
#######################################################
#                                                     #
#                        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        1.34     1.34
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.34     1.34
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    69       2_B - 70_B        0.97     1.36
  LCS_AVERAGE:     95.46

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      3   71   71      3    5    5    5    7   11   13   24   47   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     69   71   71     16   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     69   71   71     12   50   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     69   71   71      4   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     69   71   71     17   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     69   71   71     21   47   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     69   71   71     21   49   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     69   71   71     16   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     69   71   71     16   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     69   71   71     17   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     69   71   71     14   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     69   71   71      9   30   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     69   71   71      9   39   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     69   71   71     23   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     69   71   71     21   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     69   71   71     17   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     69   71   71     16   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     69   71   71     16   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     69   71   71     15   37   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     69   71   71     15   37   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     69   71   71     17   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     69   71   71     16   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     69   71   71     15   37   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     69   71   71     15   46   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     69   71   71     18   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     69   71   71     17   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     69   71   71     15   37   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     69   71   71     15   41   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     69   71   71     18   51   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     69   71   71     11   50   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     69   71   71      5   40   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     69   71   71     15   40   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     69   71   71     15   40   68   68   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     69   71   71      3    5   14   44   69   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     48   71   71      3    4    7   15   38   70   70   70   70   70   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  98.49  (  95.46  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     23     51     68     68     69     70     70     70     70     70     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  32.39  71.83  95.77  95.77  97.18  98.59  98.59  98.59  98.59  98.59 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.38   0.68   0.91   0.91   0.97   1.06   1.06   1.06   1.06   1.06   1.34   1.34   1.34   1.34   1.34   1.34   1.34   1.34   1.34   1.34
GDT RMS_ALL_AT   1.46   1.39   1.37   1.37   1.36   1.36   1.36   1.36   1.36   1.36   1.34   1.34   1.34   1.34   1.34   1.34   1.34   1.34   1.34   1.34

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  E    31_B      E    31_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     7.261     0    0.062   0.062     7.645   15.119   15.119
LGA    S     2_B      S     2_B     0.965     0    0.144   0.710     3.148   69.762   68.175
LGA    V     3_B      V     3_B     0.760     0    0.074   0.854     2.237   88.214   81.837
LGA    S     4_B      S     4_B     0.862     0    0.110   0.565     1.736   88.214   84.524
LGA    K     5_B      K     5_B     0.915     0    0.145   1.096     3.551   83.810   74.603
LGA    W     6_B      W     6_B     0.909     0    0.036   0.096     1.009   90.476   89.830
LGA    S     7_B      S     7_B     0.880     0    0.083   0.637     3.226   90.476   83.730
LGA    T     8_B      T     8_B     0.723     0    0.045   0.993     2.943   90.476   80.952
LGA    D     9_B      D     9_B     0.710     0    0.032   0.804     3.744   90.476   77.202
LGA    E    10_B      E    10_B     0.932     0    0.041   1.091     3.672   90.476   75.714
LGA    V    11_B      V    11_B     0.699     0    0.034   0.113     1.041   90.476   89.184
LGA    S    12_B      S    12_B     0.991     0    0.027   0.709     1.964   88.214   84.524
LGA    E    13_B      E    13_B     1.129     0    0.046   1.377     6.626   85.952   62.063
LGA    F    14_B      F    14_B     0.855     0    0.029   0.085     0.916   90.476   90.476
LGA    I    15_B      I    15_B     0.808     0    0.029   0.644     1.669   90.476   87.143
LGA    Q    16_B      Q    16_B     0.993     0    0.073   1.072     2.664   90.476   81.905
LGA    S    17_B      S    17_B     0.977     0    0.080   0.094     0.993   90.476   90.476
LGA    L    18_B      L    18_B     0.843     0    0.038   0.106     1.124   88.214   90.536
LGA    P    19_B      P    19_B     0.997     0    0.547   0.917     3.410   78.095   79.592
LGA    G    20_B      G    20_B     1.010     0    0.129   0.129     1.710   81.548   81.548
LGA    C    21_B      C    21_B     0.867     0    0.134   0.154     1.281   88.214   85.952
LGA    E    22_B      E    22_B     0.787     0    0.071   0.676     2.347   90.476   84.603
LGA    E    23_B      E    23_B     0.574     0    0.187   0.898     3.299   92.857   81.376
LGA    H    24_B      H    24_B     0.443     0    0.143   0.281     1.372  100.000   92.524
LGA    G    25_B      G    25_B     0.618     0    0.041   0.041     0.646   90.476   90.476
LGA    K    26_B      K    26_B     0.831     0    0.031   0.803     1.909   90.476   84.550
LGA    V    27_B      V    27_B     0.935     0    0.022   1.112     3.254   90.476   81.020
LGA    F    28_B      F    28_B     0.664     0    0.038   0.092     1.355   90.476   88.874
LGA    K    29_B      K    29_B     0.836     0    0.030   0.845     2.913   85.952   79.947
LGA    D    30_B      D    30_B     1.388     0    0.091   0.129     2.275   81.429   74.107
LGA    E    31_B      E    31_B     1.166     0    0.118   0.671     2.723   83.690   74.180
LGA    Q    32_B      Q    32_B     1.181     0    0.048   1.213     2.988   83.690   79.788
LGA    I    33_B      I    33_B     0.590     0    0.097   0.111     0.887   90.476   92.857
LGA    D    34_B      D    34_B     0.625     0    0.024   0.197     1.112   92.857   89.405
LGA    G    35_B      G    35_B     0.513     0    0.037   0.037     0.584   95.238   95.238
LGA    E    36_B      E    36_B     0.683     0    0.030   0.777     3.286   90.476   77.407
LGA    A    37_B      A    37_B     0.731     0    0.041   0.043     0.937   90.476   90.476
LGA    F    38_B      F    38_B     0.355     0    0.038   0.365     1.791  100.000   88.355
LGA    L    39_B      L    39_B     0.306     0    0.117   0.958     2.408   92.976   87.500
LGA    L    40_B      L    40_B     0.478     0    0.173   1.056     2.489   92.976   85.298
LGA    M    41_B      M    41_B     0.462     0    0.017   0.939     2.757  100.000   86.905
LGA    T    42_B      T    42_B     0.327     0    0.041   0.046     0.564   95.238   97.279
LGA    Q    43_B      Q    43_B     0.934     0    0.028   1.257     4.331   90.476   73.598
LGA    T    44_B      T    44_B     1.044     0    0.044   0.953     3.474   85.952   77.143
LGA    D    45_B      D    45_B     0.716     0    0.029   0.183     1.278   90.476   89.345
LGA    I    46_B      I    46_B     0.425     0    0.058   0.114     1.425   92.857   90.536
LGA    V    47_B      V    47_B     1.139     0    0.022   1.138     3.729   83.690   77.279
LGA    K    48_B      K    48_B     1.611     0    0.136   1.196    10.307   77.143   47.407
LGA    I    49_B      I    49_B     1.456     0    0.026   0.626     2.764   81.429   73.155
LGA    M    50_B      M    50_B     0.613     0    0.049   0.854     2.764   95.238   86.429
LGA    S    51_B      S    51_B     0.206     0    0.035   0.707     2.799  100.000   92.857
LGA    I    52_B      I    52_B     0.448     0    0.026   0.111     1.105   95.238   91.726
LGA    K    53_B      K    53_B     0.827     0    0.091   1.424     3.775   88.214   72.381
LGA    E    54_B      E    54_B     1.022     0    0.023   0.695     3.432   83.690   74.392
LGA    G    55_B      G    55_B     1.462     0    0.037   0.037     1.525   79.286   79.286
LGA    P    56_B      P    56_B     1.412     0    0.721   0.681     3.883   69.762   73.537
LGA    A    57_B      A    57_B     0.635     0    0.062   0.064     0.990   90.476   92.381
LGA    E    58_B      E    58_B     1.022     0    0.041   0.620     3.659   83.690   70.159
LGA    K    59_B      K    59_B     1.472     0    0.033   0.728     2.097   81.429   75.767
LGA    I    60_B      I    60_B     1.033     0    0.031   0.081     1.210   85.952   84.821
LGA    F    61_B      F    61_B     0.388     0    0.073   0.153     0.937   97.619   95.671
LGA    N    62_B      N    62_B     0.485     0    0.044   0.409     1.212   97.619   91.786
LGA    S    63_B      S    63_B     1.269     0    0.050   0.682     1.502   81.548   81.508
LGA    I    64_B      I    64_B     1.332     0    0.024   0.162     1.751   79.286   79.286
LGA    L    65_B      L    65_B     0.892     0    0.053   0.912     2.357   90.476   85.060
LGA    M    66_B      M    66_B     0.869     0    0.032   0.880     2.703   90.476   84.107
LGA    F    67_B      F    67_B     1.259     0    0.032   0.816     3.530   81.429   66.970
LGA    K    68_B      K    68_B     1.214     0    0.051   0.789     3.597   81.429   76.243
LGA    A    69_B      A    69_B     1.289     0    0.649   0.621     2.611   75.357   76.571
LGA    A    70_B      A    70_B     2.755     0    0.144   0.145     2.924   57.143   57.143
LGA    E    71_B      E    71_B     3.624     0    0.660   1.387     7.100   40.714   34.656

# 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):     1.343          1.380                  1.816           86.041   80.401

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     70    1.06    91.549    96.609     6.043

LGA_LOCAL      RMSD:   1.058  Number of atoms:   70  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.359  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.343  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.766850 * X  +  -0.563564 * Y  +  -0.307143 * Z  +  23.453176
  Y_new =   0.044158 * X  +   0.523738 * Y  +  -0.850734 * Z  +  72.699463
  Z_new =   0.640305 * X  +   0.638823 * Y  +   0.426514 * Z  +   7.678402 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.057520 -0.694896  0.982109   [DEG:    3.2957  -39.8146   56.2707 ]
ZXZ: -0.346469  1.130161  0.786557   [DEG:  -19.8512   64.7535   45.0664 ]
 
# END of job
