
#######################################################
#                                                     #
#                        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   68 (  529),  selected   67 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   67 , 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:    67       2_A - 68_A        0.94     0.94
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.94     0.94
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.94     0.94
  LCS_AVERAGE:    100.00

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_A     S     2_A     67   67   67     11   25   49   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     67   67   67     17   41   57   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     67   67   67     11   38   57   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     67   67   67     11   41   58   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     67   67   67     18   50   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     67   67   67     26   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     67   67   67     17   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     67   67   67     24   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     67   67   67     47   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     67   67   67     37   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     67   67   67     48   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     67   67   67     28   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     67   67   67     34   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     67   67   67     50   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     67   67   67     45   56   60   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     67   67   67     14   54   59   62   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     67   67   67      3   33   60   62   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     67   67   67     17   50   58   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     50     56     60     64     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  74.63  83.58  89.55  95.52  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.35   0.54   0.78   0.86   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94
GDT RMS_ALL_AT   1.07   1.10   1.00   0.95   0.95   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94   0.94

# Checking swapping
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    64_A      E    64_A
#   possible swapping detected:  Y    65_A      Y    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     3.113     0    0.040   0.062     3.293   55.476   54.841
LGA    P     3_A      P     3_A     2.181     0    0.016   0.026     2.925   66.905   63.810
LGA    E     4_A      E     4_A     2.130     0    0.017   1.036     5.595   68.810   53.915
LGA    E     5_A      E     5_A     1.956     0    0.050   0.615     5.069   72.976   58.519
LGA    Q     6_A      Q     6_A     1.425     0    0.022   0.654     2.341   81.548   78.730
LGA    K     7_A      K     7_A     0.735     0    0.027   0.893     4.570   92.857   75.873
LGA    Q     8_A      Q     8_A     0.982     0    0.016   1.435     5.764   90.595   65.926
LGA    M     9_A      M     9_A     0.757     0    0.029   0.683     1.231   90.476   88.274
LGA    L    10_A      L    10_A     0.464     0    0.034   0.081     1.132   97.619   92.917
LGA    G    11_A      G    11_A     0.641     0    0.077   0.077     0.641   97.619   97.619
LGA    E    12_A      E    12_A     0.370     0    0.030   0.806     3.144  100.000   87.354
LGA    A    13_A      A    13_A     0.250     0    0.037   0.041     0.490  100.000  100.000
LGA    I    14_A      I    14_A     0.185     0    0.022   0.061     0.256  100.000  100.000
LGA    Y    15_A      Y    15_A     0.212     0    0.030   0.191     0.816  100.000   96.825
LGA    P    16_A      P    16_A     0.169     0    0.045   0.041     0.245  100.000  100.000
LGA    K    17_A      K    17_A     0.197     0    0.053   0.726     3.053  100.000   89.471
LGA    V    18_A      V    18_A     0.209     0    0.036   0.056     0.289  100.000  100.000
LGA    A    19_A      A    19_A     0.304     0    0.045   0.047     0.361  100.000  100.000
LGA    A    20_A      A    20_A     0.411     0    0.027   0.036     0.592   97.619   98.095
LGA    S    21_A      S    21_A     0.287     0    0.061   0.074     0.729   97.619   96.825
LGA    Q    22_A      Q    22_A     0.231     0    0.085   0.188     0.679   97.619   95.767
LGA    P    23_A      P    23_A     0.501     0    0.022   0.040     0.606   95.238   94.558
LGA    E    24_A      E    24_A     0.366     0    0.092   0.616     2.250   92.976   89.841
LGA    L    25_A      L    25_A     0.331     0    0.030   0.045     0.619  100.000   97.619
LGA    A    26_A      A    26_A     0.410     0    0.039   0.047     0.543  100.000   98.095
LGA    G    27_A      G    27_A     0.558     0    0.038   0.038     0.558   95.238   95.238
LGA    K    28_A      K    28_A     0.353     0    0.009   1.194     6.135  100.000   74.603
LGA    L    29_A      L    29_A     0.189     0    0.018   0.131     0.891  100.000   97.619
LGA    T    30_A      T    30_A     0.375     0    0.030   0.067     0.613  100.000   98.639
LGA    G    31_A      G    31_A     0.464     0    0.058   0.058     0.464  100.000  100.000
LGA    M    32_A      M    32_A     0.200     0    0.011   0.130     0.612  100.000   98.810
LGA    I    33_A      I    33_A     0.322     0    0.052   0.077     0.565  100.000   98.810
LGA    L    34_A      L    34_A     0.211     0    0.034   0.077     0.498  100.000  100.000
LGA    E    35_A      E    35_A     0.620     0    0.125   1.058     4.766   90.595   68.995
LGA    L    36_A      L    36_A     0.629     0    0.019   0.069     0.685   90.476   91.667
LGA    P    37_A      P    37_A     0.849     0    0.048   0.316     1.742   90.476   86.667
LGA    V    38_A      V    38_A     0.912     0    0.025   0.055     1.036   90.476   87.891
LGA    T    39_A      T    39_A     0.857     0    0.015   0.048     0.913   90.476   90.476
LGA    E    40_A      E    40_A     0.558     0    0.029   0.832     3.833   92.857   79.947
LGA    L    41_A      L    41_A     0.648     0    0.018   0.088     0.713   90.476   91.667
LGA    L    42_A      L    42_A     0.783     0    0.035   0.054     1.239   90.476   87.083
LGA    H    43_A      H    43_A     0.533     0    0.035   1.108     2.655   90.476   85.667
LGA    L    44_A      L    44_A     0.623     0    0.019   0.126     0.743   90.476   92.857
LGA    L    45_A      L    45_A     0.999     0    0.075   1.373     3.058   88.214   78.810
LGA    E    46_A      E    46_A     0.970     0    0.036   0.818     3.223   88.214   72.857
LGA    E    47_A      E    47_A     0.797     0    0.038   1.076     4.010   90.476   75.185
LGA    S    48_A      S    48_A     0.532     0    0.023   0.636     2.658   92.857   86.508
LGA    E    49_A      E    49_A     0.567     0    0.073   0.269     1.362   95.238   89.577
LGA    A    50_A      A    50_A     0.362     0    0.017   0.018     0.475  100.000  100.000
LGA    L    51_A      L    51_A     0.128     0    0.026   0.128     0.578  100.000   98.810
LGA    D    52_A      D    52_A     0.138     0    0.019   0.068     0.177  100.000  100.000
LGA    A    53_A      A    53_A     0.326     0    0.032   0.037     0.609  100.000   98.095
LGA    K    54_A      K    54_A     0.191     0    0.013   0.524     1.522  100.000   93.810
LGA    V    55_A      V    55_A     0.121     0    0.037   0.054     0.217  100.000  100.000
LGA    N    56_A      N    56_A     0.186     0    0.010   0.117     0.316  100.000  100.000
LGA    E    57_A      E    57_A     0.151     0    0.032   0.634     1.902  100.000   88.889
LGA    A    58_A      A    58_A     0.411     0    0.027   0.030     0.555   97.619   96.190
LGA    L    59_A      L    59_A     0.531     0    0.006   0.337     1.068   92.857   91.726
LGA    E    60_A      E    60_A     0.614     0    0.048   0.263     2.021   90.476   83.704
LGA    V    61_A      V    61_A     0.622     0    0.009   0.053     0.935   92.857   91.837
LGA    L    62_A      L    62_A     1.205     0    0.016   1.398     3.607   83.690   75.655
LGA    K    63_A      K    63_A     1.358     0    0.020   0.517     3.336   81.429   72.540
LGA    E    64_A      E    64_A     0.744     0    0.021   0.903     2.555   88.214   78.254
LGA    Y    65_A      Y    65_A     1.301     0    0.045   1.059     6.122   77.381   59.563
LGA    Q    66_A      Q    66_A     2.341     0    0.089   0.134     5.481   66.786   49.947
LGA    Q    67_A      Q    67_A     2.043     0    0.395   0.590     4.686   66.905   54.921
LGA    N    68_A      N    68_A     2.053     0    0.224   0.997     4.270   58.333   64.643

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     519    519  100.00                67
SUMMARY(RMSD_GDC):     0.941          0.943                  1.593           91.791   86.612

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.94    94.776    97.512     6.438

LGA_LOCAL      RMSD:   0.941  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.941  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.941  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.952862 * X  +  -0.302498 * Y  +   0.023438 * Z  +  -3.620167
  Y_new =  -0.301177 * X  +  -0.952383 * Y  +  -0.047527 * Z  + -11.515742
  Z_new =   0.036698 * X  +   0.038228 * Y  +  -0.998595 * Z  +   0.515225 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.306139 -0.036707  3.103330   [DEG:  -17.5405   -2.1031  177.8077 ]
ZXZ:  0.458151  3.088576  0.764992   [DEG:   26.2501  176.9624   43.8308 ]
 
# END of job
