
#######################################################
#                                                     #
#                        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   71 (  560),  selected   69 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   69 , 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:    69       3_B - 71_B        0.82     0.82
  LCS_AVERAGE:     97.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    69       3_B - 71_B        0.82     0.82
  LCS_AVERAGE:     97.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    69       3_B - 71_B        0.82     0.82
  LCS_AVERAGE:     97.18

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

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     38     63     66     67     69     69     69     69     69     69     69     69     69     69     69     69     69     69     69     69 
GDT PERCENT_AT  53.52  88.73  92.96  94.37  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18
GDT RMS_LOCAL    0.33   0.51   0.60   0.66   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82
GDT RMS_ALL_AT   0.91   0.90   0.85   0.83   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82   0.82

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  E    13_B      E    13_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:  F    38_B      F    38_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B
#   possible swapping detected:  F    61_B      F    61_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    V     3_B      V     3_B     0.389     0    0.099   0.115     0.530   95.238   97.279
LGA    S     4_B      S     4_B     0.762     0    0.070   0.150     0.991   90.476   90.476
LGA    K     5_B      K     5_B     0.676     0    0.041   0.919     4.702   90.476   72.540
LGA    W     6_B      W     6_B     0.807     0    0.058   0.144     0.934   90.476   90.476
LGA    S     7_B      S     7_B     0.763     0    0.021   0.098     1.050   90.476   88.968
LGA    T     8_B      T     8_B     0.717     0    0.035   0.166     0.838   90.476   90.476
LGA    D     9_B      D     9_B     0.493     0    0.065   0.860     3.918   97.619   82.738
LGA    E    10_B      E    10_B     0.477     0    0.027   0.209     1.570  100.000   90.741
LGA    V    11_B      V    11_B     0.615     0    0.017   0.061     0.836   90.476   90.476
LGA    S    12_B      S    12_B     0.652     0    0.024   0.093     0.748   90.476   90.476
LGA    E    13_B      E    13_B     0.373     0    0.042   1.093     5.015  100.000   77.566
LGA    F    14_B      F    14_B     0.487     0    0.020   0.180     1.567   95.238   88.139
LGA    I    15_B      I    15_B     0.579     0    0.027   0.635     1.583   92.857   89.464
LGA    Q    16_B      Q    16_B     0.519     0    0.030   0.126     0.660   92.857   93.651
LGA    S    17_B      S    17_B     0.782     0    0.035   0.059     0.911   90.476   90.476
LGA    L    18_B      L    18_B     0.748     0    0.104   0.140     0.748   90.476   90.476
LGA    P    19_B      P    19_B     0.985     0    0.077   0.382     2.469   88.214   81.701
LGA    G    20_B      G    20_B     0.842     0    0.139   0.139     1.381   88.214   88.214
LGA    C    21_B      C    21_B     0.421     0    0.024   0.053     0.591  100.000   98.413
LGA    E    22_B      E    22_B     0.384     0    0.051   0.174     1.171  100.000   95.820
LGA    E    23_B      E    23_B     0.267     0    0.076   0.954     5.593  100.000   73.386
LGA    H    24_B      H    24_B     0.195     0    0.052   0.137     0.757  100.000   97.143
LGA    G    25_B      G    25_B     0.262     0    0.019   0.019     0.428  100.000  100.000
LGA    K    26_B      K    26_B     0.480     0    0.015   0.552     2.029   95.238   91.852
LGA    V    27_B      V    27_B     0.746     0    0.050   1.162     3.457   90.476   82.177
LGA    F    28_B      F    28_B     0.309     0    0.020   0.033     0.447  100.000  100.000
LGA    K    29_B      K    29_B     0.711     0    0.035   0.781     2.720   90.595   82.169
LGA    D    30_B      D    30_B     1.234     0    0.091   0.136     1.748   83.690   79.345
LGA    E    31_B      E    31_B     1.170     0    0.016   0.115     1.504   81.429   80.476
LGA    Q    32_B      Q    32_B     1.197     0    0.078   0.691     2.557   81.429   74.974
LGA    I    33_B      I    33_B     0.752     0    0.050   0.616     1.746   90.476   88.274
LGA    D    34_B      D    34_B     0.827     0    0.032   0.188     1.490   90.476   87.083
LGA    G    35_B      G    35_B     0.649     0    0.077   0.077     0.721   95.238   95.238
LGA    E    36_B      E    36_B     0.600     0    0.030   0.993     3.112   90.476   82.963
LGA    A    37_B      A    37_B     0.543     0    0.044   0.047     0.582   92.857   94.286
LGA    F    38_B      F    38_B     0.377     0    0.024   0.283     0.561  100.000   98.268
LGA    L    39_B      L    39_B     0.415     0    0.050   0.237     0.596   97.619   97.619
LGA    L    40_B      L    40_B     0.249     0    0.105   0.189     0.700   97.619   96.429
LGA    M    41_B      M    41_B     0.195     0    0.093   0.137     0.446  100.000  100.000
LGA    T    42_B      T    42_B     0.588     0    0.016   0.147     0.765   92.857   91.837
LGA    Q    43_B      Q    43_B     0.656     0    0.010   0.296     2.720   92.857   83.862
LGA    T    44_B      T    44_B     0.652     0    0.021   0.151     1.178   92.857   90.544
LGA    D    45_B      D    45_B     0.405     0    0.020   0.148     0.567  100.000   97.619
LGA    I    46_B      I    46_B     0.530     0    0.030   0.055     0.869   90.476   90.476
LGA    V    47_B      V    47_B     0.496     0    0.035   0.044     0.513  100.000   97.279
LGA    K    48_B      K    48_B     0.740     0    0.058   0.988     5.265   90.476   75.926
LGA    I    49_B      I    49_B     0.825     0    0.041   0.094     0.841   90.476   90.476
LGA    M    50_B      M    50_B     0.848     0    0.021   0.684     1.825   90.476   88.333
LGA    S    51_B      S    51_B     0.713     0    0.066   0.081     0.811   95.238   93.651
LGA    I    52_B      I    52_B     0.482     0    0.025   0.031     0.554   97.619   96.429
LGA    K    53_B      K    53_B     0.400     0    0.049   0.782     4.394  100.000   83.598
LGA    E    54_B      E    54_B     0.361     0    0.045   0.804     3.296  100.000   83.915
LGA    G    55_B      G    55_B     0.178     0    0.045   0.045     0.211  100.000  100.000
LGA    P    56_B      P    56_B     0.110     0    0.016   0.316     1.038  100.000   97.347
LGA    A    57_B      A    57_B     0.170     0    0.030   0.033     0.266  100.000  100.000
LGA    E    58_B      E    58_B     0.301     0    0.026   0.792     3.504  100.000   84.815
LGA    K    59_B      K    59_B     0.293     0    0.024   0.062     0.573  100.000   98.942
LGA    I    60_B      I    60_B     0.291     0    0.014   0.022     0.332  100.000  100.000
LGA    F    61_B      F    61_B     0.301     0    0.044   0.047     0.483  100.000  100.000
LGA    N    62_B      N    62_B     0.387     0    0.013   0.087     0.523  100.000   98.810
LGA    S    63_B      S    63_B     0.307     0    0.025   0.086     0.343  100.000  100.000
LGA    I    64_B      I    64_B     0.532     0    0.011   0.066     0.627   95.238   92.857
LGA    L    65_B      L    65_B     0.415     0    0.029   0.099     0.910   95.238   96.429
LGA    M    66_B      M    66_B     0.714     0    0.027   0.653     2.963   88.214   78.750
LGA    F    67_B      F    67_B     1.126     0    0.028   0.164     1.688   81.548   85.584
LGA    K    68_B      K    68_B     1.609     0    0.068   1.003     2.390   72.976   75.820
LGA    A    69_B      A    69_B     1.882     0    0.079   0.084     2.230   68.810   69.619
LGA    A    70_B      A    70_B     2.426     0    0.155   0.166     3.482   59.167   61.905
LGA    E    71_B      E    71_B     3.026     0    0.058   0.632     3.830   50.119   47.884

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       69     276    276  100.00     543    543  100.00                71
SUMMARY(RMSD_GDC):     0.816          0.846                  1.232           89.955   86.380

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   71   71    4.0     69    0.82    94.366    96.003     7.533

LGA_LOCAL      RMSD:   0.816  Number of atoms:   69  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.816  Number of assigned atoms:   69 
Std_ASGN_ATOMS RMSD:   0.816  Standard rmsd on all 69 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.348448 * X  +  -0.704539 * Y  +  -0.618230 * Z  + -16.378010
  Y_new =   0.031510 * X  +  -0.650389 * Y  +   0.758947 * Z  +  36.446354
  Z_new =  -0.936798 * X  +  -0.283934 * Y  +  -0.204427 * Z  +   0.568318 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.090185  1.213364 -2.194805   [DEG:    5.1672   69.5206 -125.7531 ]
ZXZ: -2.458019  1.776674 -1.865086   [DEG: -140.8341  101.7959 -106.8615 ]
 
# END of job
