
#######################################################
#                                                     #
#                        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        4.62    28.91
  LCS_AVERAGE:     53.51

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31      35_A - 65_A        1.99    28.82
  LONGEST_CONTINUOUS_SEGMENT:    31      38_A - 68_A        1.99    29.32
  LCS_AVERAGE:     36.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      33_A - 55_A        0.99    29.04
  LCS_AVERAGE:     25.06

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      4    9   13   16   19   21   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     10   15   16   18   22   22   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      7   15   16   18   22   22   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     10   15   16   18   22   22   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     10   15   16   19   22   22   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     10   15   16   19   22   22   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     10   15   16   19   22   22   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     10   15   16   19   22   22   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     10   15   16   19   22   22   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     10   15   16   19   22   22   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     10   15   16   19   22   22   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     10   15   16   19   22   22   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      5   15   16   19   22   22   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      9   15   16   19   22   22   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      9   15   16   19   22   22   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      9   15   16   19   22   22   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      9   13   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     N    19_A     N    19_A     16   23   24      9   13   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    20_A     E    20_A     16   23   24      9   13   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    21_A     E    21_A     16   23   24      9   13   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   27 
LCS_GDT     A    22_A     A    22_A     16   23   24      9   13   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   27   38   42 
LCS_GDT     L    23_A     L    23_A     16   23   37      9   13   16   19   22   22   23   23   23   23   23   23   23   23   23   23   27   37   41   44 
LCS_GDT     R    24_A     R    24_A     16   23   44      5   13   16   19   22   22   23   23   23   23   23   23   23   24   28   32   38   42   43   45 
LCS_GDT     Q    33_A     Q    33_A     23   30   46      9   16   20   23   24   27   29   32   36   37   39   42   42   42   44   45   45   45   46   46 
LCS_GDT     L    34_A     L    34_A     23   30   46     12   18   20   23   24   27   29   35   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     L    35_A     L    35_A     23   31   46     12   18   21   25   27   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     S    36_A     S    36_A     23   31   46     12   18   21   25   27   31   34   36   37   39   41   42   42   42   44   45   45   45   46   46 
LCS_GDT     G    37_A     G    37_A     23   31   46     12   18   21   25   27   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     I    38_A     I    38_A     23   31   46     12   18   21   25   27   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     V    39_A     V    39_A     23   31   46     12   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     Q    40_A     Q    40_A     23   31   46     12   18   21   25   27   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     Q    41_A     Q    41_A     23   31   46     12   18   21   25   27   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     Q    42_A     Q    42_A     23   31   46     12   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     N    43_A     N    43_A     23   31   46     12   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     N    44_A     N    44_A     23   31   46     12   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     L    45_A     L    45_A     23   31   46     12   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     L    46_A     L    46_A     23   31   46      9   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     R    47_A     R    47_A     23   31   46      7   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     A    48_A     A    48_A     23   31   46     12   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     I    49_A     I    49_A     23   31   46      7   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     E    50_A     E    50_A     23   31   46     10   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     A    51_A     A    51_A     23   31   46     10   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     Q    52_A     Q    52_A     23   31   46     10   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     Q    53_A     Q    53_A     23   31   46     10   17   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     H    54_A     H    54_A     23   31   46     10   16   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     L    55_A     L    55_A     23   31   46      8   18   21   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     L    56_A     L    56_A     22   31   46     10   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     Q    57_A     Q    57_A     20   31   46     10   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     L    58_A     L    58_A     20   31   46     10   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     T    59_A     T    59_A     20   31   46     10   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     V    60_A     V    60_A     20   31   46     10   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     W    61_A     W    61_A     20   31   46      7   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     G    62_A     G    62_A     20   31   46      7   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     I    63_A     I    63_A     20   31   46      7   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     K    64_A     K    64_A     20   31   46      7   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     Q    65_A     Q    65_A     20   31   46      7   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     L    66_A     L    66_A     20   31   46      7   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     Q    67_A     Q    67_A     20   31   46      7   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     A    68_A     A    68_A     20   31   46      6   15   20   25   28   31   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     R    69_A     R    69_A     18   30   46      4    9   16   22   27   30   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     I    70_A     I    70_A     15   30   46      4    9   16   22   27   30   34   36   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     L    71_A     L    71_A     14   30   46      4    8   13   17   23   28   33   35   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     A    72_A     A    72_A     10   28   46      4    8   10   15   20   24   30   35   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     V    73_A     V    73_A     10   23   46      4    8   10   12   15   22   27   33   37   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     E    74_A     E    74_A     10   19   46      5    8   10   12   14   17   23   29   36   40   41   42   42   43   44   45   45   45   46   46 
LCS_GDT     R    75_A     R    75_A     10   16   46      5    8   10   12   14   15   18   22   26   32   38   40   42   43   44   45   45   45   46   46 
LCS_GDT     Y    76_A     Y    76_A      9   14   46      5    8   10   12   12   14   16   19   22   25   28   35   38   43   44   45   45   45   46   46 
LCS_GDT     L    77_A     L    77_A      9   14   46      5    8   10   12   12   13   16   17   19   23   28   33   40   43   44   45   45   45   46   46 
LCS_GDT     R    78_A     R    78_A      9   14   46      5    8    9   11   11   13   14   16   18   20   21   24   26   28   32   33   38   40   46   46 
LCS_GDT     D    79_A     D    79_A      3    4   36      3    3    3    4    5    7    8   12   12   14   14   15   16   17   18   19   19   21   22   25 
LCS_GDT     Q    80_A     Q    80_A      3    3   20      3    3    3    4    4    6    6    7    9   11   12   12   14   14   16   16   16   17   18   18 
LCS_GDT     Q    81_A     Q    81_A      3    3   17      3    3    3    4    4    6    8    9   10   11   12   13   14   15   16   16   16   17   18   18 
LCS_AVERAGE  LCS_A:  38.22  (  25.06   36.09   53.51 )

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     21     25     28     31     34     36     37     40     41     42     42     43     44     45     45     45     46     46 
GDT PERCENT_AT  16.67  25.00  29.17  34.72  38.89  43.06  47.22  50.00  51.39  55.56  56.94  58.33  58.33  59.72  61.11  62.50  62.50  62.50  63.89  63.89
GDT RMS_LOCAL    0.25   0.64   0.83   1.31   1.68   1.99   2.30   2.49   2.61   3.19   3.25   3.42   3.42   4.07   4.13   4.26   4.26   4.26   4.62   4.62
GDT RMS_ALL_AT  29.80  29.29  28.93  28.75  29.79  29.32  29.44  29.14  29.23  29.35  29.26  29.09  29.09  29.26  29.17  29.03  29.03  29.03  28.91  28.91

# Checking swapping
#   possible swapping detected:  E    13_A      E    13_A
#   possible swapping detected:  E    20_A      E    20_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    75.991     0    0.131   1.124    77.308    0.000    0.000
LGA    S     3_A      S     3_A    72.688     0    0.145   0.663    74.419    0.000    0.000
LGA    L     4_A      L     4_A    69.308     0    0.031   1.437    71.150    0.000    0.000
LGA    I     5_A      I     5_A    67.979     0    0.036   0.659    73.114    0.000    0.000
LGA    E     6_A      E     6_A    65.416     0    0.060   0.952    70.508    0.000    0.000
LGA    E     7_A      E     7_A    61.445     0    0.029   0.746    63.473    0.000    0.000
LGA    L     8_A      L     8_A    58.698     0    0.056   0.197    63.110    0.000    0.000
LGA    I     9_A      I     9_A    57.453     0    0.032   0.588    62.060    0.000    0.000
LGA    R    10_A      R    10_A    54.597     0    0.050   1.398    60.056    0.000    0.000
LGA    R    11_A      R    11_A    50.380     0    0.056   1.531    52.465    0.000    0.000
LGA    S    12_A      S    12_A    48.764     0    0.078   0.082    51.858    0.000    0.000
LGA    E    13_A      E    13_A    47.306     0    0.035   1.210    50.690    0.000    0.000
LGA    E    14_A      E    14_A    43.858     0    0.043   1.293    46.730    0.000    0.000
LGA    Q    15_A      Q    15_A    39.829     0    0.093   1.152    41.775    0.000    0.000
LGA    Q    16_A      Q    16_A    39.125     0    0.041   0.977    40.941    0.000    0.000
LGA    R    17_A      R    17_A    37.621     0    0.035   1.430    42.982    0.000    0.000
LGA    R    18_A      R    18_A    33.950     0    0.051   1.159    38.962    0.000    0.000
LGA    N    19_A      N    19_A    30.785     0    0.073   0.337    34.275    0.000    0.000
LGA    E    20_A      E    20_A    30.562     0    0.021   1.329    33.588    0.000    0.000
LGA    E    21_A      E    21_A    29.740     0    0.035   1.220    32.844    0.000    0.000
LGA    A    22_A      A    22_A    25.540     0    0.066   0.064    27.235    0.000    0.000
LGA    L    23_A      L    23_A    24.167     0    0.113   0.957    29.434    0.000    0.000
LGA    R    24_A      R    24_A    24.043     0    0.226   1.443    32.990    0.000    0.000
LGA    Q    33_A      Q    33_A     7.582     0    0.077   0.885    10.147   11.190    5.397
LGA    L    34_A      L    34_A     6.258     0    0.027   0.921    11.253   23.452   14.345
LGA    L    35_A      L    35_A     3.363     0    0.037   1.312     4.566   49.048   49.048
LGA    S    36_A      S    36_A     4.024     0    0.036   0.066     5.317   43.452   37.698
LGA    G    37_A      G    37_A     4.468     0    0.049   0.049     4.468   41.905   41.905
LGA    I    38_A      I    38_A     2.591     0    0.023   0.899     3.588   65.357   61.429
LGA    V    39_A      V    39_A     0.953     0    0.054   0.890     3.041   83.690   77.007
LGA    Q    40_A      Q    40_A     2.543     0    0.039   1.094     8.302   66.905   40.370
LGA    Q    41_A      Q    41_A     1.753     0    0.048   0.844     4.043   79.405   65.661
LGA    Q    42_A      Q    42_A     0.995     0    0.047   0.994     1.924   86.190   82.646
LGA    N    43_A      N    43_A     2.140     0    0.042   0.725     5.398   70.952   57.560
LGA    N    44_A      N    44_A     1.253     0    0.034   0.178     3.164   90.714   75.000
LGA    L    45_A      L    45_A     1.125     0    0.044   1.035     3.272   81.786   74.524
LGA    L    46_A      L    46_A     2.319     0    0.042   1.182     4.872   64.881   58.869
LGA    R    47_A      R    47_A     1.775     0    0.020   0.238     3.240   72.857   67.965
LGA    A    48_A      A    48_A     1.392     0    0.034   0.052     2.203   73.095   73.048
LGA    I    49_A      I    49_A     2.915     0    0.045   0.176     3.998   55.476   53.690
LGA    E    50_A      E    50_A     2.903     0    0.040   0.533     3.051   57.143   57.196
LGA    A    51_A      A    51_A     2.250     0    0.036   0.046     2.462   64.762   64.762
LGA    Q    52_A      Q    52_A     2.527     0    0.043   1.045     3.927   59.048   59.894
LGA    Q    53_A      Q    53_A     2.860     0    0.040   1.039     3.225   57.143   58.042
LGA    H    54_A      H    54_A     2.677     0    0.037   1.091     5.733   57.143   45.286
LGA    L    55_A      L    55_A     2.594     0    0.056   1.120     4.545   60.952   56.786
LGA    L    56_A      L    56_A     2.316     0    0.039   1.357     4.919   64.762   57.798
LGA    Q    57_A      Q    57_A     2.165     0    0.026   0.784     4.190   66.786   56.190
LGA    L    58_A      L    58_A     2.125     0    0.060   1.420     5.952   68.810   58.690
LGA    T    59_A      T    59_A     1.708     0    0.044   0.044     1.948   72.857   72.857
LGA    V    60_A      V    60_A     1.632     0    0.041   1.263     3.926   77.143   69.932
LGA    W    61_A      W    61_A     1.674     0    0.079   1.378     8.847   77.143   41.599
LGA    G    62_A      G    62_A     1.075     0    0.051   0.051     1.322   81.429   81.429
LGA    I    63_A      I    63_A     1.184     0    0.031   0.211     1.426   81.429   81.429
LGA    K    64_A      K    64_A     1.474     0    0.039   1.359     7.288   77.143   57.037
LGA    Q    65_A      Q    65_A     1.821     0    0.061   1.022     5.535   69.048   54.339
LGA    L    66_A      L    66_A     2.577     0    0.082   0.248     3.628   59.048   55.476
LGA    Q    67_A      Q    67_A     2.447     0    0.107   1.283     4.856   57.500   52.222
LGA    A    68_A      A    68_A     3.154     0    0.060   0.059     4.177   46.905   48.952
LGA    R    69_A      R    69_A     4.101     0    0.054   0.889     5.757   36.190   36.537
LGA    I    70_A      I    70_A     4.422     0    0.075   0.254     5.775   31.786   35.238
LGA    L    71_A      L    71_A     5.639     0    0.036   0.189     7.548   19.286   18.452
LGA    A    72_A      A    72_A     7.135     0    0.084   0.082     9.595    9.167   10.000
LGA    V    73_A      V    73_A     9.010     0    0.021   0.860    10.849    2.262    1.905
LGA    E    74_A      E    74_A     9.408     0    0.051   0.636    12.177    1.071    2.593
LGA    R    75_A      R    75_A    11.777     0    0.076   0.979    14.766    0.000    5.931
LGA    Y    76_A      Y    76_A    14.774     0    0.037   1.128    21.158    0.000    0.000
LGA    L    77_A      L    77_A    15.737     0    0.113   0.938    18.384    0.000    0.000
LGA    R    78_A      R    78_A    17.285     0    0.626   0.665    18.924    0.000    0.000
LGA    D    79_A      D    79_A    21.399     0    0.630   0.559    25.761    0.000    0.000
LGA    Q    80_A      Q    80_A    26.441     0    0.728   1.108    30.029    0.000    0.000
LGA    Q    81_A      Q    81_A    30.138     0    0.563   1.183    33.194    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):    22.414         21.927                 22.921           33.560   30.232

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     36    2.49    43.056    42.795     1.388

LGA_LOCAL      RMSD:   2.494  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  29.143  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  22.414  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.997045 * X  +   0.071731 * Y  +   0.027478 * Z  + -18.926769
  Y_new =  -0.075906 * X  +   0.974890 * Y  +   0.209349 * Z  +  14.831815
  Z_new =  -0.011771 * X  +  -0.210816 * Y  +   0.977455 * Z  +  51.768890 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.075985  0.011771 -0.212425   [DEG:   -4.3536    0.6744  -12.1711 ]
ZXZ:  3.011086  0.212746 -3.085816   [DEG:  172.5226   12.1894 -176.8042 ]
 
# END of job
