
#######################################################
#                                                     #
#                        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:    34      57_A - 90_A        4.58    38.29
  LCS_AVERAGE:     23.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28      61_A - 88_A        1.92    42.85
  LCS_AVERAGE:     15.86

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      62_A - 84_A        0.96    42.59
  LCS_AVERAGE:     11.03

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      3    4   10      0    3    3    4    5    5    6    7    8    8    8    9   10   10   10   10   10   10   10   12 
LCS_GDT     K    28_A     K    28_A      3    4   10      3    3    3    3    5    5    6    7    8    8    8    9   10   10   10   10   10   12   12   13 
LCS_GDT     C    29_A     C    29_A      4    5   14      3    4    4    4    5    5    6    7    8    8    8    9   10   10   10   10   11   12   17   17 
LCS_GDT     H    30_A     H    30_A      4    5   16      3    4    4    4    4    6    6    7    8   10   10   11   13   14   15   15   16   17   18   18 
LCS_GDT     F    31_A     F    31_A      4    9   16      3    4    4    7    7   10   11   11   11   12   13   13   14   14   15   15   16   17   18   18 
LCS_GDT     D    32_A     D    32_A      6   10   16      3    4    6    7    9   10   11   11   12   12   13   13   14   14   15   15   16   17   18   18 
LCS_GDT     K    33_A     K    33_A      6   10   16      4    4    6    6    9   10   11   11   12   12   13   13   14   14   15   15   16   17   18   18 
LCS_GDT     C    34_A     C    34_A      6   10   16      4    4    6    7    9   10   11   11   12   12   13   13   14   14   15   15   16   17   18   18 
LCS_GDT     N    35_A     N    35_A      6   10   16      4    4    6    7    9   10   11   11   12   12   13   13   14   14   15   15   16   17   18   18 
LCS_GDT     K    36_A     K    36_A      6   10   16      4    5    6    7    9   10   11   11   12   12   13   13   14   14   15   15   16   17   18   18 
LCS_GDT     S    37_A     S    37_A      6   10   16      3    5    6    7    9   10   11   11   12   12   13   13   14   14   15   15   16   17   18   18 
LCS_GDT     Y    38_A     Y    38_A      5   10   16      3    5    5    7    9   10   11   11   12   12   13   13   14   14   15   15   16   17   18   18 
LCS_GDT     N    39_A     N    39_A      5   10   16      3    5    5    7    9   10   11   11   12   12   13   13   14   14   15   15   16   17   18   18 
LCS_GDT     W    40_A     W    40_A      5   10   16      3    5    5    7    9   10   11   11   12   12   13   13   14   14   15   15   16   17   18   18 
LCS_GDT     R    41_A     R    41_A      4   10   16      4    4    5    7    9   10   11   11   12   12   13   13   14   14   15   15   16   19   19   19 
LCS_GDT     K    42_A     K    42_A      5    7   16      4    5    5    5    7    7    8    8    9   11   12   12   13   14   15   15   16   19   19   19 
LCS_GDT     K    43_A     K    43_A      5    7   16      4    5    5    5    7    7    8    8    8   11   11   11   12   12   13   15   16   19   19   19 
LCS_GDT     Y    44_A     Y    44_A      5    7   16      4    5    5    5    7    7    8    8    9   11   11   13   14   14   15   15   16   19   19   19 
LCS_GDT     G    45_A     G    45_A      5    7   16      4    5    5    7    8    8   11   11   12   12   13   13   14   14   15   15   16   19   19   19 
LCS_GDT     K    46_A     K    46_A      5    7   16      4    5    5    5    7    7    8    9   12   12   13   13   14   14   15   15   16   19   19   19 
LCS_GDT     L    47_A     L    47_A      3    7   13      1    3    3    5    7    7    8    8    8   11   12   12   14   14   15   15   16   19   19   19 
LCS_GDT     R    48_A     R    48_A      3    4   13      3    3    3    4    4    5    6    8    8   11   11   11   12   12   13   14   16   19   19   19 
LCS_GDT     L    49_A     L    49_A      3    3   13      3    3    3    3    3    5    5    7    8   11   11   12   12   16   17   19   21   23   25   28 
LCS_GDT     V    50_A     V    50_A      3    3   13      3    3    3    3    3    4    4    5    7   11   11   12   14   16   17   19   21   23   25   28 
LCS_GDT     D    51_A     D    51_A      3    3   13      1    3    3    3    3    4    5    5    8   11   11   12   14   16   17   19   21   23   25   28 
LCS_GDT     H    52_A     H    52_A      3    3   13      0    3    3    3    3    3    5    6    8    8   10   12   15   17   20   24   24   26   28   30 
LCS_GDT     A    53_A     A    53_A      3    4   13      2    3    3    4    5    6    6    7    9   10   13   15   19   20   22   26   27   31   31   32 
LCS_GDT     F    54_A     F    54_A      3    4   13      3    3    3    4    4    5    6    7    9   10   12   15   19   20   22   26   27   31   31   32 
LCS_GDT     T    55_A     T    55_A      3    5   13      3    3    3    4    5    6    7    9   11   12   14   14   17   19   20   24   24   29   30   32 
LCS_GDT     H    56_A     H    56_A      4    7   13      3    4    4    6    7    8    8   10   11   12   14   15   17   20   22   26   29   31   31   32 
LCS_GDT     V    57_A     V    57_A      4    7   34      3    4    4    6    7    8    8   10   11   13   15   19   22   27   28   29   32   33   33   34 
LCS_GDT     P    58_A     P    58_A      4    7   34      3    4    4    6    7    8    9   13   17   20   24   28   29   29   31   32   32   33   33   34 
LCS_GDT     H    59_A     H    59_A      4   27   34      3    4    4    5   11   18   23   25   28   28   28   29   31   31   32   32   32   33   33   34 
LCS_GDT     L    60_A     L    60_A      5   27   34      3    4   14   21   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     K    61_A     K    61_A     19   28   34      4   13   22   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     M    62_A     M    62_A     23   28   34      8   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     K    63_A     K    63_A     23   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     C    64_A     C    64_A     23   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     N    65_A     N    65_A     23   28   34      5    9   21   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     F    66_A     F    66_A     23   28   34      5   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     C    67_A     C    67_A     23   28   34      4   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     D    68_A     D    68_A     23   28   34      4   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     Y    69_A     Y    69_A     23   28   34      4   13   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     M    70_A     M    70_A     23   28   34      4   12   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     C    71_A     C    71_A     23   28   34      7   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     K    72_A     K    72_A     23   28   34      4   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     G    73_A     G    73_A     23   28   34      6   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     I    74_A     I    74_A     23   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     R    75_A     R    75_A     23   28   34      4   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     N    76_A     N    76_A     23   28   34      9   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     I    77_A     I    77_A     23   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     R    78_A     R    78_A     23   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     L    79_A     L    79_A     23   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     H    80_A     H    80_A     23   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     H    81_A     H    81_A     23   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     K    82_A     K    82_A     23   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     K    83_A     K    83_A     23   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     S    84_A     S    84_A     23   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     H    85_A     H    85_A     20   28   34      5   17   22   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     P    86_A     P    86_A      6   28   34      5    5    5    6    6   18   26   26   27   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     D    87_A     D    87_A      6   28   34      5    5    5    6    6    8   11   15   26   28   28   29   31   31   32   32   32   32   33   34 
LCS_GDT     E    88_A     E    88_A      6   28   34     11   17   23   26   27   27   27   27   28   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     Q    89_A     Q    89_A      6    6   34      3    4    5    6    6   13   19   22   27   28   30   30   31   31   32   32   32   33   33   34 
LCS_GDT     L    90_A     L    90_A      3    3   34      0    3    3    3    4   13   14   22   24   27   30   30   31   31   32   32   32   33   33   34 
LCS_AVERAGE  LCS_A:  16.86  (  11.03   15.86   23.69 )

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     17     23     26     27     27     27     27     28     28     30     30     31     31     32     32     32     33     33     34 
GDT PERCENT_AT  10.48  16.19  21.90  24.76  25.71  25.71  25.71  25.71  26.67  26.67  28.57  28.57  29.52  29.52  30.48  30.48  30.48  31.43  31.43  32.38
GDT RMS_LOCAL    0.33   0.59   0.90   1.08   1.34   1.34   1.34   1.34   1.97   1.73   2.39   2.39   2.67   2.67   3.08   3.08   3.08   4.40   3.82   4.58
GDT RMS_ALL_AT  42.56  42.88  42.77  42.43  41.96  41.96  41.96  41.96  41.44  42.04  40.90  40.90  41.20  41.20  40.69  40.69  40.69  38.00  39.63  38.29

# Checking swapping
#   possible swapping detected:  F    31_A      F    31_A
#   possible swapping detected:  D    32_A      D    32_A
#   possible swapping detected:  Y    44_A      Y    44_A
#   possible swapping detected:  D    51_A      D    51_A
#   possible swapping detected:  F    54_A      F    54_A
#   possible swapping detected:  F    66_A      F    66_A
#   possible swapping detected:  D    68_A      D    68_A
#   possible swapping detected:  Y    69_A      Y    69_A
#   possible swapping detected:  D    87_A      D    87_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    I    27_A      I    27_A    72.666     0    0.065   0.659    74.504    0.000    0.000
LGA    K    28_A      K    28_A    71.239     0    0.324   0.321    73.544    0.000    0.000
LGA    C    29_A      C    29_A    70.508     0    0.597   0.817    71.840    0.000    0.000
LGA    H    30_A      H    30_A    71.724     0    0.262   0.398    75.276    0.000    0.000
LGA    F    31_A      F    31_A    68.138     0    0.629   0.728    69.324    0.000    0.000
LGA    D    32_A      D    32_A    67.996     0    0.616   1.140    69.463    0.000    0.000
LGA    K    33_A      K    33_A    73.745     0    0.421   0.715    79.778    0.000    0.000
LGA    C    34_A      C    34_A    73.921     0    0.132   0.713    75.355    0.000    0.000
LGA    N    35_A      N    35_A    79.401     0    0.181   0.266    84.455    0.000    0.000
LGA    K    36_A      K    36_A    77.765     0    0.094   1.041    77.895    0.000    0.000
LGA    S    37_A      S    37_A    76.894     0    0.059   0.625    79.387    0.000    0.000
LGA    Y    38_A      Y    38_A    73.513     0    0.055   0.086    74.445    0.000    0.000
LGA    N    39_A      N    39_A    75.237     0    0.077   0.197    80.121    0.000    0.000
LGA    W    40_A      W    40_A    70.461     0    0.571   0.410    72.704    0.000    0.000
LGA    R    41_A      R    41_A    67.677     0    0.625   1.009    76.851    0.000    0.000
LGA    K    42_A      K    42_A    64.167     0    0.033   0.784    67.517    0.000    0.000
LGA    K    43_A      K    43_A    63.016     0    0.095   0.594    67.166    0.000    0.000
LGA    Y    44_A      Y    44_A    60.536     0    0.029   1.087    71.225    0.000    0.000
LGA    G    45_A      G    45_A    55.591     0    0.112   0.112    57.785    0.000    0.000
LGA    K    46_A      K    46_A    52.791     0    0.629   1.511    55.604    0.000    0.000
LGA    L    47_A      L    47_A    48.842     0    0.587   0.952    50.309    0.000    0.000
LGA    R    48_A      R    48_A    49.857     0    0.624   1.222    58.439    0.000    0.000
LGA    L    49_A      L    49_A    46.188     0    0.561   1.050    50.217    0.000    0.000
LGA    V    50_A      V    50_A    40.955     0    0.571   1.467    42.967    0.000    0.000
LGA    D    51_A      D    51_A    37.660     0    0.647   1.003    39.121    0.000    0.000
LGA    H    52_A      H    52_A    37.819     0    0.613   1.325    42.909    0.000    0.000
LGA    A    53_A      A    53_A    32.598     0    0.611   0.603    34.524    0.000    0.000
LGA    F    54_A      F    54_A    27.662     0    0.590   0.977    29.130    0.000    0.000
LGA    T    55_A      T    55_A    26.412     0    0.478   0.966    29.567    0.000    0.000
LGA    H    56_A      H    56_A    25.089     0    0.571   0.453    32.512    0.000    0.000
LGA    V    57_A      V    57_A    18.113     0    0.032   0.091    20.354    0.000    0.000
LGA    P    58_A      P    58_A    14.507     0    0.255   0.426    17.090    0.000    0.000
LGA    H    59_A      H    59_A     8.423     0    0.698   1.273    15.017    7.857    3.619
LGA    L    60_A      L    60_A     3.880     0    0.439   1.403     7.002   39.524   29.940
LGA    K    61_A      K    61_A     1.617     0    0.034   0.963     6.007   77.381   60.794
LGA    M    62_A      M    62_A     0.465     0    0.041   0.891     3.929   92.976   87.024
LGA    K    63_A      K    63_A     0.674     0    0.034   1.118     6.664   95.238   70.529
LGA    C    64_A      C    64_A     0.109     0    0.028   0.059     1.234   92.976   93.730
LGA    N    65_A      N    65_A     1.889     0    0.048   0.067     3.061   72.976   66.071
LGA    F    66_A      F    66_A     1.096     0    0.199   1.295     7.917   79.286   50.346
LGA    C    67_A      C    67_A     1.146     0    0.601   0.628     3.412   75.833   79.206
LGA    D    68_A      D    68_A     1.102     0    0.221   0.339     3.724   88.333   72.083
LGA    Y    69_A      Y    69_A     1.503     0    0.054   0.118     5.072   77.143   56.865
LGA    M    70_A      M    70_A     1.492     0    0.052   0.966     4.573   79.286   62.738
LGA    C    71_A      C    71_A     0.624     0    0.035   0.876     1.828   88.214   86.032
LGA    K    72_A      K    72_A     1.393     0    0.603   0.891     5.209   77.619   60.794
LGA    G    73_A      G    73_A     1.532     0    0.085   0.085     2.050   72.976   72.976
LGA    I    74_A      I    74_A     1.290     0    0.041   0.098     1.365   81.429   81.429
LGA    R    75_A      R    75_A     1.396     0    0.023   0.895     4.497   81.429   75.411
LGA    N    76_A      N    76_A     1.313     0    0.009   0.170     1.423   81.429   81.429
LGA    I    77_A      I    77_A     0.588     0    0.087   0.939     2.171   92.857   85.119
LGA    R    78_A      R    78_A     0.102     0    0.032   1.624     8.141   97.619   63.290
LGA    L    79_A      L    79_A     0.640     0    0.047   0.072     0.922   92.857   91.667
LGA    H    80_A      H    80_A     0.783     0    0.022   0.131     1.022   90.476   89.571
LGA    H    81_A      H    81_A     0.561     0    0.140   1.169     2.369   86.071   82.810
LGA    K    82_A      K    82_A     0.818     0    0.037   0.550     2.527   90.476   79.947
LGA    K    83_A      K    83_A     0.750     0    0.106   1.172     4.065   90.476   81.693
LGA    S    84_A      S    84_A     1.264     0    0.071   0.073     1.585   79.286   80.000
LGA    H    85_A      H    85_A     1.673     0    0.188   0.220    10.150   70.833   35.571
LGA    P    86_A      P    86_A     6.162     0    0.109   0.178     8.389   20.238   17.007
LGA    D    87_A      D    87_A     7.205     0    0.070   1.022    10.386   18.690    9.821
LGA    E    88_A      E    88_A     0.925     0    0.570   1.156     7.573   55.952   38.519
LGA    Q    89_A      Q    89_A     7.454     0    0.514   0.580    10.594   11.071   12.857
LGA    L    90_A      L    90_A     8.631     0    0.162   0.631    10.136    2.500    9.881

# 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):    17.990         17.743                 18.995           21.536   18.750

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64  105    4.0     27    1.34    24.286    22.993     1.878

LGA_LOCAL      RMSD:   1.338  Number of atoms:   27  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  41.965  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:  17.990  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.341519 * X  +  -0.936091 * Y  +  -0.084250 * Z  +  -0.505216
  Y_new =   0.863597 * X  +   0.277166 * Y  +   0.421164 * Z  + -32.006058
  Z_new =  -0.370897 * X  +  -0.216593 * Y  +   0.903063 * Z  +  57.045307 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.194209  0.379974 -0.235397   [DEG:   68.4231   21.7709  -13.4872 ]
ZXZ: -2.944159  0.443948 -2.099347   [DEG: -168.6879   25.4363 -120.2837 ]
 
# END of job
