
#######################################################
#                                                     #
#                        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 (  529),  selected   67 , name one
# Molecule2: number of CA atoms   67 (  519),  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       2_A - 68_A        0.93     0.93
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.93     0.93
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.93     0.93
  LCS_AVERAGE:    100.00

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     S     2_A     S     2_A     67   67   67     11   19   51   58   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     67   67   67     11   39   56   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     67   67   67     11   31   52   60   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     67   67   67     11   39   56   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     67   67   67     16   53   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     67   67   67     13   57   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     67   67   67     16   57   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     67   67   67     16   57   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     67   67   67     29   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     67   67   67     20   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     67   67   67     29   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     67   67   67     39   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     67   67   67     36   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     67   67   67     37   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     67   67   67     37   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     67   67   67     26   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     67   67   67     41   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     67   67   67     39   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     67   67   67     32   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     67   67   67     17   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     67   67   67     17   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     67   67   67     17   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     67   67   67     17   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     67   67   67     17   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     67   67   67     17   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     67   67   67     15   58   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     67   67   67      3   45   63   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     41     58     63     65     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  61.19  86.57  94.03  97.01  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.54   0.67   0.79   0.85   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93
GDT RMS_ALL_AT   1.10   1.08   0.99   0.95   0.94   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93

# Checking swapping
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    49_A      E    49_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  Y    65_A      Y    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     3.226     0    0.041   0.043     3.927   55.476   51.429
LGA    P     3_A      P     3_A     2.227     0    0.038   0.308     2.655   66.786   64.830
LGA    E     4_A      E     4_A     2.409     0    0.047   0.182     2.735   66.786   62.275
LGA    E     5_A      E     5_A     1.931     0    0.047   1.168     4.752   75.119   63.280
LGA    Q     6_A      Q     6_A     1.154     0    0.018   0.654     2.298   85.952   79.683
LGA    K     7_A      K     7_A     0.815     0    0.019   0.788     2.412   92.857   84.815
LGA    Q     8_A      Q     8_A     0.865     0    0.024   0.865     3.341   90.476   85.026
LGA    M     9_A      M     9_A     0.692     0    0.059   0.804     1.455   95.238   89.464
LGA    L    10_A      L    10_A     0.329     0    0.070   0.298     0.662  100.000   97.619
LGA    G    11_A      G    11_A     0.491     0    0.026   0.026     0.745   95.238   95.238
LGA    E    12_A      E    12_A     0.671     0    0.037   0.201     0.938   90.476   90.476
LGA    A    13_A      A    13_A     0.779     0    0.035   0.040     0.832   90.476   90.476
LGA    I    14_A      I    14_A     0.627     0    0.033   1.335     4.404   90.476   76.429
LGA    Y    15_A      Y    15_A     0.667     0    0.033   0.121     1.076   90.476   89.722
LGA    P    16_A      P    16_A     0.728     0    0.024   0.175     1.338   90.476   89.184
LGA    K    17_A      K    17_A     0.664     0    0.018   0.535     1.237   92.857   89.524
LGA    V    18_A      V    18_A     0.509     0    0.018   0.155     0.627   90.476   90.476
LGA    A    19_A      A    19_A     0.594     0    0.033   0.035     0.643   90.476   90.476
LGA    A    20_A      A    20_A     0.575     0    0.060   0.088     0.757   90.476   90.476
LGA    S    21_A      S    21_A     0.446     0    0.119   0.142     1.337  100.000   93.810
LGA    Q    22_A      Q    22_A     0.405     0    0.044   0.153     0.719   95.238   97.884
LGA    P    23_A      P    23_A     0.874     0    0.036   0.323     1.413   85.952   89.252
LGA    E    24_A      E    24_A     1.024     0    0.071   1.242     3.841   83.690   66.984
LGA    L    25_A      L    25_A     0.887     0    0.040   1.082     3.778   90.476   82.321
LGA    A    26_A      A    26_A     0.762     0    0.025   0.045     0.808   90.476   90.476
LGA    G    27_A      G    27_A     0.998     0    0.064   0.064     1.022   88.214   88.214
LGA    K    28_A      K    28_A     0.922     0    0.045   0.548     2.376   90.476   84.603
LGA    L    29_A      L    29_A     0.546     0    0.050   1.046     4.520   95.238   78.333
LGA    T    30_A      T    30_A     0.459     0    0.805   0.875     3.305   82.857   88.844
LGA    G    31_A      G    31_A     0.566     0    0.101   0.101     0.612   95.238   95.238
LGA    M    32_A      M    32_A     0.422     0    0.042   0.185     0.617  100.000   97.619
LGA    I    33_A      I    33_A     0.295     0    0.033   0.257     0.849  100.000   97.619
LGA    L    34_A      L    34_A     0.203     0    0.025   0.133     0.524  100.000   98.810
LGA    E    35_A      E    35_A     0.317     0    0.073   1.049     3.419   97.619   78.042
LGA    L    36_A      L    36_A     0.448     0    0.058   0.251     0.630   95.238   95.238
LGA    P    37_A      P    37_A     0.813     0    0.027   0.384     1.427   92.857   90.544
LGA    V    38_A      V    38_A     0.943     0    0.039   0.185     1.708   90.476   85.374
LGA    T    39_A      T    39_A     0.592     0    0.024   1.203     2.849   95.238   85.034
LGA    E    40_A      E    40_A     0.338     0    0.028   0.786     2.272  100.000   89.947
LGA    L    41_A      L    41_A     0.519     0    0.020   1.009     2.673   92.857   85.476
LGA    L    42_A      L    42_A     0.528     0    0.051   0.894     2.422   95.238   86.429
LGA    H    43_A      H    43_A     0.406     0    0.025   0.206     1.122  100.000   93.429
LGA    L    44_A      L    44_A     0.496     0    0.030   0.135     0.677   95.238   94.048
LGA    L    45_A      L    45_A     0.956     0    0.058   0.109     1.532   85.952   82.619
LGA    E    46_A      E    46_A     1.016     0    0.046   0.752     3.425   85.952   69.471
LGA    E    47_A      E    47_A     0.778     0    0.048   1.020     3.567   90.476   76.720
LGA    S    48_A      S    48_A     0.135     0    0.030   0.656     2.076  100.000   94.127
LGA    E    49_A      E    49_A     0.736     0    0.104   0.707     3.711   97.619   82.540
LGA    A    50_A      A    50_A     0.400     0    0.022   0.020     0.500  100.000   98.095
LGA    L    51_A      L    51_A     0.139     0    0.029   0.235     0.640  100.000   98.810
LGA    D    52_A      D    52_A     0.463     0    0.024   0.915     3.506   97.619   79.881
LGA    A    53_A      A    53_A     0.547     0    0.029   0.028     0.644   92.857   92.381
LGA    K    54_A      K    54_A     0.476     0    0.027   0.560     1.997   97.619   89.735
LGA    V    55_A      V    55_A     0.388     0    0.009   0.058     0.510  100.000   98.639
LGA    N    56_A      N    56_A     0.366     0    0.056   0.130     0.506   97.619   98.810
LGA    E    57_A      E    57_A     0.427     0    0.057   0.391     3.234  100.000   80.847
LGA    A    58_A      A    58_A     0.415     0    0.031   0.028     0.425  100.000  100.000
LGA    L    59_A      L    59_A     0.360     0    0.029   0.406     2.223   95.238   87.381
LGA    E    60_A      E    60_A     0.841     0    0.024   0.722     2.566   88.214   82.804
LGA    V    61_A      V    61_A     0.991     0    0.029   0.074     1.195   85.952   86.599
LGA    L    62_A      L    62_A     1.043     0    0.020   0.562     2.543   83.690   80.714
LGA    K    63_A      K    63_A     1.181     0    0.054   1.434     4.543   81.429   70.529
LGA    E    64_A      E    64_A     1.429     0    0.029   0.181     2.595   79.286   71.270
LGA    Y    65_A      Y    65_A     1.334     0    0.032   1.057     7.963   81.429   52.897
LGA    Q    66_A      Q    66_A     1.132     0    0.162   0.558     3.873   88.333   74.762
LGA    Q    67_A      Q    67_A     0.933     0    0.152   1.242     4.823   85.952   73.704
LGA    N    68_A      N    68_A     1.169     0    0.111   0.938     5.824   66.310   56.071

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     519    519  100.00                67
SUMMARY(RMSD_GDC):     0.934          0.964                  1.596           90.668   84.834

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.93    95.896    98.187     6.482

LGA_LOCAL      RMSD:   0.934  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.934  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.934  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.688415 * X  +  -0.366445 * Y  +  -0.625941 * Z  +   9.889184
  Y_new =  -0.725003 * X  +  -0.373053 * Y  +  -0.578967 * Z  +  17.688494
  Z_new =  -0.021350 * X  +   0.852379 * Y  +  -0.522489 * Z  +   7.332162 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.811278  0.021351  2.120703   [DEG:  -46.4828    1.2233  121.5074 ]
ZXZ: -0.824364  2.120564 -0.025042   [DEG:  -47.2326  121.4994   -1.4348 ]
 
# END of job
