
#######################################################
#                                                     #
#                        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   64 (  548),  selected   64 , name one
# Molecule2: number of CA atoms  105 (  864),  selected   64 , 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:    36      54_A - 89_A        4.99    21.64
  LONGEST_CONTINUOUS_SEGMENT:    36      55_A - 90_A        4.29    22.82
  LCS_AVERAGE:     33.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31      59_A - 89_A        1.76    25.93
  LONGEST_CONTINUOUS_SEGMENT:    31      60_A - 90_A        1.86    26.07
  LCS_AVERAGE:     24.20

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28      61_A - 88_A        0.97    26.23
  LCS_AVERAGE:     16.16

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
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     I    27_A     I    27_A      5    7   35      7   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   35   38 
LCS_GDT     K    28_A     K    28_A      5    7   35      7   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   35   36 
LCS_GDT     C    29_A     C    29_A      5    7   35      6   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   35   36 
LCS_GDT     H    30_A     H    30_A      5    7   35      7   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   35   35 
LCS_GDT     F    31_A     F    31_A      5    7   35      3    4    5   16   20   26   30   30   31   32   32   32   32   33   33   33   33   35   35   35 
LCS_GDT     D    32_A     D    32_A      4   13   35      3    6   18   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   35   35 
LCS_GDT     K    33_A     K    33_A      4   13   35      3    3    4    4    5    7    9   16   26   30   32   32   32   33   33   33   33   34   34   34 
LCS_GDT     C    34_A     C    34_A      8   23   35      4   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   35   35 
LCS_GDT     N    35_A     N    35_A      8   23   35      4    6   18   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   35   35 
LCS_GDT     K    36_A     K    36_A      8   23   35      7   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   37   39 
LCS_GDT     S    37_A     S    37_A      8   23   35      7   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   37   39 
LCS_GDT     Y    38_A     Y    38_A      8   23   35      6   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   35   37   38   40 
LCS_GDT     N    39_A     N    39_A      8   23   35      6    7   18   20   23   27   30   30   31   32   32   32   32   33   33   33   35   37   38   40 
LCS_GDT     W    40_A     W    40_A      8   23   35      3    9   18   20   23   27   30   30   31   32   32   32   32   33   33   33   35   37   38   40 
LCS_GDT     R    41_A     R    41_A      8   23   35      4    6   14   20   23   27   30   30   31   32   32   32   32   33   33   33   33   37   38   40 
LCS_GDT     K    42_A     K    42_A      6   23   35      4    5    7   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   36   38 
LCS_GDT     K    43_A     K    43_A      6   23   35      4    5   18   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   36   37 
LCS_GDT     Y    44_A     Y    44_A      6   23   35      4    5    7   12   21   27   30   30   31   32   32   32   32   33   33   33   33   35   36   37 
LCS_GDT     G    45_A     G    45_A     12   23   35      3    7   16   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   36   38 
LCS_GDT     K    46_A     K    46_A     12   23   35      3    5   13   20   22   26   30   30   31   32   32   32   32   33   33   33   33   35   36   38 
LCS_GDT     L    47_A     L    47_A     12   23   35      8   10   13   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   36   38 
LCS_GDT     R    48_A     R    48_A     12   23   35      8   10   16   20   23   27   30   30   31   32   32   32   32   33   33   33   35   37   38   40 
LCS_GDT     L    49_A     L    49_A     12   23   35      8   10   16   20   23   27   30   30   31   32   32   32   32   33   33   33   35   37   38   40 
LCS_GDT     V    50_A     V    50_A     12   23   35      8   11   16   20   23   27   30   30   31   32   32   32   32   33   33   33   33   35   38   40 
LCS_GDT     D    51_A     D    51_A     12   23   35      8   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   33   37   38   40 
LCS_GDT     H    52_A     H    52_A     12   23   35      8   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   35   37   38   40 
LCS_GDT     A    53_A     A    53_A     12   23   35      8   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   35   37   38   40 
LCS_GDT     F    54_A     F    54_A     12   23   36      8   11   18   20   23   27   30   30   31   32   32   32   32   33   33   33   35   37   38   40 
LCS_GDT     T    55_A     T    55_A     12   23   36      8   10   18   20   23   27   30   30   31   32   32   32   32   33   33   35   35   37   38   40 
LCS_GDT     H    56_A     H    56_A     12   23   36      3   10   11   20   23   27   30   30   31   32   32   32   32   33   34   35   35   37   38   40 
LCS_GDT     V    57_A     V    57_A      4   14   36      3    4    5    6   16   17   26   30   31   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     P    58_A     P    58_A      5   30   36      3    4    5   12   23   26   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     H    59_A     H    59_A      5   31   36      3    4    7   11   21   22   29   29   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     L    60_A     L    60_A      5   31   36      3    4    5    6    7   19   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     K    61_A     K    61_A     28   31   36     10   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     M    62_A     M    62_A     28   31   36      7   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     K    63_A     K    63_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     C    64_A     C    64_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     N    65_A     N    65_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     F    66_A     F    66_A     28   31   36      7   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     C    67_A     C    67_A     28   31   36      3   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     D    68_A     D    68_A     28   31   36      4   10   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     Y    69_A     Y    69_A     28   31   36      6   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     M    70_A     M    70_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     C    71_A     C    71_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     K    72_A     K    72_A     28   31   36      4   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   35   38   40 
LCS_GDT     G    73_A     G    73_A     28   31   36      4   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   35   36   36 
LCS_GDT     I    74_A     I    74_A     28   31   36      4   16   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   35   36   39 
LCS_GDT     R    75_A     R    75_A     28   31   36      5   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   35   36   36 
LCS_GDT     N    76_A     N    76_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   35   36   39 
LCS_GDT     I    77_A     I    77_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     R    78_A     R    78_A     28   31   36      6   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   35   37   39 
LCS_GDT     L    79_A     L    79_A     28   31   36      6   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   35   37   39 
LCS_GDT     H    80_A     H    80_A     28   31   36      9   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     H    81_A     H    81_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     K    82_A     K    82_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     K    83_A     K    83_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   35   38   40 
LCS_GDT     S    84_A     S    84_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     H    85_A     H    85_A     28   31   36     11   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     P    86_A     P    86_A     28   31   36      5   21   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     D    87_A     D    87_A     28   31   36      4   17   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     E    88_A     E    88_A     28   31   36      3   16   25   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     Q    89_A     Q    89_A     21   31   36      3    4   17   29   29   29   31   31   32   32   32   32   33   33   34   35   35   37   38   40 
LCS_GDT     L    90_A     L    90_A      3   31   36      3    3    3    3    4    4   15   28   30   30   30   30   32   33   33   33   35   35   36   39 
LCS_AVERAGE  LCS_A:  24.75  (  16.16   24.20   33.88 )

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     21     25     29     29     29     31     31     32     32     32     32     33     33     34     35     35     37     38     40 
GDT PERCENT_AT  10.48  20.00  23.81  27.62  27.62  27.62  29.52  29.52  30.48  30.48  30.48  30.48  31.43  31.43  32.38  33.33  33.33  35.24  36.19  38.10
GDT RMS_LOCAL    0.38   0.64   0.78   1.02   1.02   1.02   1.85   1.85   2.02   2.02   2.02   2.02   2.73   2.34   3.55   4.10   4.10   6.05   6.17   6.44
GDT RMS_ALL_AT  26.51  26.26  26.14  26.27  26.27  26.27  25.57  25.57  25.57  25.57  25.57  25.57  24.85  25.60  23.81  22.74  22.74  11.36  11.35  11.31

# Checking swapping
#   possible swapping detected:  F    31_A      F    31_A
#   possible swapping detected:  Y    44_A      Y    44_A
#   possible swapping detected:  E    88_A      E    88_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    I    27_A      I    27_A    42.771     0    0.169   0.820    45.942    0.000    0.000
LGA    K    28_A      K    28_A    39.124     0    0.095   0.796    43.578    0.000    0.000
LGA    C    29_A      C    29_A    34.155     0    0.048   0.819    35.469    0.000    0.000
LGA    H    30_A      H    30_A    36.191     0    0.657   0.866    40.712    0.000    0.000
LGA    F    31_A      F    31_A    31.171     0    0.563   1.074    32.813    0.000    0.000
LGA    D    32_A      D    32_A    29.498     0    0.631   0.905    32.206    0.000    0.000
LGA    K    33_A      K    33_A    28.966     0    0.024   1.014    30.514    0.000    0.000
LGA    C    34_A      C    34_A    26.393     0    0.670   0.753    28.967    0.000    0.000
LGA    N    35_A      N    35_A    30.889     0    0.034   0.870    35.358    0.000    0.000
LGA    K    36_A      K    36_A    28.658     0    0.113   0.676    33.045    0.000    0.000
LGA    S    37_A      S    37_A    34.088     0    0.075   0.577    36.566    0.000    0.000
LGA    Y    38_A      Y    38_A    35.872     0    0.061   0.143    40.429    0.000    0.000
LGA    N    39_A      N    39_A    41.657     0    0.302   1.101    42.618    0.000    0.000
LGA    W    40_A      W    40_A    46.175     0    0.110   0.996    50.913    0.000    0.000
LGA    R    41_A      R    41_A    52.004     0    0.068   1.059    53.392    0.000    0.000
LGA    K    42_A      K    42_A    57.368     0    0.021   0.770    63.720    0.000    0.000
LGA    K    43_A      K    43_A    57.942     0    0.052   0.632    62.894    0.000    0.000
LGA    Y    44_A      Y    44_A    51.535     0    0.172   1.033    53.645    0.000    0.000
LGA    G    45_A      G    45_A    49.388     0    0.051   0.051    50.829    0.000    0.000
LGA    K    46_A      K    46_A    43.176     0    0.560   0.823    47.272    0.000    0.000
LGA    L    47_A      L    47_A    38.190     0    0.029   1.451    40.062    0.000    0.000
LGA    R    48_A      R    48_A    33.119     0    0.026   1.118    35.424    0.000    0.000
LGA    L    49_A      L    49_A    33.463     0    0.051   1.423    36.569    0.000    0.000
LGA    V    50_A      V    50_A    32.942     0    0.036   0.051    37.150    0.000    0.000
LGA    D    51_A      D    51_A    28.063     0    0.016   0.191    30.673    0.000    0.000
LGA    H    52_A      H    52_A    24.779     0    0.060   0.208    26.404    0.000    0.000
LGA    A    53_A      A    53_A    25.992     0    0.106   0.129    28.436    0.000    0.000
LGA    F    54_A      F    54_A    22.891     0    0.115   1.646    27.783    0.000    0.000
LGA    T    55_A      T    55_A    16.864     0    0.557   1.004    19.458    0.000    0.000
LGA    H    56_A      H    56_A    16.077     0    0.375   1.127    19.980    0.000    0.000
LGA    V    57_A      V    57_A    11.840     0    0.113   0.156    14.909    1.548    0.884
LGA    P    58_A      P    58_A     5.679     0    0.205   0.231     8.956   19.762   16.871
LGA    H    59_A      H    59_A     5.333     0    0.352   1.185    10.520   30.238   12.810
LGA    L    60_A      L    60_A     4.989     0    0.066   0.938    10.420   46.786   25.060
LGA    K    61_A      K    61_A     1.434     0    0.625   0.842     7.589   81.548   46.138
LGA    M    62_A      M    62_A     1.309     0    0.045   1.046     5.409   81.429   68.333
LGA    K    63_A      K    63_A     1.032     0    0.078   0.641     2.244   81.429   83.598
LGA    C    64_A      C    64_A     0.860     0    0.128   0.161     1.077   92.857   90.556
LGA    N    65_A      N    65_A     0.881     0    0.059   1.162     3.580   90.476   80.119
LGA    F    66_A      F    66_A     1.428     0    0.196   0.428     2.287   79.286   75.281
LGA    C    67_A      C    67_A     1.003     0    0.607   0.623     2.074   79.524   81.667
LGA    D    68_A      D    68_A     2.679     0    0.144   0.933     4.625   59.048   49.048
LGA    Y    69_A      Y    69_A     1.514     0    0.087   0.345     3.762   77.143   68.690
LGA    M    70_A      M    70_A     1.287     0    0.024   0.210     1.443   81.429   82.560
LGA    C    71_A      C    71_A     1.353     0    0.091   0.829     1.788   81.429   80.000
LGA    K    72_A      K    72_A     0.895     0    0.664   0.727     6.842   74.286   53.651
LGA    G    73_A      G    73_A     0.785     0    0.088   0.088     0.785   95.238   95.238
LGA    I    74_A      I    74_A     1.268     0    0.049   0.085     2.698   83.690   75.298
LGA    R    75_A      R    75_A     1.201     0    0.028   1.096     5.812   85.952   66.320
LGA    N    76_A      N    76_A     0.664     0    0.030   0.201     1.449   90.476   89.345
LGA    I    77_A      I    77_A     0.520     0    0.115   0.221     0.976   92.857   94.048
LGA    R    78_A      R    78_A     1.007     0    0.014   0.118     1.941   83.690   79.134
LGA    L    79_A      L    79_A     1.262     0    0.040   0.077     2.268   85.952   77.381
LGA    H    80_A      H    80_A     0.550     0    0.013   0.226     0.694   95.238   93.333
LGA    H    81_A      H    81_A     0.449     0    0.168   0.376     0.907   97.619   94.286
LGA    K    82_A      K    82_A     0.508     0    0.268   0.811     5.153   86.071   68.254
LGA    K    83_A      K    83_A     0.345     0    0.048   0.656     3.283   92.976   83.545
LGA    S    84_A      S    84_A     0.520     0    0.049   0.566     1.624   92.857   89.127
LGA    H    85_A      H    85_A     0.638     0    0.176   0.237     0.757   90.476   94.286
LGA    P    86_A      P    86_A     0.964     0    0.030   0.043     1.810   85.952   82.789
LGA    D    87_A      D    87_A     2.177     0    0.019   1.061     5.536   64.881   50.179
LGA    E    88_A      E    88_A     2.382     0    0.535   0.597     3.504   63.095   57.513
LGA    Q    89_A      Q    89_A     2.332     0    0.051   1.318     8.800   60.952   36.667
LGA    L    90_A      L    90_A     7.208     0    0.143   0.678    11.623   13.333    6.905

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     548    548  100.00               105
SUMMARY(RMSD_GDC):    10.792         10.694                 12.159           23.995   21.418

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64  105    4.0     31    1.85    27.619    27.164     1.593

LGA_LOCAL      RMSD:   1.846  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  25.571  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:  10.792  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.599445 * X  +   0.769108 * Y  +  -0.221672 * Z  +  -0.381824
  Y_new =   0.721021 * X  +   0.639119 * Y  +   0.267687 * Z  + -42.676048
  Z_new =   0.347555 * X  +   0.000634 * Y  +  -0.937659 * Z  +   9.429550 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.264383 -0.354963  3.140917   [DEG:  129.7396  -20.3379  179.9613 ]
ZXZ: -2.449950  2.786629  1.568973   [DEG: -140.3718  159.6621   89.8956 ]
 
# END of job
