
#######################################################
#                                                     #
#                        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   67 (  528),  selected   67 , name one
# Molecule2: number of CA atoms   92 (  680),  selected   67 , 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:    67      12_A - 78_A        1.85     1.85
  LCS_AVERAGE:     72.83

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67      12_A - 78_A        1.85     1.85
  LCS_AVERAGE:     72.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      12_A - 33_A        0.97     2.85
  LCS_AVERAGE:     16.39

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     R    12_A     R    12_A     22   67   67      6   23   37   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     R    13_A     R    13_A     22   67   67      8   38   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    14_A     K    14_A     22   67   67      8   38   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    15_A     G    15_A     22   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    16_A     S    16_A     22   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    17_A     V    17_A     22   67   67     20   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    18_A     K    18_A     22   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     W    19_A     W    19_A     22   67   67     20   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    20_A     F    20_A     22   67   67     12   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    21_A     D    21_A     22   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    22_A     T    22_A     22   67   67      6   14   41   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    23_A     Q    23_A     22   67   67      6   33   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    24_A     K    24_A     22   67   67      6   19   35   50   56   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    25_A     G    25_A     22   67   67      6   14   35   50   56   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    26_A     F    26_A     22   67   67      7   30   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     22   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    28_A     F    28_A     22   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    29_A     I    29_A     22   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     22   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    31_A     P    31_A     22   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    32_A     D    32_A     22   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    33_A     D    33_A     22   67   67      3   31   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    34_A     G    34_A     11   67   67      3    7    8   16   42   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    35_A     G    35_A     13   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    36_A     D    36_A     13   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    37_A     D    37_A     13   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    38_A     L    38_A     13   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    39_A     F    39_A     13   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    40_A     V    40_A     13   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    41_A     H    41_A     13   67   67      6   26   45   52   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    42_A     Q    42_A     13   67   67     15   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    43_A     S    43_A     13   67   67     19   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    44_A     S    44_A     13   67   67      6   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    45_A     I    45_A     13   67   67     19   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     R    46_A     R    46_A     13   67   67      3   33   44   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    47_A     S    47_A     13   67   67      8   35   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    48_A     E    48_A      6   67   67      3    5   24   34   45   59   62   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    49_A     G    49_A      6   67   67      3    7   19   46   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    50_A     F    50_A      6   67   67      3    3   12   48   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     R    51_A     R    51_A     15   67   67     10   33   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    52_A     S    52_A     15   67   67     10   35   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    53_A     L    53_A     15   67   67     17   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    54_A     A    54_A     15   67   67     17   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    55_A     A    55_A     15   67   67     10   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    56_A     E    56_A     15   67   67      3   36   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     15   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     15   67   67      7   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    59_A     V    59_A     15   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     15   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    61_A     F    61_A     15   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    62_A     E    62_A     15   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    63_A     V    63_A     15   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     15   67   67     19   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    65_A     I    65_A     15   67   67      3    9   29   46   55   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    66_A     D    66_A     13   67   67      3    9   18   36   50   58   61   64   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    67_A     N    67_A      3   67   67      3    3    3   49   56   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A      3   67   67      9   35   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    69_A     N    69_A      3   67   67      3    4    7    9   28   56   58   61   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     R    70_A     R    70_A      9   67   67     19   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    71_A     P    71_A      9   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    72_A     K    72_A      9   67   67      9   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    73_A     A    73_A      9   67   67      9   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    74_A     I    74_A      9   67   67      9   36   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    75_A     D    75_A      9   67   67     19   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    76_A     V    76_A      9   67   67     23   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    77_A     S    77_A      9   67   67     17   39   47   53   57   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    78_A     G    78_A      9   67   67      8   11   29   47   55   60   63   65   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A:  54.01  (  16.39   72.83   72.83 )

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     23     39     47     53     57     60     63     65     66     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  25.00  42.39  51.09  57.61  61.96  65.22  68.48  70.65  71.74  72.83  72.83  72.83  72.83  72.83  72.83  72.83  72.83  72.83  72.83  72.83
GDT RMS_LOCAL    0.36   0.56   0.75   0.96   1.15   1.33   1.51   1.67   1.75   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85
GDT RMS_ALL_AT   1.99   1.94   1.93   1.90   1.88   1.86   1.86   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85

# Checking swapping
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  D    33_A      D    33_A
#   possible swapping detected:  D    36_A      D    36_A
#   possible swapping detected:  E    48_A      E    48_A
#   possible swapping detected:  F    50_A      F    50_A
#   possible swapping detected:  E    56_A      E    56_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  F    61_A      F    61_A
#   possible swapping detected:  E    62_A      E    62_A
#   possible swapping detected:  D    75_A      D    75_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    R    12_A      R    12_A     2.198     0    0.197   1.468     6.176   51.071   45.281
LGA    R    13_A      R    13_A     1.014     0    0.090   0.398     3.073   85.952   72.121
LGA    K    14_A      K    14_A     0.964     0    0.034   0.882     3.814   88.214   72.487
LGA    G    15_A      G    15_A     0.432     0    0.080   0.080     0.662   97.619   97.619
LGA    S    16_A      S    16_A     0.462     0    0.039   0.057     1.004   92.976   92.143
LGA    V    17_A      V    17_A     0.632     0    0.139   0.222     1.331   88.214   90.544
LGA    K    18_A      K    18_A     0.623     0    0.048   0.996     2.534   92.857   81.111
LGA    W    19_A      W    19_A     0.523     0    0.061   0.583     2.128   95.238   84.252
LGA    F    20_A      F    20_A     0.884     0    0.123   0.166     1.622   88.214   83.160
LGA    D    21_A      D    21_A     0.413     0    0.036   0.907     3.923   90.595   76.369
LGA    T    22_A      T    22_A     2.039     0    0.095   0.089     3.238   67.024   62.857
LGA    Q    23_A      Q    23_A     2.254     0    0.024   1.243     5.952   59.524   54.497
LGA    K    24_A      K    24_A     3.156     0    0.026   0.762     4.269   48.571   47.354
LGA    G    25_A      G    25_A     3.018     0    0.025   0.025     3.018   55.357   55.357
LGA    F    26_A      F    26_A     1.653     0    0.050   0.196     2.121   81.667   74.589
LGA    G    27_A      G    27_A     0.246     0    0.078   0.078     0.439  100.000  100.000
LGA    F    28_A      F    28_A     0.161     0    0.025   0.249     1.075  100.000   93.203
LGA    I    29_A      I    29_A     0.213     0    0.067   0.538     1.284  100.000   94.107
LGA    T    30_A      T    30_A     0.428     0    0.070   0.916     2.252  100.000   89.728
LGA    P    31_A      P    31_A     0.323     0    0.129   0.461     1.187  100.000   95.986
LGA    D    32_A      D    32_A     0.825     0    0.023   0.851     2.452   92.857   83.988
LGA    D    33_A      D    33_A     1.835     0    0.202   0.370     5.194   63.690   49.940
LGA    G    34_A      G    34_A     3.988     0    0.622   0.622     3.988   55.595   55.595
LGA    G    35_A      G    35_A     0.198     0    0.378   0.378     1.442   95.357   95.357
LGA    D    36_A      D    36_A     0.420     0    0.040   0.866     3.438  100.000   85.952
LGA    D    37_A      D    37_A     0.619     0    0.060   0.635     1.733   90.476   88.333
LGA    L    38_A      L    38_A     0.537     0    0.023   1.215     2.757   90.476   84.286
LGA    F    39_A      F    39_A     0.676     0    0.036   0.383     2.130   90.476   84.113
LGA    V    40_A      V    40_A     0.805     0    0.040   0.062     1.573   83.810   85.374
LGA    H    41_A      H    41_A     2.316     0    0.089   0.369     6.032   72.976   48.571
LGA    Q    42_A      Q    42_A     1.748     0    0.032   0.931     2.802   77.143   73.386
LGA    S    43_A      S    43_A     0.683     0    0.116   0.597     3.074   85.952   79.206
LGA    S    44_A      S    44_A     0.762     0    0.098   0.648     2.177   88.214   84.683
LGA    I    45_A      I    45_A     0.754     0    0.090   0.710     1.961   83.810   86.131
LGA    R    46_A      R    46_A     2.082     0    0.523   0.813     9.692   75.119   40.779
LGA    S    47_A      S    47_A     1.167     0    0.073   0.087     2.990   67.143   73.413
LGA    E    48_A      E    48_A     4.592     0    0.640   1.518    11.926   31.548   16.931
LGA    G    49_A      G    49_A     3.636     0    0.414   0.414     4.265   45.119   45.119
LGA    F    50_A      F    50_A     2.603     0    0.517   0.808     7.098   55.952   39.394
LGA    R    51_A      R    51_A     2.163     0    0.493   1.125     3.626   72.976   65.931
LGA    S    52_A      S    52_A     1.323     0    0.047   0.644     3.252   79.286   74.762
LGA    L    53_A      L    53_A     0.546     0    0.040   0.234     1.560   92.857   90.655
LGA    A    54_A      A    54_A     0.418     0    0.073   0.084     0.680  100.000   98.095
LGA    A    55_A      A    55_A     1.087     0    0.616   0.600     3.573   74.167   75.619
LGA    E    56_A      E    56_A     1.523     0    0.247   1.208     7.294   81.548   56.296
LGA    E    57_A      E    57_A     0.937     0    0.056   0.998     4.836   83.690   71.164
LGA    A    58_A      A    58_A     1.476     0    0.050   0.085     2.180   81.429   78.095
LGA    V    59_A      V    59_A     0.966     0    0.065   0.213     1.017   88.214   90.544
LGA    E    60_A      E    60_A     0.839     0    0.040   0.267     1.698   88.214   83.545
LGA    F    61_A      F    61_A     0.788     0    0.040   0.113     1.046   88.214   89.654
LGA    E    62_A      E    62_A     0.822     0    0.031   1.535     6.949   90.476   61.852
LGA    V    63_A      V    63_A     0.711     0    0.048   1.278     2.773   90.476   82.041
LGA    E    64_A      E    64_A     0.990     0    0.085   0.561     2.797   79.643   74.180
LGA    I    65_A      I    65_A     3.543     0    0.576   1.424     5.996   41.667   45.000
LGA    D    66_A      D    66_A     4.730     0    0.098   1.155    10.046   45.476   25.119
LGA    N    67_A      N    67_A     3.108     0    0.736   1.423     4.722   46.905   45.417
LGA    N    68_A      N    68_A     1.210     0    0.219   0.925     7.446   83.690   55.893
LGA    N    69_A      N    69_A     5.060     0    0.277   0.730    10.060   36.667   20.298
LGA    R    70_A      R    70_A     0.840     0    0.244   1.010     6.270   88.452   65.238
LGA    P    71_A      P    71_A     0.795     0    0.034   0.385     1.025   90.476   89.184
LGA    K    72_A      K    72_A     0.777     0    0.018   0.707     1.939   90.476   86.561
LGA    A    73_A      A    73_A     0.954     0    0.033   0.039     1.757   83.810   83.333
LGA    I    74_A      I    74_A     1.682     0    0.052   1.364     3.686   81.548   69.643
LGA    D    75_A      D    75_A     1.280     0    0.071   0.902     4.231   81.429   72.738
LGA    V    76_A      V    76_A     1.340     0    0.049   0.078     1.708   79.286   80.204
LGA    S    77_A      S    77_A     1.593     0    0.134   0.593     2.978   77.143   74.524
LGA    G    78_A      G    78_A     3.039     0    0.195   0.195     3.366   53.571   53.571

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     528    528  100.00                92
SUMMARY(RMSD_GDC):     1.849          1.880                  2.826           57.615   52.418

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   67   92    4.0     65    1.67    60.870    66.137     3.667

LGA_LOCAL      RMSD:   1.673  Number of atoms:   65  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.852  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   1.849  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.993436 * X  +  -0.068205 * Y  +  -0.091828 * Z  + -29.719151
  Y_new =   0.011961 * X  +  -0.736445 * Y  +   0.676391 * Z  +  29.833548
  Z_new =  -0.113759 * X  +  -0.673050 * Y  +  -0.730796 * Z  +   7.174287 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.012039  0.114006 -2.397305   [DEG:    0.6898    6.5321 -137.3555 ]
ZXZ: -3.006656  2.390283 -2.974155   [DEG: -172.2687  136.9532 -170.4065 ]
 
# END of job
