
#######################################################
#                                                     #
#                        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        1.82     1.82
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.82     1.82
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       6_A - 39_A        1.00     2.58
  LCS_AVERAGE:     39.46

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   16   38   49   56   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   14   33   46   56   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   14   33   48   56   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   56   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      4   24   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     34   63   63      5   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     34   63   63      5   26   35   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     34   63   63      9   25   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     34   63   63      7   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     34   63   63     11   26   35   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     34   63   63     11   26   35   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     34   63   63      7   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     34   63   63      4   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     34   63   63      4   19   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     34   63   63      4   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     34   63   63      5   23   31   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     34   63   63     10   25   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     34   63   63      4   19   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     34   63   63     10   26   37   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     34   63   63      6   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     34   63   63     11   26   37   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     34   63   63     11   24   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     34   63   63     11   26   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     34   63   63     11   23   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     34   63   63      4   23   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     34   63   63      9   26   38   49   56   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   20   34   42   55   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      3   20   28   41   55   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     14   63   63      3    9   24   45   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     14   63   63      7   23   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   63   63      6   23   38   49   56   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   10   29   47   56   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   21   35   49   56   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   23   38   49   56   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   23   37   56   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    9   29   49   56   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    9   24   49   56   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   56   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      7   23   38   49   56   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      5   21   38   49   56   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   19   34   49   56   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      4   14   27   40   56   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      5   12   26   38   48   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      5   13   27   39   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      5   10   29   47   56   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     11   23   38   49   56   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   22   38   49   56   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      5   10   35   47   56   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   16   33   39   52   58   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   14   21   38   45   57   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.82  (  39.46  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     56     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  88.89  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    0.37   0.67   1.18   1.36   1.53   1.68   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82
GDT RMS_ALL_AT   2.13   2.91   1.90   1.89   1.85   1.83   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82   1.82

# 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     1.379     0    0.133   0.133     2.182   79.524   79.524
LGA    S     2_A      S     2_A     2.398     0    0.213   0.788     3.925   66.786   60.079
LGA    S     3_A      S     3_A     2.153     0    0.125   0.678     5.555   68.810   58.968
LGA    F     4_A      F     4_A     1.655     0    0.066   0.242     3.649   72.857   61.688
LGA    C     5_A      C     5_A     1.767     0    0.120   0.802     2.720   72.857   70.238
LGA    D     6_A      D     6_A     1.766     0    0.107   1.136     6.021   72.857   55.238
LGA    S     7_A      S     7_A     2.128     0    0.114   0.703     3.782   68.810   63.889
LGA    K     8_A      K     8_A     1.449     0    0.112   0.710     5.756   79.286   66.085
LGA    C     9_A      C     9_A     1.484     0    0.048   0.059     1.733   77.143   78.571
LGA    G    10_A      G    10_A     1.504     0    0.115   0.115     1.540   77.143   77.143
LGA    V    11_A      V    11_A     1.866     0    0.057   0.072     2.137   72.857   71.701
LGA    R    12_A      R    12_A     1.634     0    0.057   1.335     7.949   75.000   53.550
LGA    C    13_A      C    13_A     0.942     0    0.634   0.717     2.558   79.881   81.905
LGA    S    14_A      S    14_A     1.245     0    0.101   0.624     1.984   79.286   78.571
LGA    K    15_A      K    15_A     1.143     0    0.100   0.649     4.149   81.429   69.312
LGA    A    16_A      A    16_A     1.083     0    0.626   0.562     2.653   75.357   76.571
LGA    G    17_A      G    17_A     2.411     0    0.043   0.043     2.795   62.857   62.857
LGA    Y    18_A      Y    18_A     1.856     0    0.300   1.361     8.014   72.976   50.635
LGA    Q    19_A      Q    19_A     1.360     0    0.105   1.124     3.773   85.952   75.556
LGA    E    20_A      E    20_A     1.623     0    0.027   0.785     4.224   72.976   61.323
LGA    R    21_A      R    21_A     2.165     0    0.054   1.275    11.941   68.810   36.277
LGA    C    22_A      C    22_A     1.452     0    0.068   0.081     1.681   77.143   77.143
LGA    L    23_A      L    23_A     1.090     0    0.055   0.286     2.127   81.429   79.345
LGA    K    24_A      K    24_A     1.809     0    0.069   1.123     9.734   75.000   47.143
LGA    Y    25_A      Y    25_A     2.013     0    0.123   0.577     3.169   68.810   66.429
LGA    C    26_A      C    26_A     1.011     0    0.040   0.093     1.300   85.952   85.952
LGA    G    27_A      G    27_A     0.780     0    0.056   0.056     1.291   85.952   85.952
LGA    I    28_A      I    28_A     1.598     0    0.043   0.751     4.657   79.286   66.012
LGA    C    29_A      C    29_A     1.252     0    0.101   0.111     1.769   85.952   83.016
LGA    C    30_A      C    30_A     0.732     0    0.104   0.110     1.060   88.214   90.556
LGA    E    31_A      E    31_A     0.591     0    0.023   0.769     3.710   90.476   78.519
LGA    K    32_A      K    32_A     0.996     0    0.056   0.892     2.138   90.476   80.741
LGA    C    33_A      C    33_A     1.033     0    0.223   0.230     1.955   79.286   83.016
LGA    H    34_A      H    34_A     1.255     0    0.083   1.222     3.103   81.548   72.762
LGA    C    35_A      C    35_A     1.203     0    0.085   0.608     2.284   81.429   77.222
LGA    V    36_A      V    36_A     1.108     0    0.075   0.305     2.295   85.952   80.408
LGA    P    37_A      P    37_A     0.704     0    0.011   0.080     1.010   88.214   89.184
LGA    S    38_A      S    38_A     1.243     0    0.249   0.659     4.954   83.810   71.905
LGA    G    39_A      G    39_A     1.640     0    0.081   0.081     2.549   66.905   66.905
LGA    T    40_A      T    40_A     2.777     0    0.502   0.432     3.930   55.595   56.327
LGA    Y    41_A      Y    41_A     3.042     0    0.131   0.302     3.943   57.381   49.683
LGA    G    42_A      G    42_A     2.255     0    0.636   0.636     4.515   54.524   54.524
LGA    N    43_A      N    43_A     1.102     0    0.195   0.801     4.491   83.690   67.560
LGA    K    44_A      K    44_A     1.185     0    0.052   1.041     8.042   77.143   57.407
LGA    D    45_A      D    45_A     2.033     0    0.091   1.043     3.711   70.833   62.262
LGA    E    46_A      E    46_A     1.385     0    0.133   0.171     2.455   83.810   75.979
LGA    C    47_A      C    47_A     0.857     0    0.102   0.225     2.307   79.524   77.381
LGA    P    48_A      P    48_A     2.300     0    0.245   0.430     2.863   68.810   69.524
LGA    C    49_A      C    49_A     1.872     0    0.089   0.215     2.200   72.976   73.016
LGA    Y    50_A      Y    50_A     1.938     0    0.080   0.782     5.281   72.857   53.492
LGA    R    51_A      R    51_A     1.252     0    0.044   1.225     5.683   83.690   63.939
LGA    D    52_A      D    52_A     0.219     0    0.130   0.792     3.443   92.857   80.179
LGA    L    53_A      L    53_A     1.054     0    0.025   0.688     4.084   83.690   72.798
LGA    K    54_A      K    54_A     1.374     0    0.031   0.983     2.800   75.119   71.323
LGA    N    55_A      N    55_A     2.571     0    0.091   0.307     2.933   59.048   60.952
LGA    S    56_A      S    56_A     3.809     0    0.156   0.568     6.094   42.024   37.063
LGA    K    57_A      K    57_A     3.257     0    0.037   0.773     5.848   51.786   40.899
LGA    G    58_A      G    58_A     2.137     0    0.041   0.041     2.349   68.810   68.810
LGA    N    59_A      N    59_A     0.675     0    0.033   0.243     2.141   92.857   89.643
LGA    P    60_A      P    60_A     1.726     0    0.084   0.331     2.927   75.000   69.524
LGA    K    61_A      K    61_A     2.424     0    0.038   0.958     3.152   59.167   60.794
LGA    C    62_A      C    62_A     3.303     0    0.120   0.512     4.239   48.452   46.825
LGA    P    63_A      P    63_A     3.695     0    0.301   0.281     4.160   43.452   44.354

# 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):     1.821          1.850                  2.741           74.482   67.875

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.82    79.762    89.822     3.279

LGA_LOCAL      RMSD:   1.821  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.821  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.821  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.058999 * X  +   0.510896 * Y  +   0.857615 * Z  +  -8.907278
  Y_new =   0.360154 * X  +   0.790357 * Y  +  -0.495606 * Z  +   3.887437
  Z_new =  -0.931026 * X  +   0.338113 * Y  +  -0.137371 * Z  +  -4.917553 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.408423  1.197213  1.956711   [DEG:   80.6967   68.5952  112.1113 ]
ZXZ:  1.046794  1.708603 -1.222444   [DEG:   59.9769   97.8958  -70.0409 ]
 
# END of job
