
#######################################################
#                                                     #
#                        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        2.09     2.09
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_A - 61_A        2.00     2.09
  LCS_AVERAGE:     96.20

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.98     3.56
  LCS_AVERAGE:     36.79

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   61   63      3    6   25   43   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   61   63      3   14   29   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   61   63      3   13   29   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   61   63      3   13   29   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   61   63      4   20   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   61   63      4   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   61   63      4   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   61   63      8   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   61   63      4   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   61   63      4   19   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   61   63      3   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   61   63      4   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   61   63      4   21   29   40   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   61   63      8   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   61   63      4   20   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   61   63      8   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   61   63      9   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   61   63     11   25   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   61   63     11   22   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   61   63     11   21   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   61   63      9   21   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   61   63     10   21   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     25   61   63     11   21   29   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     25   61   63      9   20   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   61   63      4   20   32   39   50   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     17   61   63      3   12   26   36   47   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   61   63      3    8   19   39   51   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   61   63      5   19   29   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   61   63      3   17   29   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   61   63      3    8   24   39   51   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     13   61   63      4   15   29   42   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   61   63      4   18   29   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   61   63      5    8   19   34   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     13   61   63      5   11   29   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     13   61   63      5   11   25   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     13   61   63      5    8   29   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     13   61   63      5   17   29   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     13   61   63      3   18   29   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     13   61   63      4   15   25   41   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     13   61   63      4   12   24   34   49   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     13   61   63      4   11   24   34   40   51   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     13   61   63      4   12   24   34   43   55   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     12   61   63      4   10   24   39   49   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   61   63      6   17   28   43   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   61   63     11   21   32   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   61   63      4   10   25   44   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   55   63      8   16   32   37   49   56   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   11   30   37   43   52   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.66  (  36.79   96.20  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     25     32     44     53     57     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  39.68  50.79  69.84  84.13  90.48  96.83 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.69   0.93   1.42   1.62   1.75   2.00   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09
GDT RMS_ALL_AT   2.49   3.79   3.55   2.40   2.19   2.16   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09

# Checking swapping
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  Y    50_A      Y    50_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     2.077     0    0.113   0.113     2.737   71.190   71.190
LGA    S     2_A      S     2_A     2.284     0    0.157   0.782     3.542   68.810   61.429
LGA    S     3_A      S     3_A     2.360     0    0.133   0.318     4.325   64.762   58.889
LGA    F     4_A      F     4_A     1.754     0    0.074   0.373     3.360   70.833   63.593
LGA    C     5_A      C     5_A     1.984     0    0.078   0.116     2.658   72.857   68.889
LGA    D     6_A      D     6_A     2.081     0    0.100   1.079     6.009   64.762   51.190
LGA    S     7_A      S     7_A     2.558     0    0.111   0.237     2.870   60.952   60.952
LGA    K     8_A      K     8_A     1.668     0    0.113   0.669     3.910   72.857   67.407
LGA    C     9_A      C     9_A     1.718     0    0.047   0.211     1.822   72.857   72.857
LGA    G    10_A      G    10_A     1.627     0    0.088   0.088     1.674   75.000   75.000
LGA    V    11_A      V    11_A     2.174     0    0.019   0.109     2.551   64.762   63.673
LGA    R    12_A      R    12_A     1.945     0    0.029   1.137     6.536   72.857   54.459
LGA    C    13_A      C    13_A     0.996     0    0.530   0.603     2.305   81.786   81.667
LGA    S    14_A      S    14_A     1.463     0    0.058   0.648     2.469   79.286   77.222
LGA    K    15_A      K    15_A     1.353     0    0.077   0.707     4.578   79.286   66.984
LGA    A    16_A      A    16_A     1.316     0    0.654   0.590     2.626   75.357   76.571
LGA    G    17_A      G    17_A     2.853     0    0.060   0.060     3.061   57.262   57.262
LGA    Y    18_A      Y    18_A     2.694     0    0.357   1.312     7.099   59.048   46.111
LGA    Q    19_A      Q    19_A     1.452     0    0.074   0.951     2.583   81.429   75.026
LGA    E    20_A      E    20_A     2.453     0    0.024   0.689     7.535   60.952   38.413
LGA    R    21_A      R    21_A     2.760     0    0.045   1.503    12.954   60.952   29.870
LGA    C    22_A      C    22_A     1.683     0    0.084   0.151     1.918   72.857   74.286
LGA    L    23_A      L    23_A     1.385     0    0.029   0.130     2.521   77.143   74.107
LGA    K    24_A      K    24_A     2.017     0    0.049   1.566    11.376   68.810   43.545
LGA    Y    25_A      Y    25_A     2.160     0    0.126   0.478     2.894   66.786   64.841
LGA    C    26_A      C    26_A     1.218     0    0.049   0.683     2.639   81.429   77.381
LGA    G    27_A      G    27_A     0.998     0    0.022   0.022     1.306   85.952   85.952
LGA    I    28_A      I    28_A     1.687     0    0.018   1.436     6.864   79.286   61.190
LGA    C    29_A      C    29_A     1.430     0    0.102   0.652     4.164   83.690   74.127
LGA    C    30_A      C    30_A     0.840     0    0.091   0.830     2.436   88.214   86.270
LGA    E    31_A      E    31_A     0.837     0    0.073   0.957     3.959   85.952   73.862
LGA    K    32_A      K    32_A     1.204     0    0.051   1.256     4.896   83.690   69.841
LGA    C    33_A      C    33_A     1.231     0    0.140   0.169     2.025   77.262   80.159
LGA    H    34_A      H    34_A     1.450     0    0.141   1.044     6.912   79.286   53.381
LGA    C    35_A      C    35_A     1.326     0    0.025   0.193     1.819   81.429   78.571
LGA    V    36_A      V    36_A     1.252     0    0.067   0.287     2.341   81.429   76.599
LGA    P    37_A      P    37_A     0.829     0    0.029   0.366     1.036   88.214   91.905
LGA    S    38_A      S    38_A     1.274     0    0.273   0.687     4.935   81.548   70.397
LGA    G    39_A      G    39_A     1.694     0    0.038   0.038     2.546   66.905   66.905
LGA    T    40_A      T    40_A     3.037     0    0.511   0.406     4.114   50.476   54.558
LGA    Y    41_A      Y    41_A     3.154     0    0.207   1.320    10.882   55.476   30.992
LGA    G    42_A      G    42_A     2.581     0    0.667   0.667     4.566   50.714   50.714
LGA    N    43_A      N    43_A     1.222     0    0.177   0.999     4.592   83.690   66.845
LGA    K    44_A      K    44_A     1.281     0    0.022   0.966     7.883   77.143   54.656
LGA    D    45_A      D    45_A     2.331     0    0.113   0.718     5.108   68.810   55.595
LGA    E    46_A      E    46_A     1.922     0    0.093   0.626     3.511   75.000   66.138
LGA    C    47_A      C    47_A     1.252     0    0.043   0.624     2.578   72.976   71.746
LGA    P    48_A      P    48_A     2.276     0    0.162   0.428     2.664   70.833   70.680
LGA    C    49_A      C    49_A     1.649     0    0.098   0.229     1.936   77.143   78.651
LGA    Y    50_A      Y    50_A     1.728     0    0.122   0.802     5.428   72.857   55.159
LGA    R    51_A      R    51_A     1.145     0    0.033   1.308     5.537   83.690   67.186
LGA    D    52_A      D    52_A     0.109     0    0.052   0.683     2.856  100.000   86.667
LGA    L    53_A      L    53_A     0.995     0    0.111   0.917     4.793   85.952   73.214
LGA    K    54_A      K    54_A     1.692     0    0.030   1.079     4.803   70.952   64.762
LGA    N    55_A      N    55_A     2.988     0    0.059   0.111     3.437   55.476   56.310
LGA    S    56_A      S    56_A     4.455     0    0.024   0.491     6.364   37.262   32.937
LGA    K    57_A      K    57_A     4.253     0    0.204   0.851     6.669   38.690   30.212
LGA    G    58_A      G    58_A     3.001     0    0.046   0.046     3.301   57.381   57.381
LGA    N    59_A      N    59_A     0.895     0    0.038   0.212     1.958   90.833   86.310
LGA    P    60_A      P    60_A     1.486     0    0.090   0.368     3.184   77.143   69.728
LGA    K    61_A      K    61_A     2.598     0    0.065   1.174     3.750   55.833   56.931
LGA    C    62_A      C    62_A     3.615     0    0.118   0.546     4.497   43.452   42.381
LGA    P    63_A      P    63_A     4.038     0    0.479   0.499     4.263   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):     2.087          2.096                  3.167           71.242   64.195

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    2.09    77.381    86.692     2.881

LGA_LOCAL      RMSD:   2.087  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.087  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.087  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.871439 * X  +  -0.359254 * Y  +  -0.333961 * Z  +   3.230922
  Y_new =  -0.256221 * X  +  -0.247176 * Y  +   0.934481 * Z  +  -1.282100
  Z_new =  -0.418263 * X  +   0.899911 * Y  +   0.123350 * Z  +  -1.983798 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.855631  0.431533  1.434576   [DEG: -163.6156   24.7250   82.1951 ]
ZXZ: -2.798362  1.447131 -0.435079   [DEG: -160.3344   82.9145  -24.9282 ]
 
# END of job
