
#######################################################
#                                                     #
#                        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        1.81     1.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.81     1.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       4_A - 36_A        0.97     2.80
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.93     2.76
  LONGEST_CONTINUOUS_SEGMENT:    33       7_A - 39_A        1.00     2.52
  LCS_AVERAGE:     38.73

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     11   63   63      2   19   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   63   63      3   15   32   46   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   63   63      3   15   32   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     33   63   63      3   14   36   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     33   63   63      5   23   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     33   63   63      4   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     33   63   63      4   26   35   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     33   63   63      9   24   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     33   63   63      4   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     33   63   63     11   26   35   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     33   63   63     11   26   37   49   57   60   63   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   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     33   63   63      4   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     33   63   63      4   18   38   49   57   60   63   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   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     33   63   63      5   25   31   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     33   63   63     11   25   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     33   63   63      4   19   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     33   63   63      9   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     33   63   63     11   26   37   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     33   63   63      6   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     33   63   63     10   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     33   63   63     10   25   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     33   63   63     11   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     33   63   63      9   25   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     33   63   63     10   25   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     33   63   63     10   26   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     26   63   63      4   21   34   43   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     24   63   63      4   21   28   43   55   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     15   63   63      4    8   26   47   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     15   63   63     10   25   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     15   63   63      7   25   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   63   63      5   12   30   48   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   63   63      5   20   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   63   63      5   25   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   63   63      5    8   26   38   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   63   63      5   10   30   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   63   63      5   10   25   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   63   63      5    9   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   63   63      5   25   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   63   63      3   20   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   63   63      4   20   33   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   63   63      3   13   27   41   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   63   63      6   12   26   37   47   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   63   63      6   13   27   40   54   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   63   63      6   10   30   48   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   63   63     10   25   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   63   63     11   25   38   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   63   63      6   10   35   49   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   63   63      4   17   33   40   53   59   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   63   63      3   15   26   38   46   58   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.58  (  38.73  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     11     26     38     49     57     60     63     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  41.27  60.32  77.78  90.48  95.24 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.67   1.16   1.33   1.54   1.66   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81
GDT RMS_ALL_AT   2.49   2.86   1.91   1.91   1.82   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81

# Checking swapping
#   possible swapping detected:  F     4_A      F     4_A
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  E    46_A      E    46_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     1.272     0    0.212   0.212     1.722   86.190   86.190
LGA    S     2_A      S     2_A     2.369     0    0.205   0.788     3.881   66.786   60.079
LGA    S     3_A      S     3_A     2.127     0    0.130   0.679     5.508   68.810   58.968
LGA    F     4_A      F     4_A     1.660     0    0.055   0.235     3.543   72.857   61.688
LGA    C     5_A      C     5_A     1.762     0    0.119   0.799     2.744   72.857   70.238
LGA    D     6_A      D     6_A     1.717     0    0.108   1.136     5.941   72.857   55.774
LGA    S     7_A      S     7_A     2.078     0    0.123   0.710     3.802   68.810   63.889
LGA    K     8_A      K     8_A     1.406     0    0.111   0.637     5.088   79.286   68.360
LGA    C     9_A      C     9_A     1.505     0    0.050   0.061     1.748   75.000   77.143
LGA    G    10_A      G    10_A     1.510     0    0.112   0.112     1.554   77.143   77.143
LGA    V    11_A      V    11_A     1.846     0    0.054   0.071     2.136   72.857   71.701
LGA    R    12_A      R    12_A     1.611     0    0.058   1.324     7.941   75.000   53.550
LGA    C    13_A      C    13_A     0.985     0    0.649   0.731     2.613   79.881   81.905
LGA    S    14_A      S    14_A     1.216     0    0.051   0.635     1.931   81.548   80.079
LGA    K    15_A      K    15_A     1.166     0    0.118   0.641     4.106   81.429   69.312
LGA    A    16_A      A    16_A     1.085     0    0.631   0.568     2.657   75.357   78.381
LGA    G    17_A      G    17_A     2.410     0    0.038   0.038     2.730   62.857   62.857
LGA    Y    18_A      Y    18_A     1.875     0    0.298   1.354     7.919   72.976   51.706
LGA    Q    19_A      Q    19_A     1.417     0    0.114   0.993     2.558   83.690   75.979
LGA    E    20_A      E    20_A     1.719     0    0.027   0.783     4.388   72.976   59.048
LGA    R    21_A      R    21_A     2.196     0    0.047   1.253    11.746   68.810   36.277
LGA    C    22_A      C    22_A     1.429     0    0.071   0.086     1.658   77.143   77.143
LGA    L    23_A      L    23_A     1.114     0    0.057   0.327     2.223   81.429   78.274
LGA    K    24_A      K    24_A     1.793     0    0.074   1.126     9.733   75.000   47.407
LGA    Y    25_A      Y    25_A     1.962     0    0.131   0.612     3.188   70.833   67.103
LGA    C    26_A      C    26_A     1.001     0    0.041   0.094     1.322   85.952   85.952
LGA    G    27_A      G    27_A     0.755     0    0.052   0.052     1.252   85.952   85.952
LGA    I    28_A      I    28_A     1.569     0    0.043   0.752     4.611   79.286   67.024
LGA    C    29_A      C    29_A     1.240     0    0.102   0.109     1.768   85.952   83.016
LGA    C    30_A      C    30_A     0.742     0    0.108   0.112     1.066   88.214   90.556
LGA    E    31_A      E    31_A     0.599     0    0.026   0.757     3.544   90.476   80.317
LGA    K    32_A      K    32_A     0.933     0    0.058   0.899     2.398   90.476   80.741
LGA    C    33_A      C    33_A     0.968     0    0.224   0.229     1.890   83.810   86.032
LGA    H    34_A      H    34_A     1.192     0    0.080   1.248     3.222   83.690   72.095
LGA    C    35_A      C    35_A     1.172     0    0.082   0.612     2.243   85.952   81.667
LGA    V    36_A      V    36_A     1.039     0    0.076   0.306     2.205   85.952   81.633
LGA    P    37_A      P    37_A     0.682     0    0.014   0.083     1.017   88.214   89.184
LGA    S    38_A      S    38_A     1.257     0    0.244   0.657     4.938   83.810   71.905
LGA    G    39_A      G    39_A     1.590     0    0.071   0.071     2.399   68.810   68.810
LGA    T    40_A      T    40_A     2.727     0    0.532   0.459     3.855   55.595   56.327
LGA    Y    41_A      Y    41_A     3.071     0    0.099   0.286     4.120   57.381   48.095
LGA    G    42_A      G    42_A     2.181     0    0.636   0.636     4.404   57.857   57.857
LGA    N    43_A      N    43_A     1.090     0    0.208   0.799     4.652   83.690   66.012
LGA    K    44_A      K    44_A     1.167     0    0.055   1.052     7.941   77.143   57.672
LGA    D    45_A      D    45_A     1.965     0    0.094   1.047     3.593   75.000   65.298
LGA    E    46_A      E    46_A     1.347     0    0.140   0.169     2.399   83.810   75.979
LGA    C    47_A      C    47_A     0.834     0    0.105   0.219     2.229   81.548   78.730
LGA    P    48_A      P    48_A     2.264     0    0.250   0.431     2.824   68.810   69.524
LGA    C    49_A      C    49_A     1.858     0    0.077   0.212     2.212   72.976   73.016
LGA    Y    50_A      Y    50_A     1.909     0    0.081   0.774     5.163   72.857   55.159
LGA    R    51_A      R    51_A     1.225     0    0.037   1.231     5.634   83.690   63.939
LGA    D    52_A      D    52_A     0.165     0    0.107   0.802     3.555   92.857   78.393
LGA    L    53_A      L    53_A     1.087     0    0.032   0.610     3.929   83.690   73.571
LGA    K    54_A      K    54_A     1.341     0    0.035   1.254     5.892   77.381   63.598
LGA    N    55_A      N    55_A     2.577     0    0.090   0.285     2.957   59.048   60.952
LGA    S    56_A      S    56_A     3.854     0    0.164   0.566     6.189   42.024   37.063
LGA    K    57_A      K    57_A     3.339     0    0.038   0.777     5.991   51.786   39.735
LGA    G    58_A      G    58_A     2.128     0    0.042   0.042     2.365   68.810   68.810
LGA    N    59_A      N    59_A     0.625     0    0.028   0.280     2.056   92.857   89.643
LGA    P    60_A      P    60_A     1.638     0    0.087   0.322     2.795   75.000   70.680
LGA    K    61_A      K    61_A     2.340     0    0.035   0.949     3.090   61.190   62.540
LGA    C    62_A      C    62_A     3.271     0    0.124   0.517     4.281   50.119   47.937
LGA    P    63_A      P    63_A     3.607     0    0.288   0.269     4.108   43.452   45.306

# 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):     1.805          1.828                  2.736           75.040   68.268

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.81    79.762    89.926     3.307

LGA_LOCAL      RMSD:   1.805  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.805  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.805  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.334928 * X  +   0.903865 * Y  +   0.266180 * Z  +  -8.691213
  Y_new =  -0.111278 * X  +   0.242575 * Y  +  -0.963729 * Z  +   3.368739
  Z_new =  -0.935650 * X  +  -0.352400 * Y  +   0.019335 * Z  +  -4.627808 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.820822  1.210095 -1.515984   [DEG: -161.6212   69.3334  -86.8595 ]
ZXZ:  0.269479  1.551460 -1.931001   [DEG:   15.4400   88.8921 -110.6382 ]
 
# END of job
