
#######################################################
#                                                     #
#                        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   83 (  684),  selected   72 , name one
# Molecule2: number of CA atoms   72 (  603),  selected   72 , 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:    46      33_A - 78_A        4.89    29.31
  LCS_AVERAGE:     53.03

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34      38_A - 71_A        1.96    30.07
  LCS_AVERAGE:     38.50

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      33_A - 55_A        0.95    29.56
  LCS_AVERAGE:     25.66

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   72
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     T     2_A     T     2_A     17   23   24      5   13   16   18   21   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     S     3_A     S     3_A     17   23   24      7   13   16   18   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L     4_A     L     4_A     17   23   24      9   13   16   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     I     5_A     I     5_A     17   23   24      9   13   16   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E     6_A     E     6_A     17   23   24      9   13   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E     7_A     E     7_A     17   23   24      9   13   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L     8_A     L     8_A     17   23   24      9   13   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     I     9_A     I     9_A     17   23   24      9   13   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    10_A     R    10_A     17   23   24      9   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    11_A     R    11_A     17   23   24      9   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     S    12_A     S    12_A     17   23   24      9   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    13_A     E    13_A     17   23   24      6   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    14_A     E    14_A     17   23   24      6   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Q    15_A     Q    15_A     17   23   24      6   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Q    16_A     Q    16_A     17   23   24      6   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    17_A     R    17_A     17   23   24      5   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    18_A     R    18_A     17   23   24      5   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     N    19_A     N    19_A     17   23   24      6   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    20_A     E    20_A     17   23   24      6   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    21_A     E    21_A     17   23   24      6   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   30 
LCS_GDT     A    22_A     A    22_A     17   23   24      6   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   24   33   40   45 
LCS_GDT     L    23_A     L    23_A     17   23   29      6   14   17   21   22   23   23   23   23   23   23   23   23   23   23   23   25   31   41   45 
LCS_GDT     R    24_A     R    24_A     17   23   44      6   14   17   21   22   23   23   23   23   23   23   23   23   23   30   37   40   42   46   46 
LCS_GDT     Q    33_A     Q    33_A     23   33   46     11   16   21   23   26   29   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     L    34_A     L    34_A     23   33   46     12   18   22   24   27   29   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     L    35_A     L    35_A     23   33   46     12   18   22   26   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     S    36_A     S    36_A     23   33   46     12   18   22   26   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     G    37_A     G    37_A     23   33   46     12   18   22   26   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     I    38_A     I    38_A     23   34   46     12   18   22   26   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     V    39_A     V    39_A     23   34   46     12   18   22   26   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     Q    40_A     Q    40_A     23   34   46     11   18   22   26   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     Q    41_A     Q    41_A     23   34   46     11   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     Q    42_A     Q    42_A     23   34   46     12   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     N    43_A     N    43_A     23   34   46     12   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     N    44_A     N    44_A     23   34   46     12   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     L    45_A     L    45_A     23   34   46     12   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     L    46_A     L    46_A     23   34   46     12   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     R    47_A     R    47_A     23   34   46     12   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     A    48_A     A    48_A     23   34   46     10   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     I    49_A     I    49_A     23   34   46     10   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     E    50_A     E    50_A     23   34   46     10   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     A    51_A     A    51_A     23   34   46     10   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     Q    52_A     Q    52_A     23   34   46     10   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     Q    53_A     Q    53_A     23   34   46     10   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     H    54_A     H    54_A     23   34   46     10   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     L    55_A     L    55_A     23   34   46     10   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     L    56_A     L    56_A     22   34   46      9   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     Q    57_A     Q    57_A     22   34   46      9   18   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     L    58_A     L    58_A     22   34   46      8   16   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     T    59_A     T    59_A     22   34   46      8   16   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     V    60_A     V    60_A     22   34   46      8   16   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     W    61_A     W    61_A     22   34   46      8   16   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     G    62_A     G    62_A     22   34   46      7   16   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     I    63_A     I    63_A     22   34   46      7   16   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     K    64_A     K    64_A     22   34   46      7   16   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     Q    65_A     Q    65_A     22   34   46      7   16   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     L    66_A     L    66_A     22   34   46      7   15   21   25   29   31   35   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     Q    67_A     Q    67_A     22   34   46      8   16   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     A    68_A     A    68_A     22   34   46      4   13   22   25   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     R    69_A     R    69_A     19   34   46      4    7   14   21   25   30   33   34   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     I    70_A     I    70_A     14   34   46      4    7   14   20   24   29   32   34   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     L    71_A     L    71_A      7   34   46      3    6   22   27   30   33   36   36   37   39   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     A    72_A     A    72_A      9   29   46      3    6    9   12   12   12   21   31   33   38   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     V    73_A     V    73_A      9   13   46      3    8    9   12   12   12   14   20   26   31   36   40   41   42   43   43   43   43   46   46 
LCS_GDT     E    74_A     E    74_A      9   13   46      3    8    9   12   16   24   30   34   37   38   40   41   41   42   43   43   43   43   46   46 
LCS_GDT     R    75_A     R    75_A      9   13   46      5    8    9   12   12   12   12   15   15   17   20   27   38   42   43   43   43   43   46   46 
LCS_GDT     Y    76_A     Y    76_A      9   13   46      3    8    9   12   12   12   12   13   15   15   16   17   18   22   30   36   40   42   46   46 
LCS_GDT     L    77_A     L    77_A      9   13   46      5    8    9   12   12   12   12   13   15   15   16   17   18   23   33   38   40   42   46   46 
LCS_GDT     R    78_A     R    78_A      9   13   46      5    8    9   12   12   12   12   13   15   15   16   17   18   21   25   30   33   37   40   44 
LCS_GDT     D    79_A     D    79_A      9   13   19      5    8    9   12   12   12   12   13   15   15   16   16   16   18   18   19   19   21   22   22 
LCS_GDT     Q    80_A     Q    80_A      9   13   19      5    8    9   12   12   12   12   13   13   15   16   16   16   16   16   19   19   19   20   20 
LCS_GDT     Q    81_A     Q    81_A      3   13   18      0    3    3    7    9    9   10   13   13   13   13   14   14   16   16   17   17   17   17   19 
LCS_AVERAGE  LCS_A:  39.06  (  25.66   38.50   53.03 )

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     12     18     22     27     30     33     36     36     37     39     40     41     41     42     43     43     43     43     46     46 
GDT PERCENT_AT  16.67  25.00  30.56  37.50  41.67  45.83  50.00  50.00  51.39  54.17  55.56  56.94  56.94  58.33  59.72  59.72  59.72  59.72  63.89  63.89
GDT RMS_LOCAL    0.30   0.61   0.89   1.32   1.51   1.85   2.14   2.11   2.23   2.49   2.71   2.87   2.87   3.15   3.41   3.41   3.41   3.41   5.42   5.42
GDT RMS_ALL_AT  30.01  29.75  29.56  30.16  30.04  29.67  29.46  29.55  29.43  29.48  29.63  29.56  29.56  29.61  29.48  29.48  29.48  29.48  28.82  28.82

# Checking swapping
#   possible swapping detected:  E     6_A      E     6_A
#   possible swapping detected:  E     7_A      E     7_A
#   possible swapping detected:  E    14_A      E    14_A
#   possible swapping detected:  E    21_A      E    21_A
#   possible swapping detected:  Y    76_A      Y    76_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T     2_A      T     2_A    77.515     0    0.095   1.159    77.925    0.000    0.000
LGA    S     3_A      S     3_A    73.102     0    0.104   0.673    75.106    0.000    0.000
LGA    L     4_A      L     4_A    68.547     0    0.031   1.082    70.758    0.000    0.000
LGA    I     5_A      I     5_A    68.570     0    0.026   0.171    74.647    0.000    0.000
LGA    E     6_A      E     6_A    67.150     0    0.053   0.798    72.413    0.000    0.000
LGA    E     7_A      E     7_A    61.747     0    0.033   1.140    64.184    0.000    0.000
LGA    L     8_A      L     8_A    58.861     0    0.058   0.128    62.356    0.000    0.000
LGA    I     9_A      I     9_A    59.201     0    0.040   0.970    64.026    0.000    0.000
LGA    R    10_A      R    10_A    56.222     0    0.048   2.219    60.357    0.000    0.000
LGA    R    11_A      R    11_A    50.856     0    0.032   1.427    53.337    0.000    0.000
LGA    S    12_A      S    12_A    49.763     0    0.104   0.693    51.745    0.000    0.000
LGA    E    13_A      E    13_A    48.971     0    0.026   1.047    53.436    0.000    0.000
LGA    E    14_A      E    14_A    45.138     0    0.057   1.132    47.862    0.000    0.000
LGA    Q    15_A      Q    15_A    40.631     0    0.084   0.913    42.737    0.000    0.000
LGA    Q    16_A      Q    16_A    40.235     0    0.033   1.308    43.589    0.000    0.000
LGA    R    17_A      R    17_A    38.714     0    0.044   0.917    47.516    0.000    0.000
LGA    R    18_A      R    18_A    34.867     0    0.043   1.087    36.957    0.000    0.000
LGA    N    19_A      N    19_A    31.344     0    0.033   1.032    33.039    0.000    0.000
LGA    E    20_A      E    20_A    31.338     0    0.036   1.220    36.319    0.000    0.000
LGA    E    21_A      E    21_A    29.847     0    0.029   1.192    35.010    0.000    0.000
LGA    A    22_A      A    22_A    25.140     0    0.042   0.046    27.137    0.000    0.000
LGA    L    23_A      L    23_A    23.909     0    0.122   1.183    26.377    0.000    0.000
LGA    R    24_A      R    24_A    23.461     0    0.222   0.629    33.179    0.000    0.000
LGA    Q    33_A      Q    33_A     5.108     0    0.075   1.062     6.617   30.238   23.545
LGA    L    34_A      L    34_A     4.186     0    0.042   1.170     8.056   40.476   30.119
LGA    L    35_A      L    35_A     3.281     0    0.041   0.564     5.321   53.810   47.381
LGA    S    36_A      S    36_A     2.989     0    0.026   0.696     4.691   57.262   51.746
LGA    G    37_A      G    37_A     2.483     0    0.038   0.038     2.742   64.881   64.881
LGA    I    38_A      I    38_A     1.715     0    0.013   0.181     3.606   77.381   67.560
LGA    V    39_A      V    39_A     0.943     0    0.043   0.151     1.905   88.214   81.633
LGA    Q    40_A      Q    40_A     0.652     0    0.019   0.287     0.799   95.238   94.709
LGA    Q    41_A      Q    41_A     0.452     0    0.045   0.244     1.788   97.619   88.677
LGA    Q    42_A      Q    42_A     0.607     0    0.072   0.332     1.404   90.595   89.577
LGA    N    43_A      N    43_A     1.062     0    0.033   0.435     2.542   83.690   79.583
LGA    N    44_A      N    44_A     0.705     0    0.011   1.018     3.355   85.952   76.786
LGA    L    45_A      L    45_A     1.717     0    0.035   0.116     2.239   72.976   73.988
LGA    L    46_A      L    46_A     2.047     0    0.050   0.976     4.205   66.786   63.333
LGA    R    47_A      R    47_A     2.084     0    0.038   0.561     4.166   64.762   58.268
LGA    A    48_A      A    48_A     2.109     0    0.037   0.055     2.315   64.762   64.762
LGA    I    49_A      I    49_A     2.283     0    0.028   0.160     2.665   64.762   64.821
LGA    E    50_A      E    50_A     2.334     0    0.059   0.174     2.643   62.857   63.915
LGA    A    51_A      A    51_A     2.328     0    0.018   0.032     2.449   64.762   64.762
LGA    Q    52_A      Q    52_A     2.284     0    0.044   0.935     4.528   64.762   57.037
LGA    Q    53_A      Q    53_A     2.651     0    0.000   0.120     2.973   59.048   57.989
LGA    H    54_A      H    54_A     2.274     0    0.065   1.235     7.379   66.786   45.143
LGA    L    55_A      L    55_A     1.891     0    0.059   1.375     4.559   72.976   66.786
LGA    L    56_A      L    56_A     1.749     0    0.046   1.245     4.021   75.000   66.429
LGA    Q    57_A      Q    57_A     1.447     0    0.028   1.370     4.890   81.548   63.757
LGA    L    58_A      L    58_A     1.054     0    0.072   0.153     2.487   88.333   78.631
LGA    T    59_A      T    59_A     0.656     0    0.046   1.161     3.555   90.476   77.687
LGA    V    60_A      V    60_A     0.848     0    0.027   0.127     1.487   95.238   89.320
LGA    W    61_A      W    61_A     0.767     0    0.066   1.237     6.272   90.595   62.245
LGA    G    62_A      G    62_A     1.538     0    0.067   0.067     2.386   75.238   75.238
LGA    I    63_A      I    63_A     1.921     0    0.044   1.005     4.332   72.976   62.738
LGA    K    64_A      K    64_A     0.985     0    0.069   1.246     8.182   79.405   57.460
LGA    Q    65_A      Q    65_A     2.785     0    0.041   0.993     5.595   53.810   49.418
LGA    L    66_A      L    66_A     4.044     0    0.048   0.835     5.110   41.905   36.726
LGA    Q    67_A      Q    67_A     2.635     0    0.068   0.156     3.275   57.143   59.841
LGA    A    68_A      A    68_A     3.124     0    0.054   0.063     4.795   45.833   46.667
LGA    R    69_A      R    69_A     5.645     0    0.183   0.802     8.758   23.333   13.896
LGA    I    70_A      I    70_A     5.741     0    0.092   0.114     9.037   27.738   19.286
LGA    L    71_A      L    71_A     1.439     0    0.067   0.095     7.203   57.262   44.226
LGA    A    72_A      A    72_A     7.374     0    0.050   0.094    10.761   11.071    9.810
LGA    V    73_A      V    73_A    10.857     0    0.084   0.158    13.980    0.714    0.408
LGA    E    74_A      E    74_A     8.174     0    0.093   0.972    10.600    3.095   21.111
LGA    R    75_A      R    75_A    10.315     0    0.045   1.346    14.817    0.714    0.260
LGA    Y    76_A      Y    76_A    16.316     0    0.093   1.483    24.409    0.000    0.000
LGA    L    77_A      L    77_A    18.665     0    0.071   0.155    21.110    0.000    0.000
LGA    R    78_A      R    78_A    17.268     0    0.049   1.348    21.266    0.000    0.000
LGA    D    79_A      D    79_A    21.665     0    0.283   0.301    25.741    0.000    0.000
LGA    Q    80_A      Q    80_A    26.284     0    0.724   1.263    29.341    0.000    0.000
LGA    Q    81_A      Q    81_A    30.229     0    0.420   1.087    32.666    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       72     288    288  100.00     603    603  100.00                72
SUMMARY(RMSD_GDC):    22.130         21.672                 22.657           36.973   33.502

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     36    2.11    43.056    43.824     1.627

LGA_LOCAL      RMSD:   2.113  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  29.552  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  22.130  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.617502 * X  +  -0.784993 * Y  +  -0.049779 * Z  +  33.050941
  Y_new =  -0.762769 * X  +   0.613067 * Y  +  -0.205750 * Z  +  56.949463
  Z_new =   0.192030 * X  +  -0.089082 * Y  +  -0.977338 * Z  + 280.183990 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.251335 -0.193230 -3.050697   [DEG: -128.9920  -11.0713 -174.7920 ]
ZXZ: -0.237375  2.928293  2.005145   [DEG:  -13.6006  167.7788  114.8863 ]
 
# END of job
