
#######################################################
#                                                     #
#                        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   62 (  535),  selected   62 , name one
# Molecule2: number of CA atoms  104 (  843),  selected   62 , 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:    42      47_A - 88_A        4.98    10.11
  LCS_AVERAGE:     37.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31      56_A - 86_A        1.90    13.04
  LCS_AVERAGE:     20.11

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      57_A - 79_A        0.93    13.81
  LONGEST_CONTINUOUS_SEGMENT:    23      58_A - 80_A        0.93    13.95
  LCS_AVERAGE:     12.56

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   62
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     K    27_A     K    27_A      4   12   32      4    6   13   17   20   22   25   26   26   27   27   28   30   30   32   37   39   40   43   43 
LCS_GDT     C    28_A     C    28_A      4   12   32      3    8   13   17   20   22   25   26   26   27   27   28   30   30   32   37   43   44   44   45 
LCS_GDT     H    29_A     H    29_A      4   12   32      3    4    4   12   15   19   25   26   26   27   27   27   30   30   31   31   33   34   34   34 
LCS_GDT     F    30_A     F    30_A      4   12   32      3    8   13   17   20   22   25   26   26   27   27   28   30   30   31   31   33   34   34   34 
LCS_GDT     D    31_A     D    31_A      5   12   32      3    4    7   12   14   19   25   26   26   27   27   27   30   30   31   31   33   34   34   34 
LCS_GDT     N    32_A     N    32_A      5   12   32      3    7   13   17   20   22   25   26   26   27   27   28   30   30   31   31   33   34   34   34 
LCS_GDT     C    33_A     C    33_A      7   12   32      3    7   13   17   20   22   25   26   26   27   27   28   30   30   31   31   33   34   34   34 
LCS_GDT     N    34_A     N    34_A      7   12   32      5    7    8   12   19   22   25   26   26   27   27   28   30   30   31   31   33   34   34   34 
LCS_GDT     R    35_A     R    35_A      7   12   32      5    7   13   17   20   22   25   26   26   27   27   28   30   30   31   31   33   38   43   43 
LCS_GDT     K    36_A     K    36_A      7   12   32      5    8   13   17   20   22   25   26   26   27   27   28   30   30   32   37   39   40   43   43 
LCS_GDT     I    37_A     I    37_A      7   12   32      5    7   11   17   20   22   25   26   26   27   27   30   33   36   40   42   43   44   46   47 
LCS_GDT     H    38_A     H    38_A      7   12   32      5    7   11   17   20   22   25   26   26   27   27   30   31   35   39   42   43   44   46   47 
LCS_GDT     W    39_A     W    39_A      7   10   32      5    7    8   16   20   22   24   27   29   32   35   36   38   40   41   45   46   47   48   49 
LCS_GDT     K    40_A     K    40_A      4    7   32      3    3    4    5    8   13   16   28   30   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     I    41_A     I    41_A      5    6   32      4    5    5    5   13   21   25   27   29   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     R    42_A     R    42_A      5    6   32      4    5    5    5    6   13   15   15   17   19   25   27   32   33   33   41   42   45   47   49 
LCS_GDT     Y    43_A     Y    43_A      5    6   32      4    5    5    5    6    6    9   14   17   18   21   23   28   38   43   45   46   47   48   49 
LCS_GDT     G    44_A     G    44_A      5    6   32      4    5    5    5    5    7   10   16   20   29   29   36   38   39   43   45   46   47   48   49 
LCS_GDT     K    45_A     K    45_A      5   13   32      1    5   11   17   20   22   25   26   26   27   27   28   31   38   43   45   46   47   48   49 
LCS_GDT     L    46_A     L    46_A     10   13   32      3    7   11   12   17   21   25   26   26   27   27   28   30   30   31   32   43   47   48   49 
LCS_GDT     R    47_A     R    47_A     10   13   42      6    7   11   17   20   22   25   26   26   27   27   28   30   30   35   41   46   47   48   49 
LCS_GDT     L    48_A     L    48_A     10   13   42      6    7   11   17   20   22   25   27   29   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     V    49_A     V    49_A     10   13   42      6    7   11   17   20   22   25   26   26   30   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     D    50_A     D    50_A     10   13   42      6    7   13   17   20   22   25   26   26   27   27   28   30   30   37   42   46   47   48   49 
LCS_GDT     H    51_A     H    51_A     10   13   42      6    8   13   17   20   22   25   26   26   27   27   34   37   40   41   45   46   47   48   49 
LCS_GDT     A    52_A     A    52_A     10   13   42      6    8   13   17   20   23   25   28   30   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     L    53_A     L    53_A     10   13   42      5    8   13   17   20   22   25   26   26   30   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     S    54_A     S    54_A     10   13   42      5    8   13   17   20   22   25   26   26   27   27   34   37   40   43   45   46   47   48   49 
LCS_GDT     H    55_A     H    55_A     10   13   42      5    8   13   17   20   22   25   26   29   32   33   38   38   40   43   45   46   47   48   49 
LCS_GDT     Q    56_A     Q    56_A     10   31   42      5    7   15   21   25   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     E    57_A     E    57_A     23   31   42      5   14   21   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     E    58_A     E    58_A     23   31   42      6   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     K    59_A     K    59_A     23   31   42      6   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     S    60_A     S    60_A     23   31   42      4   17   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     I    61_A     I    61_A     23   31   42     10   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     D    62_A     D    62_A     23   31   42     10   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     C    63_A     C    63_A     23   31   42     10   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     Q    64_A     Q    64_A     23   31   42     10   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     K    65_A     K    65_A     23   31   42     10   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     C    66_A     C    66_A     23   31   42      5   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     E    67_A     E    67_A     23   31   42      9   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     Y    68_A     Y    68_A     23   31   42      5   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     S    69_A     S    69_A     23   31   42     10   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     C    70_A     C    70_A     23   31   42     10   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     Q    71_A     Q    71_A     23   31   42      9   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     T    72_A     T    72_A     23   31   42      6   18   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     T    73_A     T    73_A     23   31   42      6   15   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     R    74_A     R    74_A     23   31   42      8   19   23   24   26   28   30   31   31   32   35   38   38   40   43   45   46   47   48   49 
LCS_GDT     Q    75_A     Q    75_A     23   31   42      9   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     M    76_A     M    76_A     23   31   42     10   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     R    77_A     R    77_A     23   31   42     10   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     Y    78_A     Y    78_A     23   31   42      5   17   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     H    79_A     H    79_A     23   31   42     10   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     Y    80_A     Y    80_A     23   31   42      4    7   13   22   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     K    81_A     K    81_A      7   31   42      5    7    7   13   18   27   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     K    82_A     K    82_A      7   31   42      5    7   11   15   25   27   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     I    83_A     I    83_A      7   31   42      5    7    8   22   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     H    84_A     H    84_A      7   31   42      5   19   23   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     A    85_A     A    85_A      7   31   42      5   12   20   23   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     N    86_A     N    86_A      3   31   42      4   15   20   24   26   28   30   31   31   32   36   38   38   40   43   45   46   47   48   49 
LCS_GDT     L    87_A     L    87_A      3    4   42      3    3    3    4    5   13   19   21   21   30   32   35   38   40   43   45   46   47   48   49 
LCS_GDT     K    88_A     K    88_A      3    4   42      0    3    3    3    4    5   10   13   17   24   28   33   34   38   40   42   43   44   46   47 
LCS_AVERAGE  LCS_A:  23.32  (  12.56   20.11   37.28 )

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     10     19     23     24     26     28     30     31     31     32     36     38     38     40     43     45     46     47     48     49 
GDT PERCENT_AT   9.62  18.27  22.12  23.08  25.00  26.92  28.85  29.81  29.81  30.77  34.62  36.54  36.54  38.46  41.35  43.27  44.23  45.19  46.15  47.12
GDT RMS_LOCAL    0.31   0.65   0.82   0.93   1.15   1.44   1.77   1.90   1.90   2.34   3.40   3.64   3.67   3.98   4.61   4.92   5.10   5.31   5.52   5.64
GDT RMS_ALL_AT  13.51  13.65  13.97  13.89  13.74  13.64  13.13  13.04  13.04  12.17  10.69  10.60  10.20  10.29  10.83  10.45  10.44  10.40  10.48  10.57

# Checking swapping
#   possible swapping detected:  Y    43_A      Y    43_A
#   possible swapping detected:  D    50_A      D    50_A
#   possible swapping detected:  Y    78_A      Y    78_A
#   possible swapping detected:  Y    80_A      Y    80_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    27_A      K    27_A    22.581     0    0.172   0.806    30.452    0.000    0.000
LGA    C    28_A      C    28_A    19.556     0    0.133   0.167    21.731    0.000    0.000
LGA    H    29_A      H    29_A    19.100     0    0.281   1.271    20.786    0.000    0.000
LGA    F    30_A      F    30_A    18.604     0    0.598   0.786    21.995    0.000    0.000
LGA    D    31_A      D    31_A    25.602     0    0.182   0.735    29.519    0.000    0.000
LGA    N    32_A      N    32_A    29.362     0    0.133   0.232    31.979    0.000    0.000
LGA    C    33_A      C    33_A    26.565     0    0.539   0.558    28.718    0.000    0.000
LGA    N    34_A      N    34_A    30.774     0    0.285   0.344    36.347    0.000    0.000
LGA    R    35_A      R    35_A    28.605     0    0.000   1.372    34.155    0.000    0.000
LGA    K    36_A      K    36_A    26.354     0    0.138   1.275    31.204    0.000    0.000
LGA    I    37_A      I    37_A    21.992     0    0.112   0.129    22.924    0.000    0.000
LGA    H    38_A      H    38_A    23.876     0    0.545   0.778    32.163    0.000    0.000
LGA    W    39_A      W    39_A    16.845     0    0.131   1.562    19.367    0.000    0.000
LGA    K    40_A      K    40_A    13.730     0    0.269   1.183    19.614    0.357    0.159
LGA    I    41_A      I    41_A     9.908     0    0.642   1.098    11.524    0.119    0.298
LGA    R    42_A      R    42_A    13.214     0    0.000   1.335    15.540    0.000    0.000
LGA    Y    43_A      Y    43_A    13.564     0    0.177   0.902    14.448    0.000    0.000
LGA    G    44_A      G    44_A    12.186     0    0.514   0.514    14.012    0.000    0.000
LGA    K    45_A      K    45_A    11.766     0    0.191   1.551    13.854    0.000    0.159
LGA    L    46_A      L    46_A    16.178     0    0.411   0.416    21.008    0.000    0.000
LGA    R    47_A      R    47_A    18.170     0    0.000   0.875    27.686    0.000    0.000
LGA    L    48_A      L    48_A    12.277     0    0.079   1.095    13.986    0.000    0.000
LGA    V    49_A      V    49_A     8.898     0    0.082   0.890    10.726    0.952    1.429
LGA    D    50_A      D    50_A    15.112     0    0.087   1.104    19.498    0.000    0.000
LGA    H    51_A      H    51_A    15.546     0    0.055   0.212    21.097    0.000    0.000
LGA    A    52_A      A    52_A     8.777     0    0.082   0.091    10.985    4.405    6.952
LGA    L    53_A      L    53_A     8.974     0    0.092   0.149    13.427    1.905    1.310
LGA    S    54_A      S    54_A    13.206     0    0.149   0.186    15.872    0.000    0.000
LGA    H    55_A      H    55_A    10.473     0    0.168   0.315    17.897    2.381    0.952
LGA    Q    56_A      Q    56_A     4.052     0    0.069   0.423     6.358   30.952   35.767
LGA    E    57_A      E    57_A     2.543     4    0.302   0.303     3.057   57.262   31.005
LGA    E    58_A      E    58_A     0.763     4    0.131   0.169     1.323   88.214   48.254
LGA    K    59_A      K    59_A     0.699     0    0.000   0.830     5.417   88.214   66.455
LGA    S    60_A      S    60_A     1.761     0    0.256   0.530     3.003   81.548   74.841
LGA    I    61_A      I    61_A     0.664     0    0.023   1.146     3.489   88.214   76.012
LGA    D    62_A      D    62_A     0.429     0    0.155   0.749     3.333   92.976   80.476
LGA    C    63_A      C    63_A     0.444     0    0.033   0.097     1.094   92.976   92.143
LGA    Q    64_A      Q    64_A     1.006     0    0.240   0.923     6.619   79.524   58.413
LGA    K    65_A      K    65_A     0.987     0    0.055   0.771     3.519   88.214   73.069
LGA    C    66_A      C    66_A     1.071     0    0.086   0.708     1.649   88.214   84.524
LGA    E    67_A      E    67_A     0.643     4    0.122   0.124     0.867   90.476   50.265
LGA    Y    68_A      Y    68_A     1.287     0    0.020   1.286     9.882   83.690   45.317
LGA    S    69_A      S    69_A     0.514     0    0.000   0.689     2.393   90.476   87.778
LGA    C    70_A      C    70_A     0.771     0    0.112   0.213     1.277   88.214   87.460
LGA    Q    71_A      Q    71_A     0.750     0    0.074   1.497     3.648   85.952   75.556
LGA    T    72_A      T    72_A     2.325     0    0.044   1.103     4.189   68.810   63.197
LGA    T    73_A      T    73_A     2.120     0    0.075   1.113     4.923   68.810   62.381
LGA    R    74_A      R    74_A     1.945     0    0.000   1.824     9.612   72.976   48.528
LGA    Q    75_A      Q    75_A     1.490     0    0.064   0.953     6.081   79.286   59.735
LGA    M    76_A      M    76_A     0.733     0    0.087   0.596     2.107   90.476   85.000
LGA    R    77_A      R    77_A     0.964     0    0.115   0.815     2.225   88.214   77.706
LGA    Y    78_A      Y    78_A     1.421     0    0.059   1.274     6.240   81.429   62.063
LGA    H    79_A      H    79_A     0.791     0    0.140   0.142     1.133   90.476   86.857
LGA    Y    80_A      Y    80_A     2.393     0    0.076   1.552     3.433   62.976   64.484
LGA    K    81_A      K    81_A     4.023     0    0.042   0.991    10.150   41.905   24.339
LGA    K    82_A      K    82_A     3.780     0    0.086   0.242     8.078   45.119   32.169
LGA    I    83_A      I    83_A     2.469     0    0.117   1.501     4.622   64.881   59.702
LGA    H    84_A      H    84_A     0.801     0    0.484   0.513     2.736   79.881   78.238
LGA    A    85_A      A    85_A     2.991     0    0.643   0.617     5.463   71.310   62.286
LGA    N    86_A      N    86_A     2.273     3    0.645   0.622     5.286   50.238   31.369
LGA    L    87_A      L    87_A     8.180     0    0.594   0.614    11.818   10.238    5.298
LGA    K    88_A      K    88_A     8.934     0    0.280   1.008    11.948    1.429    3.122

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       62     248    248  100.00     520    520  100.00               104
SUMMARY(RMSD_GDC):     9.332          9.200                 10.289           23.016   19.087

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62  104    4.0     31    1.90    28.606    26.668     1.552

LGA_LOCAL      RMSD:   1.897  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.043  Number of assigned atoms:   62 
Std_ASGN_ATOMS RMSD:   9.332  Standard rmsd on all 62 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.993723 * X  +   0.086040 * Y  +   0.071497 * Z  + -443.360657
  Y_new =   0.078729 * X  +  -0.991923 * Y  +   0.099455 * Z  + 316.731384
  Z_new =   0.079477 * X  +  -0.093202 * Y  +  -0.992470 * Z  + 325.394440 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.079061 -0.079561 -3.047959   [DEG:    4.5298   -4.5585 -174.6352 ]
ZXZ:  2.518298  3.018797  2.435508   [DEG:  144.2879  172.9643  139.5443 ]
 
# END of job
