
#######################################################
#                                                     #
#                        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   67 (  530),  selected   67 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   67 , 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:    67       2_B - 68_B        0.93     0.93
  LCS_AVERAGE:     94.37

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_B - 68_B        0.93     0.93
  LCS_AVERAGE:     94.37

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_B - 68_B        0.93     0.93
  LCS_AVERAGE:     94.37

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     S     2_B     S     2_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V     3_B     V     3_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S     4_B     S     4_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     5_B     K     5_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     W     6_B     W     6_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S     7_B     S     7_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T     8_B     T     8_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D     9_B     D     9_B     67   67   67     20   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    10_B     E    10_B     67   67   67     20   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    11_B     V    11_B     67   67   67     26   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    12_B     S    12_B     67   67   67     19   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    13_B     E    13_B     67   67   67     16   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    14_B     F    14_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    15_B     I    15_B     67   67   67     19   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    16_B     Q    16_B     67   67   67     19   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    17_B     S    17_B     67   67   67     20   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    18_B     L    18_B     67   67   67      8   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    19_B     P    19_B     67   67   67      8   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    20_B     G    20_B     67   67   67     19   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     C    21_B     C    21_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    22_B     E    22_B     67   67   67     28   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    23_B     E    23_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    24_B     H    24_B     67   67   67     12   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    25_B     G    25_B     67   67   67      9   30   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    26_B     K    26_B     67   67   67      9   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    27_B     V    27_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    28_B     F    28_B     67   67   67     20   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    29_B     K    29_B     67   67   67     14   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    30_B     D    30_B     67   67   67      9   60   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    31_B     E    31_B     67   67   67     20   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    32_B     Q    32_B     67   67   67     20   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_B     I    33_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    34_B     D    34_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    35_B     G    35_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    36_B     E    36_B     67   67   67     20   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    37_B     A    37_B     67   67   67     20   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    38_B     F    38_B     67   67   67     21   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    39_B     L    39_B     67   67   67     26   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    40_B     L    40_B     67   67   67     20   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    41_B     M    41_B     67   67   67     19   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    42_B     T    42_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    43_B     Q    43_B     67   67   67     17   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    44_B     T    44_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    45_B     D    45_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    46_B     I    46_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    47_B     V    47_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    48_B     K    48_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    49_B     I    49_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    50_B     M    50_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    51_B     S    51_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    52_B     I    52_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    53_B     K    53_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    54_B     E    54_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    55_B     G    55_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    56_B     P    56_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    57_B     A    57_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    58_B     E    58_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    59_B     K    59_B     67   67   67     30   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    60_B     I    60_B     67   67   67     12   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    61_B     F    61_B     67   67   67      8   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    62_B     N    62_B     67   67   67      8   60   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    63_B     S    63_B     67   67   67      8   14   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    64_B     I    64_B     67   67   67      8   12   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    65_B     L    65_B     67   67   67      8   53   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    66_B     M    66_B     67   67   67      8   14   64   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    67_B     F    67_B     67   67   67      8   12   16   49   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    68_B     K    68_B     67   67   67      8   12   16   49   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A:  94.37  (  94.37   94.37   94.37 )

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     30     60     64     65     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  42.25  84.51  90.14  91.55  94.37  94.37  94.37  94.37  94.37  94.37  94.37  94.37  94.37  94.37  94.37  94.37  94.37  94.37  94.37  94.37
GDT RMS_LOCAL    0.34   0.61   0.77   0.77   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93
GDT RMS_ALL_AT   1.07   0.99   0.94   0.94   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93   0.93

# 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:  E    36_B      E    36_B
#   possible swapping detected:  F    38_B      F    38_B
#   possible swapping detected:  D    45_B      D    45_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  F    61_B      F    61_B
#   possible swapping detected:  F    67_B      F    67_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_B      S     2_B     0.247     0    0.068   0.639     1.945   97.619   92.302
LGA    V     3_B      V     3_B     0.805     0    0.093   0.079     1.525   92.857   86.735
LGA    S     4_B      S     4_B     0.528     0    0.020   0.067     0.639   95.238   93.651
LGA    K     5_B      K     5_B     0.126     0    0.022   0.827     3.765  100.000   81.270
LGA    W     6_B      W     6_B     0.536     0    0.052   0.112     1.541   92.857   86.020
LGA    S     7_B      S     7_B     0.491     0    0.031   0.083     0.682   97.619   95.238
LGA    T     8_B      T     8_B     0.429     0    0.022   0.107     0.630   97.619   97.279
LGA    D     9_B      D     9_B     0.675     0    0.064   0.809     3.728   92.857   78.393
LGA    E    10_B      E    10_B     0.687     0    0.044   1.001     2.517   90.476   80.899
LGA    V    11_B      V    11_B     0.468     0    0.036   0.064     0.625   95.238   95.918
LGA    S    12_B      S    12_B     1.022     0    0.029   0.449     2.568   88.214   81.905
LGA    E    13_B      E    13_B     0.994     0    0.042   0.739     4.642   90.476   70.741
LGA    F    14_B      F    14_B     0.524     0    0.027   0.138     2.332   92.857   81.082
LGA    I    15_B      I    15_B     0.687     0    0.025   0.661     1.576   92.857   87.202
LGA    Q    16_B      Q    16_B     1.131     0    0.062   1.485     5.192   88.214   72.116
LGA    S    17_B      S    17_B     0.712     0    0.034   0.072     0.928   90.476   90.476
LGA    L    18_B      L    18_B     0.914     0    0.076   0.326     0.992   90.476   90.476
LGA    P    19_B      P    19_B     1.036     0    0.070   0.153     1.429   88.214   85.306
LGA    G    20_B      G    20_B     0.818     0    0.097   0.097     1.189   88.214   88.214
LGA    C    21_B      C    21_B     0.598     0    0.035   0.053     0.845   90.476   90.476
LGA    E    22_B      E    22_B     0.687     0    0.027   0.879     3.524   90.476   77.672
LGA    E    23_B      E    23_B     0.640     0    0.097   1.271     7.113   92.857   63.280
LGA    H    24_B      H    24_B     0.660     0    0.024   0.162     1.182   88.214   91.476
LGA    G    25_B      G    25_B     1.235     0    0.040   0.040     1.235   83.690   83.690
LGA    K    26_B      K    26_B     0.935     0    0.041   0.625     3.208   88.214   80.952
LGA    V    27_B      V    27_B     0.599     0    0.055   1.127     3.135   90.476   82.177
LGA    F    28_B      F    28_B     0.670     0    0.035   0.076     1.008   90.476   89.654
LGA    K    29_B      K    29_B     0.853     0    0.030   1.081     4.856   90.476   71.958
LGA    D    30_B      D    30_B     0.943     0    0.108   0.127     1.299   90.476   87.083
LGA    E    31_B      E    31_B     0.729     0    0.019   0.084     1.076   90.476   89.471
LGA    Q    32_B      Q    32_B     0.734     0    0.019   0.863     3.999   90.476   77.037
LGA    I    33_B      I    33_B     0.538     0    0.050   0.585     1.240   95.238   90.595
LGA    D    34_B      D    34_B     0.364     0    0.031   0.066     0.706   97.619   95.238
LGA    G    35_B      G    35_B     0.349     0    0.033   0.033     0.400  100.000  100.000
LGA    E    36_B      E    36_B     0.742     0    0.027   0.908     1.940   90.476   85.556
LGA    A    37_B      A    37_B     0.725     0    0.041   0.044     0.789   90.476   90.476
LGA    F    38_B      F    38_B     0.392     0    0.028   0.407     0.904   97.619   95.671
LGA    L    39_B      L    39_B     0.304     0    0.054   0.200     1.203   97.619   92.917
LGA    L    40_B      L    40_B     0.708     0    0.063   0.066     1.158   90.476   88.214
LGA    M    41_B      M    41_B     0.779     0    0.149   0.661     1.816   88.214   86.012
LGA    T    42_B      T    42_B     0.597     0    0.016   0.156     0.689   92.857   94.558
LGA    Q    43_B      Q    43_B     1.020     0    0.011   1.114     4.579   83.690   66.878
LGA    T    44_B      T    44_B     1.147     0    0.059   0.128     1.587   85.952   82.789
LGA    D    45_B      D    45_B     0.718     0    0.026   0.147     0.852   90.476   90.476
LGA    I    46_B      I    46_B     0.419     0    0.066   0.073     0.686   95.238   94.048
LGA    V    47_B      V    47_B     0.615     0    0.022   0.035     0.685   90.476   90.476
LGA    K    48_B      K    48_B     0.759     0    0.048   1.293     9.020   90.476   60.000
LGA    I    49_B      I    49_B     0.602     0    0.023   0.118     0.817   92.857   92.857
LGA    M    50_B      M    50_B     0.375     0    0.041   0.231     0.798  100.000   98.810
LGA    S    51_B      S    51_B     0.499     0    0.065   0.070     0.756   97.619   96.825
LGA    I    52_B      I    52_B     0.469     0    0.036   0.611     1.629   95.238   89.524
LGA    K    53_B      K    53_B     0.174     0    0.059   0.638     2.222  100.000   90.952
LGA    E    54_B      E    54_B     0.437     0    0.031   0.750     3.390   95.238   81.534
LGA    G    55_B      G    55_B     0.576     0    0.037   0.037     0.576   90.476   90.476
LGA    P    56_B      P    56_B     0.505     0    0.029   0.309     0.809   95.238   94.558
LGA    A    57_B      A    57_B     0.539     0    0.049   0.057     0.662   90.476   92.381
LGA    E    58_B      E    58_B     0.847     0    0.042   0.964     4.878   90.476   73.704
LGA    K    59_B      K    59_B     0.767     0    0.025   0.599     1.583   90.476   86.508
LGA    I    60_B      I    60_B     0.618     0    0.022   0.082     0.703   90.476   90.476
LGA    F    61_B      F    61_B     0.730     0    0.020   0.258     1.198   90.476   88.831
LGA    N    62_B      N    62_B     0.678     0    0.050   0.121     1.396   90.476   87.083
LGA    S    63_B      S    63_B     1.417     0    0.020   0.617     1.965   79.405   80.159
LGA    I    64_B      I    64_B     1.886     0    0.026   1.376     5.790   70.833   60.536
LGA    L    65_B      L    65_B     1.137     0    0.030   1.425     4.190   81.429   70.952
LGA    M    66_B      M    66_B     1.856     0    0.089   1.254     5.782   67.262   53.750
LGA    F    67_B      F    67_B     3.091     0    0.067   1.190     5.759   51.786   42.597
LGA    K    68_B      K    68_B     2.876     0    0.581   0.937     4.985   55.595   51.217

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     530    530  100.00                71
SUMMARY(RMSD_GDC):     0.929          0.940                  1.670           84.956   79.405

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   67   71    4.0     67    0.93    91.197    93.075     6.513

LGA_LOCAL      RMSD:   0.929  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.929  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.929  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.133159 * X  +  -0.824081 * Y  +  -0.550600 * Z  +  44.583530
  Y_new =  -0.825072 * X  +  -0.399972 * Y  +   0.399098 * Z  +  70.626656
  Z_new =  -0.549113 * X  +   0.401141 * Y  +  -0.733185 * Z  +  10.599886 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.410786  0.581303  2.640963   [DEG:  -80.8321   33.3062  151.3160 ]
ZXZ: -2.198001  2.393791 -0.939876   [DEG: -125.9362  137.1541  -53.8509 ]
 
# END of job
