
#######################################################
#                                                     #
#                        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        1.40     1.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.40     1.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    69       1_B - 69_B        0.91     1.45
  LCS_AVERAGE:     94.60

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      5   11   57   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     69   71   71     22   53   64   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     69   71   71     25   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     69   71   71     20   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     69   71   71     25   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     69   71   71     10   46   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     69   71   71     10   35   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     69   71   71     10   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     69   71   71     23   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     69   71   71     16   37   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     69   71   71     14   38   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     69   71   71     18   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     69   71   71     19   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     69   71   71      8   53   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     69   71   71     23   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     69   71   71     13   49   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     69   71   71     25   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     69   71   71     10   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     69   71   71     10   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     69   71   71     23   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     69   71   71     25   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     69   71   71     10   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     69   71   71     22   54   64   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     69   71   71     23   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     69   71   71     23   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     69   71   71     24   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     69   71   71     24   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     69   71   71     23   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     69   71   71     23   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     69   71   71     13   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     69   71   71     13   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     69   71   71     22   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     69   71   71     26   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     69   71   71     22   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     69   71   71     22   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     69   71   71     22   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     69   71   71     21   54   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     69   71   71     18   50   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     69   71   71     18   41   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     69   71   71     20   50   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     69   71   71     18   45   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     69   71   71     18   35   60   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     69   71   71     18   37   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     69   71   71     19   49   65   68   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B      4   71   71      4    4    5   26   38   48   68   69   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B      4   71   71      4    4    5    5   38   48   56   64   70   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  98.20  (  94.60  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     26     54     65     68     69     69     69     69     70     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  36.62  76.06  91.55  95.77  97.18  97.18  97.18  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
GDT RMS_LOCAL    0.36   0.62   0.84   0.87   0.91   0.91   0.91   0.91   1.16   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40
GDT RMS_ALL_AT   1.47   1.44   1.42   1.44   1.45   1.45   1.45   1.45   1.41   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  F    61_B      F    61_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.159     0    0.348   0.348     3.844   70.000   70.000
LGA    S     2_B      S     2_B     1.021     0    0.042   0.802     3.540   85.952   78.095
LGA    V     3_B      V     3_B     0.354     0    0.082   1.054     3.229  100.000   85.374
LGA    S     4_B      S     4_B     0.389     0    0.006   0.064     0.655  100.000   98.413
LGA    K     5_B      K     5_B     0.451     0    0.035   0.702     2.753  100.000   86.561
LGA    W     6_B      W     6_B     0.603     0    0.023   0.118     1.303   90.476   88.537
LGA    S     7_B      S     7_B     0.610     0    0.059   0.094     0.739   95.238   93.651
LGA    T     8_B      T     8_B     0.455     0    0.022   0.083     0.877  100.000   95.918
LGA    D     9_B      D     9_B     0.418     0    0.024   0.837     3.437   95.238   82.560
LGA    E    10_B      E    10_B     0.672     0    0.020   0.247     2.103   92.857   83.757
LGA    V    11_B      V    11_B     0.368     0    0.022   0.039     0.633   95.238   95.918
LGA    S    12_B      S    12_B     1.168     0    0.037   0.511     2.888   83.690   78.889
LGA    E    13_B      E    13_B     1.569     0    0.021   0.826     6.350   77.143   57.037
LGA    F    14_B      F    14_B     1.058     0    0.024   0.253     2.157   83.690   78.485
LGA    I    15_B      I    15_B     0.788     0    0.040   0.646     2.032   88.214   83.869
LGA    Q    16_B      Q    16_B     1.728     0    0.057   0.988     3.063   75.000   70.582
LGA    S    17_B      S    17_B     1.631     0    0.061   0.079     1.739   77.143   77.143
LGA    L    18_B      L    18_B     1.042     0    0.142   0.279     1.216   81.429   83.690
LGA    P    19_B      P    19_B     0.968     0    0.085   0.198     1.220   90.476   87.891
LGA    G    20_B      G    20_B     1.125     0    0.060   0.060     1.130   85.952   85.952
LGA    C    21_B      C    21_B     0.718     0    0.060   0.059     0.860   90.476   90.476
LGA    E    22_B      E    22_B     1.171     0    0.014   0.655     2.367   85.952   80.635
LGA    E    23_B      E    23_B     0.427     0    0.065   1.007     5.168   97.619   75.767
LGA    H    24_B      H    24_B     0.301     0    0.037   0.155     0.846   95.238   94.286
LGA    G    25_B      G    25_B     0.947     0    0.060   0.060     0.982   90.476   90.476
LGA    K    26_B      K    26_B     0.829     0    0.050   0.697     1.755   90.476   87.513
LGA    V    27_B      V    27_B     0.634     0    0.027   0.116     0.894   90.476   91.837
LGA    F    28_B      F    28_B     0.599     0    0.019   0.160     1.206   90.476   89.697
LGA    K    29_B      K    29_B     0.897     0    0.011   1.092     4.568   90.476   73.545
LGA    D    30_B      D    30_B     1.059     0    0.046   0.190     1.833   88.214   83.750
LGA    E    31_B      E    31_B     0.886     0    0.015   0.086     1.328   90.476   87.460
LGA    Q    32_B      Q    32_B     0.881     0    0.037   0.114     1.440   90.476   86.455
LGA    I    33_B      I    33_B     0.555     0    0.047   0.561     1.286   95.238   91.726
LGA    D    34_B      D    34_B     0.420     0    0.022   0.043     0.773  100.000   95.238
LGA    G    35_B      G    35_B     0.271     0    0.021   0.021     0.361  100.000  100.000
LGA    E    36_B      E    36_B     0.621     0    0.019   0.661     1.345   92.857   89.524
LGA    A    37_B      A    37_B     0.671     0    0.014   0.018     0.761   90.476   90.476
LGA    F    38_B      F    38_B     0.405     0    0.021   0.098     0.455  100.000  100.000
LGA    L    39_B      L    39_B     0.226     0    0.025   0.081     0.383  100.000  100.000
LGA    L    40_B      L    40_B     0.213     0    0.056   0.147     0.717  100.000   98.810
LGA    M    41_B      M    41_B     0.194     0    0.051   0.827     2.958  100.000   92.262
LGA    T    42_B      T    42_B     0.721     0    0.043   0.081     0.943   92.857   91.837
LGA    Q    43_B      Q    43_B     1.243     0    0.010   0.233     3.186   81.429   69.735
LGA    T    44_B      T    44_B     1.279     0    0.037   1.179     3.520   81.429   74.762
LGA    D    45_B      D    45_B     0.879     0    0.016   0.065     0.992   90.476   90.476
LGA    I    46_B      I    46_B     0.713     0    0.060   0.139     1.290   90.476   89.345
LGA    V    47_B      V    47_B     0.867     0    0.050   0.059     1.037   90.476   89.184
LGA    K    48_B      K    48_B     0.991     0    0.021   1.192     8.572   90.476   60.106
LGA    I    49_B      I    49_B     0.766     0    0.066   0.661     2.973   90.476   86.310
LGA    M    50_B      M    50_B     0.468     0    0.021   0.246     0.553   92.857   92.857
LGA    S    51_B      S    51_B     0.513     0    0.063   0.692     2.724   95.238   89.683
LGA    I    52_B      I    52_B     0.564     0    0.024   0.139     1.625   90.476   87.143
LGA    K    53_B      K    53_B     0.472     0    0.034   1.057     4.476   95.238   83.228
LGA    E    54_B      E    54_B     0.455     0    0.021   0.861     4.960   97.619   76.878
LGA    G    55_B      G    55_B     0.451     0    0.028   0.028     0.523   97.619   97.619
LGA    P    56_B      P    56_B     0.460     0    0.040   0.265     0.591  100.000   98.639
LGA    A    57_B      A    57_B     0.481     0    0.017   0.016     0.553   95.238   96.190
LGA    E    58_B      E    58_B     0.622     0    0.029   0.904     2.867   90.476   78.254
LGA    K    59_B      K    59_B     0.745     0    0.023   0.482     1.008   90.476   90.529
LGA    I    60_B      I    60_B     0.541     0    0.016   0.120     0.694   90.476   92.857
LGA    F    61_B      F    61_B     0.517     0    0.035   0.478     1.163   97.619   93.160
LGA    N    62_B      N    62_B     0.584     0    0.020   0.537     2.113   92.857   88.452
LGA    S    63_B      S    63_B     1.108     0    0.020   0.036     1.401   83.690   82.937
LGA    I    64_B      I    64_B     1.189     0    0.028   0.460     2.151   81.429   80.476
LGA    L    65_B      L    65_B     0.989     0    0.030   1.044     2.516   85.952   80.833
LGA    M    66_B      M    66_B     1.406     0    0.031   0.663     2.977   77.143   72.024
LGA    F    67_B      F    67_B     1.831     0    0.069   0.592     3.473   70.833   64.329
LGA    K    68_B      K    68_B     1.643     0    0.064   0.968     3.341   77.143   68.783
LGA    A    69_B      A    69_B     1.331     0    0.600   0.539     1.970   81.548   81.524
LGA    A    70_B      A    70_B     6.272     0    0.596   0.550     7.721   22.143   19.143
LGA    E    71_B      E    71_B     7.263     0    0.726   0.966    10.050    6.548   15.026

# 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):     1.401          1.449                  1.756           88.139   83.586

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     69    0.91    92.254    96.448     6.866

LGA_LOCAL      RMSD:   0.905  Number of atoms:   69  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.447  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.401  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.645188 * X  +   0.744872 * Y  +  -0.169996 * Z  +   2.596493
  Y_new =   0.055785 * X  +  -0.267834 * Y  +  -0.961849 * Z  +  52.055500
  Z_new =  -0.761985 * X  +   0.611090 * Y  +  -0.214356 * Z  +  36.275188 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.086249  0.866372  1.908163   [DEG:    4.9417   49.6395  109.3297 ]
ZXZ: -0.174932  1.786829 -0.894854   [DEG:  -10.0229  102.3778  -51.2714 ]
 
# END of job
