.850   77.143   67.460
LGA    G    39_A      G    39_A     1.266     0    0.050   0.050     2.170   72.976   72.976
LGA    T    40_A      T    40_A     2.454     0    0.559   1.201     4.325   60.119   61.156
LGA    Y    41_A      Y    41_A     2.924     0    0.200   1.206    10.220   62.976   34.405
LGA    G    42_A      G    42_A     3.833     0    0.572   0.572     5.540   39.524   39.524
LGA    N    43_A      N    43_A     3.009     0    0.369   1.243     5.235   44.167   47.262
LGA    K    44_A      K    44_A     2.339     0    0.139   1.304     8.288   64.762   49.788
LGA    D    45_A      D    45_A     2.902     0    0.122   1.179     7.664   60.952   43.393
LGA    E    46_A      E    46_A     2.158     0    0.115   0.814     2.896   70.952   70.317
LGA    C    47_A      C    47_A     1.109     0    0.121   0.284     2.644   72.976   70.317
LGA    P    48_A      P    48_A     2.228     0    0.170   0.382     2.650   68.810   70.748
LGA    C    49_A      C    49_A     1.867     0    0.068   0.126     2.013   70.833   72.937
LGA    Y    50_A      Y    50_A     1.563     0    0.094   1.251    10.343   75.000   42.738
LGA    R    51_A      R    51_A     1.188     0    0.037   1.264     6.214   85.952   61.558
LGA    D    52_A      D    52_A     0.975     0    0.171   0.799     2.279   81.548   78.333
LGA    L    53_A      L    53_A     1.292     0    0.163   0.850     2.880   77.381   72.262
LGA    K    54_A      K    54_A     1.112     0    0.046   0.927     4.951   83.690   65.926
LGA    N    55_A      N    55_A     1.437     0    0.061   0.223     1.924   81.429   78.214
LGA    S    56_A      S    56_A     1.720     0    0.157   0.488     3.389   70.833   66.349
LGA    K    57_A      K    57_A     1.643     0    0.041   0.757     4.501   75.000   60.212
LGA    G    58_A      G    58_A     0.730     0    0.064   0.064     0.950   90.476   90.476
LGA    N    59_A      N    59_A     0.379     0    0.123   0.287     1.099   95.238   92.917
LGA    P    60_A      P    60_A     1.224     0    0.106   0.342     2.731   81.429   75.510
LGA    K    61_A      K    61_A     2.457     0    0.223   1.083     5.160   57.738   55.873
LGA    C    62_A      C    62_A     3.481     0    0.332   0.721     4.968   45.476   43.889
LGA    P    63_A      P    63_A     3.458     0    0.533   0.519     3.458   50.000   52.041

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     472    472  100.00                63
SUMMARY(RMSD_GDC):     1.919          1.985                  2.926           73.209   66.270

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.92    77.778    88.290     3.121

LGA_LOCAL      RMSD:   1.919  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.919  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.919  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.682632 * X  +   0.166294 * Y  +  -0.711589 * Z  +   7.325340
  Y_new =   0.729411 * X  +  -0.095867 * Y  +   0.677325 * Z  +   2.637498
  Z_new =   0.044417 * X  +  -0.981405 * Y  +  -0.186739 * Z  +   8.045145 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.818514 -0.044432 -1.758826   [DEG:   46.8974   -2.5457 -100.7733 ]
ZXZ: -2.331530  1.758638  3.096365   [DEG: -133.5868  100.7625  177.4086 ]
 
# END of job
