
#######################################################
#                                                     #
#                        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   63 (  472),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  472),  selected   63 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        2.11     2.11
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    57       4_A - 60_A        1.99     2.12
  LCS_AVERAGE:     89.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.98     3.63
  LCS_AVERAGE:     35.93

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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_A     G     1_A     11   56   63      3   12   23   43   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   56   63      3   16   29   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   56   63      3   12   28   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   57   63      3   12   30   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   57   63      4   19   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   57   63      4   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   57   63      4   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   57   63      4   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   57   63      4   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   57   63     10   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   57   63     10   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   57   63      9   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   57   63      5   19   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   57   63      3   10   30   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   57   63      4   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   57   63      4   21   30   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   57   63      4   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   57   63      4   20   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   57   63      9   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   57   63     11   24   31   44   53   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   57   63     11   24   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   57   63     11   22   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   57   63     11   21   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   57   63      9   21   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   57   63     11   21   29   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     25   57   63     10   21   29   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     25   57   63      8   19   31   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   57   63      4   20   31   39   50   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   57   63      3   18   23   36   48   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   57   63      3    8   19   34   51   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     11   57   63      4   19   29   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     11   57   63      4   17   29   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      8   57   63      4    8   24   35   52   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     10   57   63      4   16   29   41   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     11   57   63      6   19   29   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     11   57   63      5    7   17   35   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     11   57   63      5   10   29   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     11   57   63      5   10   21   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     11   57   63      5    8   28   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     11   57   63      5   19   29   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     11   57   63      6   19   29   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     11   57   63      4   14   24   41   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   57   63      4   12   22   33   48   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   57   63      6   10   20   32   40   49   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   57   63      6   10   21   33   42   52   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   57   63      6   10   21   33   50   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   57   63      6   17   29   42   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   57   63     11   21   29   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   56   63      6   10   23   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   55   63      3   21   31   38   49   55   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   42   63      3   12   30   38   45   52   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  75.29  (  35.93   89.95  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     11     24     31     44     53     58     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  38.10  49.21  69.84  84.13  92.06  95.24 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.65   0.90   1.44   1.64   1.86   1.91   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11
GDT RMS_ALL_AT   3.55   3.87   3.46   2.44   2.21   2.13   2.14   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11

# Checking swapping
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  D    52_A      D    52_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     2.117     0    0.115   0.115     2.738   71.190   71.190
LGA    S     2_A      S     2_A     2.267     0    0.152   0.770     3.480   68.810   62.540
LGA    S     3_A      S     3_A     2.388     0    0.137   0.466     3.366   64.762   59.841
LGA    F     4_A      F     4_A     1.871     0    0.083   0.345     3.624   70.833   60.346
LGA    C     5_A      C     5_A     2.204     0    0.116   0.643     2.926   66.786   64.841
LGA    D     6_A      D     6_A     2.093     0    0.095   1.067     5.888   64.762   52.440
LGA    S     7_A      S     7_A     2.594     0    0.134   0.560     4.774   60.952   55.397
LGA    K     8_A      K     8_A     1.682     0    0.133   0.793     4.104   72.857   71.746
LGA    C     9_A      C     9_A     1.718     0    0.049   0.216     1.808   72.857   72.857
LGA    G    10_A      G    10_A     1.622     0    0.085   0.085     1.664   75.000   75.000
LGA    V    11_A      V    11_A     2.211     0    0.016   1.228     4.860   64.762   62.381
LGA    R    12_A      R    12_A     1.984     0    0.050   1.327     8.148   68.810   51.082
LGA    C    13_A      C    13_A     1.314     0    0.672   0.848     2.400   79.524   75.952
LGA    S    14_A      S    14_A     1.557     0    0.063   0.604     1.967   77.143   75.714
LGA    K    15_A      K    15_A     1.781     0    0.218   0.861     2.541   72.857   73.069
LGA    A    16_A      A    16_A     1.483     0    0.617   0.558     3.047   71.429   73.429
LGA    G    17_A      G    17_A     2.463     0    0.056   0.056     2.700   60.952   60.952
LGA    Y    18_A      Y    18_A     2.537     0    0.334   1.383     5.878   61.071   49.603
LGA    Q    19_A      Q    19_A     1.370     0    0.065   1.203     2.811   81.429   74.974
LGA    E    20_A      E    20_A     2.349     0    0.029   0.771     6.766   64.881   44.921
LGA    R    21_A      R    21_A     2.681     0    0.053   1.061    10.416   62.857   34.502
LGA    C    22_A      C    22_A     1.694     0    0.116   0.632     2.943   72.857   70.238
LGA    L    23_A      L    23_A     1.418     0    0.023   1.435     4.320   77.143   68.512
LGA    K    24_A      K    24_A     2.070     0    0.046   1.138     9.586   66.786   41.376
LGA    Y    25_A      Y    25_A     2.247     0    0.119   0.462     3.144   62.857   61.071
LGA    C    26_A      C    26_A     1.258     0    0.047   0.672     2.645   81.429   77.381
LGA    G    27_A      G    27_A     1.061     0    0.018   0.018     1.382   81.429   81.429
LGA    I    28_A      I    28_A     1.754     0    0.019   1.369     6.709   77.143   60.119
LGA    C    29_A      C    29_A     1.445     0    0.106   0.649     4.081   81.548   72.698
LGA    C    30_A      C    30_A     0.938     0    0.060   0.730     2.391   88.214   84.683
LGA    E    31_A      E    31_A     0.889     0    0.064   0.827     3.084   85.952   75.450
LGA    K    32_A      K    32_A     1.222     0    0.055   0.566     3.532   81.429   69.947
LGA    C    33_A      C    33_A     1.290     0    0.107   0.230     1.977   77.143   78.571
LGA    H    34_A      H    34_A     1.498     0    0.112   1.094     3.707   77.143   70.095
LGA    C    35_A      C    35_A     1.367     0    0.022   0.194     1.865   81.429   78.571
LGA    V    36_A      V    36_A     1.286     0    0.062   0.250     2.326   81.429   76.599
LGA    P    37_A      P    37_A     0.901     0    0.032   0.338     1.057   88.214   90.544
LGA    S    38_A      S    38_A     1.256     0    0.271   0.686     4.897   81.548   70.397
LGA    G    39_A      G    39_A     1.735     0    0.036   0.036     2.552   66.905   66.905
LGA    T    40_A      T    40_A     3.091     0    0.538   0.428     4.190   50.476   53.605
LGA    Y    41_A      Y    41_A     3.202     0    0.207   1.248    11.471   55.476   29.286
LGA    G    42_A      G    42_A     2.590     0    0.667   0.667     4.549   50.714   50.714
LGA    N    43_A      N    43_A     1.241     0    0.177   0.987     4.581   83.690   66.845
LGA    K    44_A      K    44_A     1.347     0    0.017   1.180     7.787   77.143   58.201
LGA    D    45_A      D    45_A     2.395     0    0.141   1.286     7.162   68.810   50.476
LGA    E    46_A      E    46_A     1.974     0    0.061   0.546     2.398   72.976   72.063
LGA    C    47_A      C    47_A     1.231     0    0.026   0.639     2.573   72.976   71.746
LGA    P    48_A      P    48_A     2.273     0    0.211   0.200     2.804   70.833   67.211
LGA    C    49_A      C    49_A     1.690     0    0.063   0.747     2.220   79.405   77.302
LGA    Y    50_A      Y    50_A     1.705     0    0.121   0.842     5.278   72.857   55.159
LGA    R    51_A      R    51_A     1.049     0    0.018   1.458     7.547   83.690   56.970
LGA    D    52_A      D    52_A     0.149     0    0.048   0.739     3.129  100.000   86.964
LGA    L    53_A      L    53_A     0.952     0    0.109   1.364     5.161   85.952   68.869
LGA    K    54_A      K    54_A     1.632     0    0.043   0.841     3.458   70.952   65.926
LGA    N    55_A      N    55_A     2.968     0    0.058   0.102     3.463   55.476   57.262
LGA    S    56_A      S    56_A     4.552     0    0.022   0.157     5.793   34.405   30.873
LGA    K    57_A      K    57_A     4.315     0    0.152   0.740     4.498   37.143   46.085
LGA    G    58_A      G    58_A     3.067     0    0.044   0.044     3.350   55.476   55.476
LGA    N    59_A      N    59_A     1.190     0    0.017   0.966     3.991   86.190   80.238
LGA    P    60_A      P    60_A     1.527     0    0.091   0.213     2.809   75.000   69.524
LGA    K    61_A      K    61_A     2.567     0    0.064   0.936     3.728   55.833   55.873
LGA    C    62_A      C    62_A     3.582     0    0.122   0.549     4.461   43.452   42.381
LGA    P    63_A      P    63_A     4.038     0    0.462   0.493     4.250   38.690   42.585

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     472    472  100.00                63
SUMMARY(RMSD_GDC):     2.110          2.112                  3.014           70.520   63.952

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    2.11    76.984    84.893     2.851

LGA_LOCAL      RMSD:   2.110  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.110  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.110  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.891055 * X  +  -0.232330 * Y  +  -0.389928 * Z  +   4.116882
  Y_new =  -0.261938 * X  +  -0.438380 * Y  +   0.859774 * Z  +  -2.558999
  Z_new =  -0.370688 * X  +   0.868243 * Y  +   0.329765 * Z  +  -6.083850 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.855683  0.379750  1.207818   [DEG: -163.6186   21.7581   69.2029 ]
ZXZ: -2.715812  1.234742 -0.403513   [DEG: -155.6046   70.7455  -23.1196 ]
 
# END of job
