
#######################################################
#                                                     #
#                        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   73 (  570),  selected   71 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   71 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.09     1.09
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.09     1.09
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    69       1_B - 69_B        0.95     1.11
  LONGEST_CONTINUOUS_SEGMENT:    69       2_B - 70_B        1.00     1.09
  LCS_AVERAGE:     96.83

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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_B     G     1_B     69   71   71      8   37   62   69   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     69   71   71     19   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     69   71   71     23   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     69   71   71     27   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     69   71   71     32   51   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     69   71   71      6   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     69   71   71     11   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     69   71   71     28   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     69   71   71     28   51   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     69   71   71     19   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     69   71   71     32   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     69   71   71     28   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     69   71   71     26   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     69   71   71     23   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     69   71   71     21   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     69   71   71     21   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     69   71   71     19   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     69   71   71     19   34   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     69   71   71     19   32   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     69   71   71     19   50   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     69   71   71     19   50   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     69   71   71     21   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     69   71   71     21   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     69   71   71     21   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     69   71   71     21   40   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     69   71   71     21   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     69   71   71     21   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     69   71   71     21   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     69   71   71     21   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     69   71   71     21   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     69   71   71     31   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     69   71   71     21   53   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     69   71   71     18   46   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     69   71   71     18   48   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     69   71   71     18   50   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     69   71   71     18   40   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     69   71   71     18   37   66   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     69   71   71      9   32   64   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     69   71   71      9   29   57   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     69   71   71      9   28   37   50   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     51   71   71      9   13   37   50   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  98.94  (  96.83  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     32     53     66     69     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  45.07  74.65  92.96  97.18  98.59 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.63   0.85   0.95   1.06   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09
GDT RMS_ALL_AT   1.42   1.25   1.14   1.11   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  F    14_B      F    14_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B
#   possible swapping detected:  F    67_B      F    67_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.138     0    0.453   0.453     3.469   67.262   67.262
LGA    S     2_B      S     2_B     1.254     0    0.051   0.076     1.848   81.548   80.079
LGA    V     3_B      V     3_B     0.886     0    0.074   0.112     1.504   90.476   85.374
LGA    S     4_B      S     4_B     1.020     0    0.041   0.168     1.547   83.690   81.508
LGA    K     5_B      K     5_B     1.060     0    0.025   0.841     5.234   83.690   64.974
LGA    W     6_B      W     6_B     1.008     0    0.037   0.138     1.889   83.690   81.531
LGA    S     7_B      S     7_B     0.838     0    0.038   0.042     0.896   90.476   90.476
LGA    T     8_B      T     8_B     0.582     0    0.066   1.139     2.573   92.857   84.558
LGA    D     9_B      D     9_B     0.164     0    0.031   0.782     3.291  100.000   84.940
LGA    E    10_B      E    10_B     0.594     0    0.042   0.360     2.167   92.857   85.661
LGA    V    11_B      V    11_B     0.420     0    0.011   0.056     0.652  100.000   98.639
LGA    S    12_B      S    12_B     0.535     0    0.033   0.107     0.924   92.857   92.063
LGA    E    13_B      E    13_B     1.092     0    0.013   0.774     4.336   83.690   69.101
LGA    F    14_B      F    14_B     1.109     0    0.076   1.363     7.069   81.548   56.017
LGA    I    15_B      I    15_B     0.636     0    0.013   0.701     2.632   90.476   86.310
LGA    Q    16_B      Q    16_B     1.060     0    0.049   0.154     1.979   83.690   81.481
LGA    S    17_B      S    17_B     1.341     0    0.007   0.662     2.160   81.429   78.651
LGA    L    18_B      L    18_B     1.021     0    0.036   0.090     1.096   81.429   87.143
LGA    P    19_B      P    19_B     1.252     0    0.012   0.386     2.232   81.429   77.823
LGA    G    20_B      G    20_B     1.307     0    0.035   0.035     1.310   81.429   81.429
LGA    C    21_B      C    21_B     0.820     0    0.043   0.049     1.024   88.214   88.968
LGA    E    22_B      E    22_B     0.938     0    0.060   0.773     4.427   88.214   70.847
LGA    E    23_B      E    23_B     0.653     0    0.083   0.824     3.496   90.476   81.164
LGA    H    24_B      H    24_B     0.668     0    0.071   0.097     1.373   90.476   85.952
LGA    G    25_B      G    25_B     0.736     0    0.040   0.040     0.859   90.476   90.476
LGA    K    26_B      K    26_B     0.869     0    0.011   0.765     1.586   90.476   83.545
LGA    V    27_B      V    27_B     1.153     0    0.047   1.063     3.661   85.952   78.571
LGA    F    28_B      F    28_B     0.579     0    0.008   0.210     1.705   90.476   88.095
LGA    K    29_B      K    29_B     0.705     0    0.009   1.057     3.409   88.214   75.556
LGA    D    30_B      D    30_B     1.391     0    0.051   0.074     1.726   81.429   77.143
LGA    E    31_B      E    31_B     1.205     0    0.015   0.136     1.789   81.429   78.571
LGA    Q    32_B      Q    32_B     1.195     0    0.019   0.834     4.301   81.429   68.624
LGA    I    33_B      I    33_B     0.650     0    0.060   0.070     0.767   92.857   92.857
LGA    D    34_B      D    34_B     0.729     0    0.014   0.120     1.425   90.476   88.214
LGA    G    35_B      G    35_B     0.789     0    0.060   0.060     0.789   90.476   90.476
LGA    E    36_B      E    36_B     1.020     0    0.017   0.066     2.245   85.952   77.831
LGA    A    37_B      A    37_B     0.815     0    0.029   0.028     0.853   90.476   90.476
LGA    F    38_B      F    38_B     0.420     0    0.065   0.251     1.201   97.619   92.338
LGA    L    39_B      L    39_B     0.295     0    0.099   0.189     0.629   97.619   96.429
LGA    L    40_B      L    40_B     0.178     0    0.018   0.077     0.518  100.000   98.810
LGA    M    41_B      M    41_B     0.401     0    0.065   0.144     0.983  100.000   95.238
LGA    T    42_B      T    42_B     0.584     0    0.017   0.042     0.654   90.476   90.476
LGA    Q    43_B      Q    43_B     0.569     0    0.011   0.078     1.029   92.857   90.529
LGA    T    44_B      T    44_B     0.531     0    0.039   0.105     0.772   95.238   93.197
LGA    D    45_B      D    45_B     0.546     0    0.013   0.113     1.015   90.476   89.345
LGA    I    46_B      I    46_B     0.638     0    0.033   0.069     0.815   90.476   90.476
LGA    V    47_B      V    47_B     0.881     0    0.045   0.051     1.158   90.476   89.184
LGA    K    48_B      K    48_B     1.389     0    0.061   0.818     5.249   79.286   66.243
LGA    I    49_B      I    49_B     1.384     0    0.034   0.086     1.816   81.429   77.143
LGA    M    50_B      M    50_B     1.000     0    0.030   0.266     1.633   88.214   84.881
LGA    S    51_B      S    51_B     0.943     0    0.023   0.045     1.414   88.214   85.952
LGA    I    52_B      I    52_B     0.545     0    0.045   0.044     0.698   90.476   92.857
LGA    K    53_B      K    53_B     0.860     0    0.026   0.651     2.615   90.476   83.069
LGA    E    54_B      E    54_B     1.124     0    0.031   0.574     2.727   81.429   74.180
LGA    G    55_B      G    55_B     1.236     0    0.067   0.067     1.370   81.429   81.429
LGA    P    56_B      P    56_B     0.857     0    0.010   0.293     0.954   90.476   90.476
LGA    A    57_B      A    57_B     0.668     0    0.031   0.031     0.778   92.857   92.381
LGA    E    58_B      E    58_B     0.870     0    0.026   0.152     1.200   90.476   87.460
LGA    K    59_B      K    59_B     0.968     0    0.014   0.101     1.537   90.476   84.497
LGA    I    60_B      I    60_B     0.542     0    0.015   0.065     0.647   95.238   96.429
LGA    F    61_B      F    61_B     0.267     0    0.064   0.109     0.601  100.000   97.403
LGA    N    62_B      N    62_B     0.556     0    0.006   0.023     1.388   95.238   89.464
LGA    S    63_B      S    63_B     1.004     0    0.015   0.038     1.350   85.952   84.444
LGA    I    64_B      I    64_B     0.855     0    0.008   0.086     1.174   88.214   88.214
LGA    L    65_B      L    65_B     0.546     0    0.028   0.136     0.979   90.476   94.048
LGA    M    66_B      M    66_B     1.245     0    0.017   0.845     2.714   81.548   79.702
LGA    F    67_B      F    67_B     1.604     0    0.020   0.468     2.070   72.976   76.797
LGA    K    68_B      K    68_B     1.746     0    0.026   0.984     2.521   70.833   70.265
LGA    A    69_B      A    69_B     2.032     0    0.083   0.086     2.335   66.786   68.000
LGA    A    70_B      A    70_B     2.913     0    0.146   0.158     3.351   53.571   54.286
LGA    E    71_B      E    71_B     3.214     0    0.023   0.675     3.718   50.000   53.333

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     553    553  100.00                71
SUMMARY(RMSD_GDC):     1.089          1.100                  1.484           86.807   83.118

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.09    92.958    97.183     5.972

LGA_LOCAL      RMSD:   1.089  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.089  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.089  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.147701 * X  +  -0.982704 * Y  +  -0.111703 * Z  +  26.203688
  Y_new =  -0.475811 * X  +  -0.028411 * Y  +   0.879089 * Z  +  40.739590
  Z_new =  -0.867057 * X  +   0.182992 * Y  +  -0.463385 * Z  +  -8.362887 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.871784  1.049265  2.765489   [DEG: -107.2453   60.1185  158.4508 ]
ZXZ: -3.015203  2.052607 -1.362800   [DEG: -172.7584  117.6057  -78.0827 ]
 
# END of job
