
#######################################################
#                                                     #
#                        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        0.69     0.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        0.69     0.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        0.69     0.69
  LCS_AVERAGE:    100.00

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     71   71   71      7   61   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     71   71   71     39   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     71   71   71     39   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     71   71   71     41   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     71   71   71     39   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     71   71   71     39   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     71   71   71     27   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     71   71   71     43   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     71   71   71     39   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     71   71   71     42   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     71   71   71     33   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     71   71   71     30   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     71   71   71     43   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     71   71   71     14   54   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     71   71   71     14   53   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     71   71   71     14   53   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     71   71   71     15   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     71   71   71     43   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     71   71   71     44   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     71   71   71     43   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     71   71   71     43   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     71   71   71     37   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     71   71   71     30   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     71   71   71     18   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     71   71   71     18   64   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     71   71   71     18   46   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     71   71   71      9   46   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     71   71   71     15   46   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
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     44     64     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  61.97  90.14  98.59 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.51   0.66   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69
GDT RMS_ALL_AT   0.78   0.71   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  F    14_B      F    14_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  F    28_B      F    28_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  F    38_B      F    38_B
#   possible swapping detected:  F    61_B      F    61_B
#   possible swapping detected:  E    71_B      E    71_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     1.661     0    0.350   0.350     2.767   80.119   80.119
LGA    S     2_B      S     2_B     0.675     0    0.039   0.715     2.885   90.476   84.921
LGA    V     3_B      V     3_B     0.295     0    0.067   0.062     0.472  100.000  100.000
LGA    S     4_B      S     4_B     0.718     0    0.035   0.155     0.957   90.476   90.476
LGA    K     5_B      K     5_B     0.654     0    0.034   0.825     4.722   92.857   72.698
LGA    W     6_B      W     6_B     0.752     0    0.037   0.114     0.799   90.476   90.476
LGA    S     7_B      S     7_B     0.647     0    0.013   0.045     0.683   90.476   92.063
LGA    T     8_B      T     8_B     0.635     0    0.047   1.083     2.630   90.476   83.197
LGA    D     9_B      D     9_B     0.344     0    0.066   0.778     3.372  100.000   84.940
LGA    E    10_B      E    10_B     0.291     0    0.022   0.244     1.481  100.000   92.751
LGA    V    11_B      V    11_B     0.404     0    0.010   0.033     0.547  100.000   97.279
LGA    S    12_B      S    12_B     0.469     0    0.022   0.117     0.549  100.000   98.413
LGA    E    13_B      E    13_B     0.308     0    0.035   0.809     3.898  100.000   81.587
LGA    F    14_B      F    14_B     0.352     0    0.029   0.200     1.485  100.000   90.649
LGA    I    15_B      I    15_B     0.369     0    0.010   0.621     1.660  100.000   95.417
LGA    Q    16_B      Q    16_B     0.432     0    0.022   0.127     0.663   97.619   97.884
LGA    S    17_B      S    17_B     0.559     0    0.027   0.032     0.666   92.857   92.063
LGA    L    18_B      L    18_B     0.533     0    0.098   0.141     0.533   92.857   95.238
LGA    P    19_B      P    19_B     0.754     0    0.057   0.386     2.272   90.476   85.510
LGA    G    20_B      G    20_B     0.647     0    0.105   0.105     1.090   88.214   88.214
LGA    C    21_B      C    21_B     0.356     0    0.018   0.093     0.519  100.000   98.413
LGA    E    22_B      E    22_B     0.537     0    0.043   0.124     1.111   92.857   90.529
LGA    E    23_B      E    23_B     0.550     0    0.048   1.191     5.346   92.857   70.370
LGA    H    24_B      H    24_B     0.257     0    0.111   0.109     0.718  100.000   97.143
LGA    G    25_B      G    25_B     0.377     0    0.018   0.018     0.463  100.000  100.000
LGA    K    26_B      K    26_B     0.460     0    0.013   0.617     2.234   97.619   92.910
LGA    V    27_B      V    27_B     0.682     0    0.057   1.117     3.361   92.857   83.469
LGA    F    28_B      F    28_B     0.190     0    0.026   0.038     0.442  100.000  100.000
LGA    K    29_B      K    29_B     0.316     0    0.017   0.795     2.569   95.238   86.190
LGA    D    30_B      D    30_B     0.810     0    0.080   0.106     1.123   90.476   87.083
LGA    E    31_B      E    31_B     0.863     0    0.023   0.097     1.222   90.476   87.460
LGA    Q    32_B      Q    32_B     0.826     0    0.044   0.486     2.222   90.476   84.603
LGA    I    33_B      I    33_B     0.500     0    0.044   0.621     1.671   92.857   91.845
LGA    D    34_B      D    34_B     0.601     0    0.033   0.129     1.092   95.238   91.726
LGA    G    35_B      G    35_B     0.392     0    0.041   0.041     0.518   97.619   97.619
LGA    E    36_B      E    36_B     0.692     0    0.048   0.101     1.742   90.476   84.550
LGA    A    37_B      A    37_B     0.599     0    0.062   0.073     0.640   92.857   94.286
LGA    F    38_B      F    38_B     0.369     0    0.032   0.222     0.629  100.000   98.268
LGA    L    39_B      L    39_B     0.439     0    0.095   0.210     0.786   97.619   95.238
LGA    L    40_B      L    40_B     0.267     0    0.111   0.187     0.736   97.619   95.238
LGA    M    41_B      M    41_B     0.132     0    0.078   0.103     0.501  100.000   98.810
LGA    T    42_B      T    42_B     0.573     0    0.039   0.045     0.716   95.238   93.197
LGA    Q    43_B      Q    43_B     0.598     0    0.013   0.698     2.873   95.238   86.878
LGA    T    44_B      T    44_B     0.485     0    0.013   0.078     0.705   97.619   95.918
LGA    D    45_B      D    45_B     0.374     0    0.021   0.166     0.792  100.000   96.429
LGA    I    46_B      I    46_B     0.545     0    0.028   0.056     0.884   92.857   91.667
LGA    V    47_B      V    47_B     0.516     0    0.028   0.043     0.672   92.857   91.837
LGA    K    48_B      K    48_B     1.162     0    0.020   0.926     5.272   83.690   70.106
LGA    I    49_B      I    49_B     1.352     0    0.076   0.119     1.461   81.429   81.429
LGA    M    50_B      M    50_B     1.221     0    0.016   0.708     1.641   81.429   81.488
LGA    S    51_B      S    51_B     0.962     0    0.020   0.026     1.432   88.214   85.952
LGA    I    52_B      I    52_B     0.430     0    0.022   0.042     0.725   97.619   96.429
LGA    K    53_B      K    53_B     0.348     0    0.029   0.667     2.823  100.000   89.418
LGA    E    54_B      E    54_B     0.409     0    0.034   0.763     3.784  100.000   82.328
LGA    G    55_B      G    55_B     0.372     0    0.020   0.020     0.381  100.000  100.000
LGA    P    56_B      P    56_B     0.251     0    0.016   0.285     0.807  100.000   98.639
LGA    A    57_B      A    57_B     0.261     0    0.020   0.025     0.358  100.000  100.000
LGA    E    58_B      E    58_B     0.415     0    0.033   0.163     0.524  100.000   98.942
LGA    K    59_B      K    59_B     0.365     0    0.052   0.095     0.531   97.619   98.942
LGA    I    60_B      I    60_B     0.190     0    0.013   0.030     0.227  100.000  100.000
LGA    F    61_B      F    61_B     0.269     0    0.038   0.054     0.644  100.000   96.537
LGA    N    62_B      N    62_B     0.355     0    0.033   0.057     0.527  100.000   98.810
LGA    S    63_B      S    63_B     0.335     0    0.023   0.051     0.392  100.000  100.000
LGA    I    64_B      I    64_B     0.377     0    0.011   0.040     0.478  100.000  100.000
LGA    L    65_B      L    65_B     0.464     0    0.017   0.142     0.772   95.238   97.619
LGA    M    66_B      M    66_B     0.666     0    0.020   0.619     3.441   90.476   76.190
LGA    F    67_B      F    67_B     0.823     0    0.050   0.297     1.311   88.214   89.654
LGA    K    68_B      K    68_B     1.069     0    0.054   0.950     2.692   83.690   80.741
LGA    A    69_B      A    69_B     1.308     0    0.059   0.069     1.510   79.286   79.714
LGA    A    70_B      A    70_B     1.731     0    0.120   0.137     2.176   70.833   71.238
LGA    E    71_B      E    71_B     1.853     0    0.128   0.696     2.269   72.857   75.026

# 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):     0.688          0.694                  1.087           94.069   90.490

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    0.69    97.535    99.117     9.016

LGA_LOCAL      RMSD:   0.688  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.688  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   0.688  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.828511 * X  +  -0.027947 * Y  +   0.559275 * Z  +  20.162212
  Y_new =  -0.116562 * X  +   0.968270 * Y  +   0.221060 * Z  +  37.737732
  Z_new =  -0.547707 * X  +  -0.248341 * Y  +   0.798964 * Z  +   4.356051 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.139771  0.579622 -0.301361   [DEG:   -8.0083   33.2099  -17.2667 ]
ZXZ:  1.947211  0.645226 -1.996489   [DEG:  111.5670   36.9687 -114.3904 ]
 
# END of job
