
#######################################################
#                                                     #
#                        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        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36       5_A - 40_A        0.97     2.79
  LCS_AVERAGE:     43.24

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      7   63   63      3    6    7   47   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   63   63      4   10   28   44   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     34   63   63      4   11   30   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     34   63   63      4   10   33   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     36   63   63      6   22   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     36   63   63      4   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     36   63   63      4   26   35   47   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     36   63   63      8   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     36   63   63      9   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     36   63   63      9   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     36   63   63      9   26   35   46   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     36   63   63      8   26   35   46   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     36   63   63      9   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     36   63   63      4   19   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     36   63   63      4   19   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     36   63   63      5   25   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     36   63   63      6   23   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     36   63   63      9   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     36   63   63     12   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     36   63   63     10   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     36   63   63     10   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     36   63   63     10   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     36   63   63     10   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     36   63   63      5   25   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     36   63   63      5   26   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     36   63   63      4   19   35   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     36   63   63     10   19   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     36   63   63      3   26   35   46   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     36   63   63      3   24   35   41   48   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     10   63   63      3    8   14   18   31   52   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     10   63   63      4    4    9   15   23   46   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     10   63   63      4   10   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A      8   63   63      4    7   24   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      8   63   63      4    7   12   28   54   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     15   63   63      4    7   28   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     16   63   63      3   19   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     16   63   63      5   15   27   46   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     16   63   63      5   15   29   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     16   63   63      5   10   30   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     16   63   63      5   15   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     16   63   63      5   19   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     16   63   63      5   17   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     16   63   63      5   19   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     16   63   63      5   19   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     16   63   63      5   19   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     16   63   63      5   19   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     16   63   63      6   19   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     16   63   63      9   19   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     16   63   63     10   18   34   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     16   63   63      5   13   30   48   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     16   63   63      5   26   35   41   55   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     16   63   63      4    4   12   37   42   52   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  81.08  (  43.24  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     12     26     35     48     57     60     61     62     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  19.05  41.27  55.56  76.19  90.48  95.24  96.83  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    9.14   0.62   0.84   1.36   1.56   1.67   1.75   1.83   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90
GDT RMS_ALL_AT   3.21   3.16   3.08   1.97   1.91   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90

# Checking swapping
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_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     2.009     0    0.151   0.151     3.094   67.262   67.262
LGA    S     2_A      S     2_A     2.389     0    0.243   0.880     3.302   68.810   62.540
LGA    S     3_A      S     3_A     1.840     0    0.068   0.666     4.708   75.119   66.111
LGA    F     4_A      F     4_A     1.543     0    0.085   0.227     3.852   77.143   61.299
LGA    C     5_A      C     5_A     1.535     0    0.116   0.818     2.508   79.286   74.524
LGA    D     6_A      D     6_A     1.594     0    0.075   1.058     5.684   72.857   56.488
LGA    S     7_A      S     7_A     2.079     0    0.096   0.553     4.237   66.905   61.587
LGA    K     8_A      K     8_A     1.612     0    0.129   0.793     6.787   75.000   61.164
LGA    C     9_A      C     9_A     1.370     0    0.032   0.052     1.604   79.286   80.000
LGA    G    10_A      G    10_A     1.582     0    0.054   0.054     1.738   75.000   75.000
LGA    V    11_A      V    11_A     2.190     0    0.059   0.073     2.630   66.786   64.830
LGA    R    12_A      R    12_A     2.062     0    0.035   0.881     4.871   70.833   56.450
LGA    C    13_A      C    13_A     0.531     0    0.640   0.716     2.727   82.143   84.921
LGA    S    14_A      S    14_A     0.836     0    0.067   0.615     1.567   88.214   84.524
LGA    K    15_A      K    15_A     1.429     0    0.107   0.669     5.147   81.429   64.021
LGA    A    16_A      A    16_A     1.532     0    0.077   0.095     1.743   75.000   76.286
LGA    G    17_A      G    17_A     1.633     0    0.195   0.195     1.716   75.000   75.000
LGA    Y    18_A      Y    18_A     1.737     0    0.265   1.009     7.548   72.976   55.833
LGA    Q    19_A      Q    19_A     0.981     0    0.057   0.938     2.275   90.476   81.693
LGA    E    20_A      E    20_A     1.546     0    0.039   0.759     3.789   72.976   62.910
LGA    R    21_A      R    21_A     2.231     0    0.077   1.552    11.651   66.786   35.455
LGA    C    22_A      C    22_A     1.660     0    0.089   0.141     1.940   72.857   75.714
LGA    L    23_A      L    23_A     1.264     0    0.021   0.268     1.764   81.429   81.488
LGA    K    24_A      K    24_A     1.864     0    0.044   1.185    10.219   72.857   46.138
LGA    Y    25_A      Y    25_A     2.043     0    0.151   0.582     2.983   66.905   69.008
LGA    C    26_A      C    26_A     1.271     0    0.030   0.095     1.353   81.429   81.429
LGA    G    27_A      G    27_A     0.925     0    0.036   0.036     1.255   85.952   85.952
LGA    I    28_A      I    28_A     1.440     0    0.019   0.748     4.443   81.429   69.702
LGA    C    29_A      C    29_A     1.156     0    0.121   0.773     4.209   85.952   77.063
LGA    C    30_A      C    30_A     0.900     0    0.127   0.115     1.130   85.952   89.048
LGA    E    31_A      E    31_A     0.867     0    0.026   0.835     4.032   90.476   77.831
LGA    K    32_A      K    32_A     0.852     0    0.035   1.198     5.642   90.476   70.212
LGA    C    33_A      C    33_A     0.882     0    0.202   0.220     1.690   83.810   86.032
LGA    H    34_A      H    34_A     1.145     0    0.144   1.244     3.512   81.548   71.238
LGA    C    35_A      C    35_A     1.069     0    0.074   0.210     1.709   83.690   80.079
LGA    V    36_A      V    36_A     1.223     0    0.037   0.221     2.464   85.952   79.184
LGA    P    37_A      P    37_A     0.829     0    0.022   0.291     1.282   88.214   87.891
LGA    S    38_A      S    38_A     1.186     0    0.268   0.669     4.646   85.952   74.683
LGA    G    39_A      G    39_A     2.444     0    0.141   0.141     3.600   57.500   57.500
LGA    T    40_A      T    40_A     3.108     0    0.259   0.347     3.899   53.571   53.197
LGA    Y    41_A      Y    41_A     4.558     0    0.379   1.106    11.846   38.810   19.444
LGA    G    42_A      G    42_A     4.229     0    0.616   0.616     5.732   34.762   34.762
LGA    N    43_A      N    43_A     1.664     0    0.229   0.967     3.775   70.833   63.571
LGA    K    44_A      K    44_A     2.120     0    0.050   0.690     4.944   62.976   59.418
LGA    D    45_A      D    45_A     2.979     0    0.209   1.162     8.043   59.048   40.893
LGA    E    46_A      E    46_A     2.167     0    0.111   0.228     2.842   70.952   64.127
LGA    C    47_A      C    47_A     1.395     0    0.054   0.680     2.572   72.976   71.746
LGA    P    48_A      P    48_A     2.444     0    0.177   0.400     2.861   68.810   69.524
LGA    C    49_A      C    49_A     1.929     0    0.073   0.178     2.212   72.976   73.016
LGA    Y    50_A      Y    50_A     1.933     0    0.157   0.745     4.777   72.857   57.024
LGA    R    51_A      R    51_A     1.200     0    0.035   1.254     5.785   83.690   63.333
LGA    D    52_A      D    52_A     0.769     0    0.189   0.784     2.560   83.810   79.643
LGA    L    53_A      L    53_A     1.468     0    0.137   0.860     2.911   73.214   69.107
LGA    K    54_A      K    54_A     1.420     0    0.049   0.915     4.668   81.429   65.767
LGA    N    55_A      N    55_A     1.575     0    0.065   0.242     1.756   72.857   75.000
LGA    S    56_A      S    56_A     1.953     0    0.160   0.488     3.482   70.833   66.349
LGA    K    57_A      K    57_A     1.781     0    0.047   0.767     4.480   72.857   59.894
LGA    G    58_A      G    58_A     0.929     0    0.057   0.057     1.140   88.214   88.214
LGA    N    59_A      N    59_A     0.482     0    0.109   0.290     1.651   95.238   93.036
LGA    P    60_A      P    60_A     1.184     0    0.126   0.334     2.832   81.429   74.354
LGA    K    61_A      K    61_A     1.967     0    0.095   1.359     4.153   66.905   61.905
LGA    C    62_A      C    62_A     2.805     0    0.524   1.099     4.700   50.833   49.921
LGA    P    63_A      P    63_A     4.473     0    0.359   0.364     6.097   52.619   39.456

# 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):     1.898          1.884                  2.913           74.511   67.632

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     62    1.83    78.968    89.195     3.213

LGA_LOCAL      RMSD:   1.830  Number of atoms:   62  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.900  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.898  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.034765 * X  +   0.942281 * Y  +  -0.333013 * Z  +   1.935696
  Y_new =   0.331069 * X  +  -0.303541 * Y  +  -0.893452 * Z  +   0.774096
  Z_new =  -0.942966 * X  +  -0.141311 * Y  +  -0.301407 * Z  +   4.571001 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.675422  1.231430 -2.703184   [DEG:   95.9946   70.5558 -154.8810 ]
ZXZ: -0.356776  1.876965 -1.719548   [DEG:  -20.4418  107.5422  -98.5228 ]
 
# END of job
