
#######################################################
#                                                     #
#                        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   71 (  606),  selected   71 , name one
# Molecule2: number of CA atoms  104 (  843),  selected   71 , 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:    32      58_A - 89_A        4.77    12.97
  LONGEST_CONTINUOUS_SEGMENT:    32      59_A - 90_A        4.78    12.77
  LCS_AVERAGE:     25.27

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      60_A - 84_A        1.75    16.34
  LONGEST_CONTINUOUS_SEGMENT:    25      61_A - 85_A        1.52    16.58
  LCS_AVERAGE:     12.74

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      61_A - 84_A        0.97    16.76
  LCS_AVERAGE:     10.64

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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     N    21_A     N    21_A      6    6    9      4    5    6    6    6    6    6    7    7    8    8    9    9   10   10   10   15   16   17   20 
LCS_GDT     K    22_A     K    22_A      6    6    9      4    5    6    6    6    6    6    7    7    8    8    9   14   16   16   17   19   23   26   28 
LCS_GDT     V    23_A     V    23_A      6    6    9      4    4    6    6    6    6    6    7    7   10   12   13   16   16   16   22   22   26   28   29 
LCS_GDT     H    24_A     H    24_A      6    6   16      4    5    6    6    6    6    8   10   14   16   18   20   23   23   25   26   28   31   31   35 
LCS_GDT     N    25_A     N    25_A      6    6   16      3    5    6    6    6    6    6    7    7   10   15   19   21   22   22   23   27   31   34   41 
LCS_GDT     I    26_A     I    26_A      6    6   16      3    5    6    6    8    9   11   13   17   19   20   21   25   30   34   36   41   44   48   51 
LCS_GDT     K    27_A     K    27_A      4    5   23      3    4    4    5    8    9   11   13   17   19   20   22   23   25   31   36   40   44   47   51 
LCS_GDT     C    28_A     C    28_A      4    5   23      3    4    4    5    8    9   11   13   17   19   20   22   23   25   27   30   35   41   45   48 
LCS_GDT     H    29_A     H    29_A      4    9   23      3    4    5    7    8    9   11   13   17   19   20   22   23   25   27   30   31   32   32   33 
LCS_GDT     F    30_A     F    30_A      3    9   23      3    3    4    6    8    9   12   14   17   19   20   22   23   25   27   30   31   32   32   33 
LCS_GDT     D    31_A     D    31_A      3    9   23      3    3    5    7    8    9   11   12   13   13   15   19   21   22   24   25   28   30   31   31 
LCS_GDT     N    32_A     N    32_A      4    9   23      3    3    5    7    8    9   11   13   13   19   20   21   23   25   26   29   31   32   32   33 
LCS_GDT     C    33_A     C    33_A      4    9   23      3    3    5    7    8    9   11   14   17   19   20   22   23   25   27   30   31   32   32   33 
LCS_GDT     N    34_A     N    34_A      4    9   23      3    4    4    6    8   10   12   14   17   19   20   22   23   25   27   30   31   32   32   33 
LCS_GDT     R    35_A     R    35_A      4    9   23      3    4    5    7    8    9   11   14   16   19   20   22   23   25   32   36   41   44   48   51 
LCS_GDT     K    36_A     K    36_A      4    9   23      3    4    4    7    8   10   12   14   17   19   20   22   23   29   35   38   41   44   48   51 
LCS_GDT     I    37_A     I    37_A      4    9   23      3    4    4    7    8   10   18   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     H    38_A     H    38_A      3    6   23      3    3    4    4    8   15   20   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     W    39_A     W    39_A      3    6   23      3    3    4    4    7    8   17   22   28   31   33   34   37   38   39   39   41   43   48   51 
LCS_GDT     K    40_A     K    40_A      3    4   23      0    3    4    4    4    9   11   12   13   14   16   19   37   38   39   39   41   43   48   51 
LCS_GDT     I    41_A     I    41_A      3    5   23      1    3    4    4    7    9   11   12   13   14   33   34   37   38   39   39   41   43   48   51 
LCS_GDT     R    42_A     R    42_A      3    5   23      3    3    4    4   10   20   21   25   28   31   33   34   37   38   39   39   41   43   48   51 
LCS_GDT     Y    43_A     Y    43_A      4    7   23      3    3    6    7    8   10   15   22   26   29   33   34   37   38   39   39   41   43   48   51 
LCS_GDT     G    44_A     G    44_A      6    7   23      3    3    5    7   10   12   16   22   26   28   31   33   37   38   39   39   41   44   48   51 
LCS_GDT     K    45_A     K    45_A      6    7   23      5    5    6    7    8   10   12   20   23   26   31   32   32   36   39   39   41   44   48   51 
LCS_GDT     L    46_A     L    46_A      6    7   23      5    5    6    7    8   10   12   14   17   19   20   22   24   28   34   36   41   44   48   51 
LCS_GDT     R    47_A     R    47_A      6    7   23      5    5    6    7    8   10   12   14   17   19   20   23   25   28   32   35   41   44   48   51 
LCS_GDT     L    48_A     L    48_A      6    7   23      5    5    6    7    8   10   12   14   17   19   20   23   26   30   34   36   41   44   48   51 
LCS_GDT     V    49_A     V    49_A      6    7   23      5    5    6    7    8   10   12   14   17   19   20   23   25   28   31   36   41   44   47   51 
LCS_GDT     D    50_A     D    50_A      4    7   23      3    4    4    5    7    9   11   13   16   18   21   23   24   27   31   34   38   41   45   48 
LCS_GDT     H    51_A     H    51_A      4    5   23      3    4    4    4    6    7   11   12   16   17   21   22   23   26   28   33   34   38   44   48 
LCS_GDT     A    52_A     A    52_A      4    5   23      3    4    4    5    7    9   12   14   17   19   21   23   23   28   31   36   41   44   46   51 
LCS_GDT     L    53_A     L    53_A      5    5   23      4    4    4    5    6    7   10   13   16   17   21   23   25   28   32   36   41   44   47   51 
LCS_GDT     S    54_A     S    54_A      5    5   23      4    4    4    5    5    6    8   11   13   17   21   23   23   27   31   36   41   43   45   48 
LCS_GDT     H    55_A     H    55_A      5    5   23      4    4    4    5    5    6    9   11   12   15   16   19   22   25   30   34   40   42   45   47 
LCS_GDT     Q    56_A     Q    56_A      5    5   23      4    4    4    5    6    7   10   12   16   17   20   22   23   27   31   36   41   43   45   49 
LCS_GDT     E    57_A     E    57_A      5    5   31      3    4    4    5    5    6    9   11   13   17   21   23   23   28   31   36   41   43   46   51 
LCS_GDT     E    58_A     E    58_A      5    6   32      4    4    5    5    7   10   11   14   17   21   26   28   31   33   34   37   41   44   48   51 
LCS_GDT     K    59_A     K    59_A      5    6   32      4    4    5    7   10   12   16   22   24   27   31   33   37   38   39   39   41   44   48   51 
LCS_GDT     S    60_A     S    60_A      5   25   32      4    4    5    5    9   12   17   23   26   29   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     I    61_A     I    61_A     24   25   32      7   18   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     D    62_A     D    62_A     24   25   32      7   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     C    63_A     C    63_A     24   25   32      7   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     Q    64_A     Q    64_A     24   25   32      7   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     K    65_A     K    65_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     C    66_A     C    66_A     24   25   32      7   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     E    67_A     E    67_A     24   25   32      3    7   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     Y    68_A     Y    68_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     S    69_A     S    69_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     C    70_A     C    70_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     Q    71_A     Q    71_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   43   48   51 
LCS_GDT     T    72_A     T    72_A     24   25   32      5   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   42   48   48 
LCS_GDT     T    73_A     T    73_A     24   25   32      5    7   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   43   48   48 
LCS_GDT     R    74_A     R    74_A     24   25   32      9   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   43   48   51 
LCS_GDT     Q    75_A     Q    75_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     M    76_A     M    76_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     R    77_A     R    77_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     Y    78_A     Y    78_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     H    79_A     H    79_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     Y    80_A     Y    80_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     K    81_A     K    81_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     K    82_A     K    82_A     24   25   32     11   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     I    83_A     I    83_A     24   25   32     10   20   22   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     H    84_A     H    84_A     24   25   32      3    4    7   23   24   24   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     A    85_A     A    85_A      3   25   32      3    3    4    5   11   21   25   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     N    86_A     N    86_A      4   15   32      3    4    4    5   11   14   17   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     L    87_A     L    87_A      4    4   32      3    4    4    4    5    6   18   25   28   31   33   34   37   38   39   39   41   44   48   51 
LCS_GDT     K    88_A     K    88_A      4    4   32      3    4    4    4    5    6    8   14   19   22   25   28   32   38   39   39   41   44   48   51 
LCS_GDT     M    89_A     M    89_A      4    4   32      3    4    4    4    4    5    7    8    9   15   17   19   22   26   31   33   38   44   48   51 
LCS_GDT     E    90_A     E    90_A      3    4   32      3    3    4    4    4    5    7    8    9   14   17   19   23   27   31   36   40   44   48   51 
LCS_GDT     G    91_A     G    91_A      3    4   14      0    3    4    5    5    5    7    9   10   16   21   21   23   26   31   34   38   44   46   51 
LCS_AVERAGE  LCS_A:  16.22  (  10.64   12.74   25.27 )

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     20     22     23     24     24     25     25     28     31     33     34     37     38     39     39     41     44     48     51 
GDT PERCENT_AT  10.58  19.23  21.15  22.12  23.08  23.08  24.04  24.04  26.92  29.81  31.73  32.69  35.58  36.54  37.50  37.50  39.42  42.31  46.15  49.04
GDT RMS_LOCAL    0.34   0.62   0.71   0.80   0.97   0.97   1.52   1.52   2.78   3.32   3.53   3.64   4.11   4.25   4.45   4.45   4.88   6.57   6.23   7.03
GDT RMS_ALL_AT  16.57  16.84  16.89  16.96  16.76  16.76  16.58  16.58  14.57  13.36  13.06  13.03  12.62  12.59  12.36  12.36  12.14  10.88  11.30  10.80

# Checking swapping
#   possible swapping detected:  Y    80_A      Y    80_A
#   possible swapping detected:  E    90_A      E    90_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    N    21_A      N    21_A    20.220     0    0.431   0.546    22.553    0.000    0.000
LGA    K    22_A      K    22_A    22.084     0    0.054   0.338    28.191    0.000    0.000
LGA    V    23_A      V    23_A    20.550     0    0.051   0.187    23.275    0.000    0.000
LGA    H    24_A      H    24_A    20.330     0    0.135   0.317    21.533    0.000    0.000
LGA    N    25_A      N    25_A    25.265     0    0.625   0.517    29.913    0.000    0.000
LGA    I    26_A      I    26_A    23.936     0    0.474   1.283    24.008    0.000    0.000
LGA    K    27_A      K    27_A    24.683     0    0.101   0.859    26.065    0.000    0.000
LGA    C    28_A      C    28_A    25.993     0    0.467   0.913    27.477    0.000    0.000
LGA    H    29_A      H    29_A    26.444     0    0.263   0.623    27.347    0.000    0.000
LGA    F    30_A      F    30_A    27.203     0    0.672   1.136    30.194    0.000    0.000
LGA    D    31_A      D    31_A    33.122     0    0.534   1.417    38.416    0.000    0.000
LGA    N    32_A      N    32_A    30.755     0    0.120   0.960    33.537    0.000    0.000
LGA    C    33_A      C    33_A    25.835     0    0.476   0.815    27.561    0.000    0.000
LGA    N    34_A      N    34_A    23.047     0    0.326   0.366    26.833    0.000    0.000
LGA    R    35_A      R    35_A    18.350     0    0.316   1.470    20.305    0.000    0.000
LGA    K    36_A      K    36_A    16.946     0    0.464   1.216    21.664    0.000    0.000
LGA    I    37_A      I    37_A    12.903     0    0.181   1.388    15.137    0.000    0.357
LGA    H    38_A      H    38_A    13.682     0    0.558   1.358    20.137    0.000    0.000
LGA    W    39_A      W    39_A    13.529     0    0.629   1.611    20.611    0.000    0.000
LGA    K    40_A      K    40_A    13.883     0    0.671   0.981    15.784    0.000    0.000
LGA    I    41_A      I    41_A    12.839     0    0.606   0.568    13.181    0.000    0.000
LGA    R    42_A      R    42_A    11.861     0    0.637   1.558    12.924    0.119    0.043
LGA    Y    43_A      Y    43_A    13.693     0    0.150   1.672    21.407    0.000    0.000
LGA    G    44_A      G    44_A    16.646     0    0.135   0.135    17.767    0.000    0.000
LGA    K    45_A      K    45_A    18.873     0    0.215   0.676    20.585    0.000    0.000
LGA    L    46_A      L    46_A    21.064     0    0.144   1.362    23.425    0.000    0.000
LGA    R    47_A      R    47_A    22.056     0    0.055   1.403    23.443    0.000    0.000
LGA    L    48_A      L    48_A    22.407     0    0.061   1.018    24.616    0.000    0.000
LGA    V    49_A      V    49_A    23.695     0    0.583   0.812    23.695    0.000    0.000
LGA    D    50_A      D    50_A    24.101     0    0.240   0.369    25.704    0.000    0.000
LGA    H    51_A      H    51_A    25.508     0    0.104   0.317    27.717    0.000    0.000
LGA    A    52_A      A    52_A    24.260     0    0.597   0.582    26.244    0.000    0.000
LGA    L    53_A      L    53_A    22.337     0    0.690   0.623    23.415    0.000    0.000
LGA    S    54_A      S    54_A    22.831     0    0.116   0.248    26.013    0.000    0.000
LGA    H    55_A      H    55_A    25.286     0    0.088   0.155    31.617    0.000    0.000
LGA    Q    56_A      Q    56_A    22.314     0    0.664   1.049    23.351    0.000    0.000
LGA    E    57_A      E    57_A    21.263     4    0.047   0.051    23.569    0.000    0.000
LGA    E    58_A      E    58_A    16.217     4    0.041   0.042    18.212    0.000    0.000
LGA    K    59_A      K    59_A    10.380     0    0.202   0.519    17.412    1.905    0.847
LGA    S    60_A      S    60_A     7.953     0    0.207   0.309     8.915   12.619   10.556
LGA    I    61_A      I    61_A     1.330     0    0.645   1.197     4.027   71.905   64.167
LGA    D    62_A      D    62_A     0.804     0    0.073   0.159     1.454   88.214   84.821
LGA    C    63_A      C    63_A     1.057     0    0.088   0.173     1.675   81.548   81.508
LGA    Q    64_A      Q    64_A     1.359     0    0.137   1.148     6.411   85.952   65.238
LGA    K    65_A      K    65_A     0.473     0    0.085   1.079     7.744   92.976   60.582
LGA    C    66_A      C    66_A     0.983     0    0.642   0.989     2.808   82.143   79.048
LGA    E    67_A      E    67_A     1.745     4    0.071   0.093     2.368   79.405   42.487
LGA    Y    68_A      Y    68_A     0.222     0    0.069   0.238     1.163   92.976   92.937
LGA    S    69_A      S    69_A     0.312     0    0.108   0.534     1.874   97.619   93.889
LGA    C    70_A      C    70_A     0.308     0    0.101   0.766     2.332  100.000   92.540
LGA    Q    71_A      Q    71_A     0.687     0    0.042   1.125     5.667   90.476   66.243
LGA    T    72_A      T    72_A     0.998     0    0.069   0.929     2.909   88.214   81.837
LGA    T    73_A      T    73_A     1.404     0    0.006   1.154     2.440   81.429   75.442
LGA    R    74_A      R    74_A     0.801     0    0.000   1.939     9.840   90.595   52.727
LGA    Q    75_A      Q    75_A     0.531     0    0.008   0.803     2.969   92.857   83.016
LGA    M    76_A      M    76_A     0.607     0    0.046   1.244     4.858   92.857   75.417
LGA    R    77_A      R    77_A     0.667     0    0.043   1.269     8.163   90.476   57.835
LGA    Y    78_A      Y    78_A     0.641     0    0.012   1.222     9.278   90.476   52.619
LGA    H    79_A      H    79_A     0.471     0    0.064   0.144     1.230   97.619   91.524
LGA    Y    80_A      Y    80_A     0.182     0    0.091   0.817     5.032   92.976   71.032
LGA    K    81_A      K    81_A     0.774     0    0.039   0.896     3.847   88.214   77.566
LGA    K    82_A      K    82_A     1.138     0    0.000   0.224     2.721   83.690   76.878
LGA    I    83_A      I    83_A     1.194     0    0.638   0.570     2.543   77.619   80.655
LGA    H    84_A      H    84_A     2.732     0    0.369   1.045    10.350   52.619   26.667
LGA    A    85_A      A    85_A     5.569     0    0.628   0.583     7.285   25.476   23.048
LGA    N    86_A      N    86_A     8.155     3    0.588   0.569     9.290    8.095    4.226
LGA    L    87_A      L    87_A     7.903     0    0.109   1.172    11.189    3.690    8.690
LGA    K    88_A      K    88_A    12.100     0    0.657   1.137    13.500    0.000    0.000
LGA    M    89_A      M    89_A    15.154     0    0.650   1.063    20.314    0.000    0.000
LGA    E    90_A      E    90_A    18.194     0    0.679   1.212    19.285    0.000    0.000
LGA    G    91_A      G    91_A    19.736     0    0.575   0.575    20.197    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     591    591  100.00               104
SUMMARY(RMSD_GDC):    10.454         10.364                 11.141           20.527   17.062

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   71  104    4.0     25    1.52    25.721    23.037     1.546

LGA_LOCAL      RMSD:   1.517  Number of atoms:   25  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  16.585  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:  10.454  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.653957 * X  +  -0.627082 * Y  +  -0.423212 * Z  + 131.532776
  Y_new =   0.443748 * X  +   0.771020 * Y  +  -0.456746 * Z  + -208.776505
  Z_new =   0.612722 * X  +   0.110892 * Y  +   0.782480 * Z  + -268.361053 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.596190 -0.659500  0.140781   [DEG:   34.1592  -37.7866    8.0662 ]
ZXZ: -0.747309  0.672158  1.391751   [DEG:  -42.8176   38.5118   79.7415 ]
 
# END of job
