
#######################################################
#                                                     #
#                        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   69 (  597),  selected   69 , name one
# Molecule2: number of CA atoms  106 (  891),  selected   69 , 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:    29      31_A - 59_A        4.99    22.96
  LONGEST_CONTINUOUS_SEGMENT:    29      32_A - 60_A        4.93    22.40
  LONGEST_CONTINUOUS_SEGMENT:    29      58_A - 86_A        4.76    17.97
  LCS_AVERAGE:     24.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      39_A - 58_A        2.00    22.96
  LCS_AVERAGE:     12.78

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      40_A - 57_A        0.96    23.15
  LCS_AVERAGE:      9.91

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   69
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     R    18_A     R    18_A      3    9   13      0    3    3    3    3    5   10   10   11   11   12   13   16   17   22   25   27   28   28   29 
LCS_GDT     K    19_A     K    19_A      7    9   13      5    5    7    7    8    9   10   10   13   15   17   18   19   20   22   25   27   28   28   29 
LCS_GDT     A    20_A     A    20_A      7    9   13      5    6    7    7    8    9   10   10   13   15   17   18   19   20   22   25   27   28   28   29 
LCS_GDT     I    21_A     I    21_A      7    9   13      5    6    7    7    8    9   10   10   13   15   17   18   19   22   22   25   27   28   28   29 
LCS_GDT     N    22_A     N    22_A      7    9   13      5    6    7    7    8    9   10   10   13   15   23   23   24   25   26   28   28   29   29   30 
LCS_GDT     F    23_A     F    23_A      7    9   13      5    6    7   13   16   18   20   21   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     D    24_A     D    24_A      7    9   13      3    6    7    7   10   12   15   19   21   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     L    25_A     L    25_A      7    9   13      1    6    7    7    8    9   10   10   13   15   17   18   25   26   28   30   31   31   33   33 
LCS_GDT     S    26_A     S    26_A      4    9   13      3    3    4    6    8    9   10   10   13   15   17   18   19   20   22   25   27   31   33   33 
LCS_GDT     T    27_A     T    27_A      3    4   13      3    3    3    3    6    8    9   10   13   15   17   18   19   20   26   27   31   34   34   34 
LCS_GDT     K    28_A     K    28_A      3    4   13      3    3    3    3    4    4    8   15   17   18   23   25   27   29   32   33   34   34   35   35 
LCS_GDT     S    29_A     S    29_A      3    4   16      3    3    3    3    4    6    8   15   17   18   23   25   27   30   32   33   34   34   35   35 
LCS_GDT     L    30_A     L    30_A      3    4   18      3    3    4    4    4    6    8   16   19   23   25   26   29   30   32   33   34   34   35   35 
LCS_GDT     E    31_A     E    31_A      3    3   29      3    4    5    8    9   14   17   19   20   23   25   26   29   30   32   33   34   34   35   35 
LCS_GDT     K    32_A     K    32_A      3    5   29      3    3    4    8    9   14   17   19   20   23   25   26   29   30   32   33   34   34   35   35 
LCS_GDT     Y    33_A     Y    33_A      4    5   29      3    3    5    7   10   14   17   19   20   24   25   25   29   29   31   33   34   34   35   36 
LCS_GDT     F    34_A     F    34_A      4    5   29      3    3    5    6    9   13   21   22   23   24   25   25   26   26   28   30   31   32   34   36 
LCS_GDT     K    35_A     K    35_A      4    5   29      3    3    5    6    9   15   21   22   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     D    36_A     D    36_A      4    5   29      3    4    5   13   15   19   21   22   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     T    37_A     T    37_A      4    5   29      3    4    5    9   14   18   20   21   22   22   24   25   25   26   27   28   28   29   31   32 
LCS_GDT     R    38_A     R    38_A      4    5   29      3    4    5    5    7    7   11   13   16   17   19   23   26   26   27   28   29   30   31   33 
LCS_GDT     E    39_A     E    39_A      4   20   29      3    4    5    8   12   19   21   22   23   24   25   25   26   26   28   30   31   32   33   34 
LCS_GDT     P    40_A     P    40_A     18   20   29      8   14   17   17   18   18   20   21   22   24   24   25   26   26   28   30   31   32   33   36 
LCS_GDT     Y    41_A     Y    41_A     18   20   29      8   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   32   34   36 
LCS_GDT     S    42_A     S    42_A     18   20   29      9   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   32   33   36 
LCS_GDT     L    43_A     L    43_A     18   20   29      8   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   32   33   34 
LCS_GDT     I    44_A     I    44_A     18   20   29      9   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   32   33   36 
LCS_GDT     K    45_A     K    45_A     18   20   29      9   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   32   33   36 
LCS_GDT     K    46_A     K    46_A     18   20   29      9   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     F    47_A     F    47_A     18   20   29      9   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     M    48_A     M    48_A     18   20   29      9   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     L    49_A     L    49_A     18   20   29      9   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     E    50_A     E    50_A     18   20   29      9   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     N    51_A     N    51_A     18   20   29      9   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     G    52_A     G    52_A     18   20   29      4   13   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     F    53_A     F    53_A     18   20   29      4   13   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     E    54_A     E    54_A     18   20   29      9   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   31   33   33 
LCS_GDT     H    55_A     H    55_A     18   20   29      4   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   31   33   36 
LCS_GDT     R    56_A     R    56_A     18   20   29      9   14   17   17   18   19   21   22   23   24   25   25   26   26   28   30   31   32   33   36 
LCS_GDT     Q    57_A     Q    57_A     18   20   29      2    4    7   17   18   19   20   22   23   24   25   25   26   26   28   30   31   32   34   36 
LCS_GDT     Y    58_A     Y    58_A      4   20   29      0    3   10   13   16   16   21   22   23   24   25   25   26   28   30   31   32   33   35   36 
LCS_GDT     S    59_A     S    59_A      7    8   29      2    5    7    7   10   14   17   19   20   22   25   26   29   30   32   33   34   34   35   36 
LCS_GDT     G    60_A     G    60_A      7    8   29      3    5    7    8    9   14   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     Y    61_A     Y    61_A      7    8   29      3    5    7    7    8   10   16   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     T    62_A     T    62_A      7    8   29      3    5    7    8   10   14   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     S    63_A     S    63_A      7    8   29      3    5    7    8    9   14   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     K    64_A     K    64_A      7    8   29      3    5    7    7    8    9   14   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     E    65_A     E    65_A      7    8   29      3    3    7    7   10   14   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     P    66_A     P    66_A      3    8   29      3    3    5    6    8    9   12   15   18   21   24   27   29   30   32   33   34   34   35   36 
LCS_GDT     I    67_A     I    67_A      3    8   29      3    3    5    7   10   15   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     N    68_A     N    68_A      3   18   29      3    3    5   13   15   17   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     E    69_A     E    69_A     15   18   29      3    3    5   15   15   16   16   18   19   21   24   27   29   30   32   33   34   34   35   36 
LCS_GDT     R    70_A     R    70_A     15   18   29      8   13   13   15   15   17   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     R    71_A     R    71_A     15   18   29      5   13   13   15   15   17   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     V    72_A     V    72_A     15   18   29      6   13   13   15   15   17   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     I    73_A     I    73_A     15   18   29      8   13   13   15   15   17   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     R    74_A     R    74_A     15   18   29      8   13   13   15   15   17   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     I    75_A     I    75_A     15   18   29      8   13   13   15   15   17   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     I    76_A     I    76_A     15   18   29      8   13   13   15   15   17   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     N    77_A     N    77_A     15   18   29      8   13   13   15   15   17   17   18   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     K    78_A     K    78_A     15   18   29      8   13   13   15   15   17   17   18   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     L    79_A     L    79_A     15   18   29      8   13   13   15   15   17   17   19   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     T    80_A     T    80_A     15   18   29      8   13   13   15   15   17   17   18   20   22   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     K    81_A     K    81_A     15   18   29      8   13   13   15   15   17   17   18   19   20   24   27   27   30   31   33   34   34   35   36 
LCS_GDT     K    82_A     K    82_A     15   18   29      3    5   11   15   15   17   17   18   20   22   24   27   29   30   32   33   34   34   35   36 
LCS_GDT     F    83_A     F    83_A     15   18   29      3   13   13   15   15   17   17   18   20   23   25   27   29   30   32   33   34   34   35   36 
LCS_GDT     T    84_A     T    84_A      4   18   29      3    3    4    4    5   13   16   17   19   20   23   27   27   30   32   33   34   34   35   35 
LCS_GDT     W    85_A     W    85_A      4   18   29      3    3   10   14   15   17   17   18   19   22   24   27   27   30   32   33   34   34   35   35 
LCS_GDT     L    86_A     L    86_A      4    4   29      3    3    5   10   14   17   17   18   20   23   25   27   29   30   32   33   34   34   35   35 
LCS_AVERAGE  LCS_A:  15.77  (   9.91   12.78   24.62 )

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      9     14     17     17     18     19     21     22     23     24     25     27     29     30     32     33     34     34     35     36 
GDT PERCENT_AT   8.49  13.21  16.04  16.04  16.98  17.92  19.81  20.75  21.70  22.64  23.58  25.47  27.36  28.30  30.19  31.13  32.08  32.08  33.02  33.96
GDT RMS_LOCAL    0.23   0.55   0.77   0.77   0.96   1.72   2.56   2.58   2.68   2.79   3.72   4.11   4.20   4.49   4.74   4.86   5.01   5.01   5.22   6.82
GDT RMS_ALL_AT  23.07  23.09  23.15  23.15  23.15  23.45  23.17  23.27  23.47  23.43  17.49  19.01  17.40  18.08  18.16  18.20  18.04  18.04  17.77  16.12

# Checking swapping
#   possible swapping detected:  F    34_A      F    34_A
#   possible swapping detected:  D    36_A      D    36_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  F    53_A      F    53_A
#   possible swapping detected:  E    54_A      E    54_A
#   possible swapping detected:  Y    58_A      Y    58_A
#   possible swapping detected:  Y    61_A      Y    61_A
#   possible swapping detected:  F    83_A      F    83_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    R    18_A      R    18_A    26.572     0    0.200   1.312    28.773    0.000    0.000
LGA    K    19_A      K    19_A    25.263     0    0.612   1.394    33.009    0.000    0.000
LGA    A    20_A      A    20_A    20.201     0    0.071   0.099    21.924    0.000    0.000
LGA    I    21_A      I    21_A    12.756     0    0.016   1.122    15.546    0.000    0.060
LGA    N    22_A      N    22_A     9.605     0    0.053   0.164    15.390    8.810    4.405
LGA    F    23_A      F    23_A     4.861     0    0.211   0.840     8.751   16.190   15.584
LGA    D    24_A      D    24_A     7.361     0    0.259   1.056     9.678   10.952    8.452
LGA    L    25_A      L    25_A    12.973     0    0.656   0.887    16.346    0.000    0.000
LGA    S    26_A      S    26_A    17.515     0    0.618   0.845    20.176    0.000    0.000
LGA    T    27_A      T    27_A    19.122     0    0.206   1.063    20.827    0.000    0.000
LGA    K    28_A      K    28_A    21.668     0    0.393   1.035    25.353    0.000    0.000
LGA    S    29_A      S    29_A    17.084     0    0.603   0.768    18.117    0.000    0.000
LGA    L    30_A      L    30_A    13.719     0    0.607   1.368    14.812    0.000    0.000
LGA    E    31_A      E    31_A    13.762     0    0.617   1.035    15.251    0.000    0.000
LGA    K    32_A      K    32_A    12.357     0    0.618   1.107    18.014    0.000    0.000
LGA    Y    33_A      Y    33_A     7.790     0    0.639   1.213    12.223    8.333    4.762
LGA    F    34_A      F    34_A     4.735     0    0.155   1.241     6.679   34.524   30.823
LGA    K    35_A      K    35_A     4.230     0    0.614   0.976     5.718   34.762   39.683
LGA    D    36_A      D    36_A     1.692     0    0.408   1.288     4.509   63.095   56.071
LGA    T    37_A      T    37_A     6.959     0    0.111   0.958    10.329   12.381    8.231
LGA    R    38_A      R    38_A     9.200     0    0.100   1.217    20.410    5.119    1.861
LGA    E    39_A      E    39_A     3.539     0    0.126   1.002     5.618   39.167   37.143
LGA    P    40_A      P    40_A     4.786     0    0.571   0.635     8.247   35.714   24.422
LGA    Y    41_A      Y    41_A     2.959     0    0.075   1.215    12.130   59.524   30.437
LGA    S    42_A      S    42_A     2.704     0    0.035   0.638     3.448   57.143   54.762
LGA    L    43_A      L    43_A     3.171     0    0.047   1.416     6.263   55.476   49.821
LGA    I    44_A      I    44_A     2.571     0    0.028   0.558     4.212   65.000   55.060
LGA    K    45_A      K    45_A     0.911     0    0.016   0.096     3.519   88.214   74.709
LGA    K    46_A      K    46_A     1.500     0    0.028   0.579     4.025   81.429   65.026
LGA    F    47_A      F    47_A     1.476     0    0.015   0.191     3.446   81.429   65.411
LGA    M    48_A      M    48_A     1.265     0    0.018   1.111     4.640   81.429   71.250
LGA    L    49_A      L    49_A     0.911     0    0.081   1.277     3.100   88.214   77.917
LGA    E    50_A      E    50_A     0.873     0    0.088   0.144     2.406   85.952   78.783
LGA    N    51_A      N    51_A     1.833     0    0.196   0.498     3.185   72.857   65.179
LGA    G    52_A      G    52_A     1.517     0    0.139   0.139     1.952   75.000   75.000
LGA    F    53_A      F    53_A     1.112     0    0.036   0.265     3.050   83.690   71.905
LGA    E    54_A      E    54_A     1.844     0    0.027   0.862     3.110   68.810   69.524
LGA    H    55_A      H    55_A     2.380     0    0.047   1.159     4.900   64.762   57.952
LGA    R    56_A      R    56_A     2.261     0    0.446   1.192     6.235   61.071   53.550
LGA    Q    57_A      Q    57_A     2.683     0    0.550   1.184    11.241   55.952   29.894
LGA    Y    58_A      Y    58_A     4.591     0    0.512   0.927     6.222   33.690   33.135
LGA    S    59_A      S    59_A    10.409     0    0.237   0.721    13.547    1.190    0.794
LGA    G    60_A      G    60_A    15.053     0    0.170   0.170    16.448    0.000    0.000
LGA    Y    61_A      Y    61_A    20.533     0    0.071   1.256    23.321    0.000    0.000
LGA    T    62_A      T    62_A    24.364     0    0.073   1.178    26.599    0.000    0.000
LGA    S    63_A      S    63_A    31.319     0    0.098   0.782    33.626    0.000    0.000
LGA    K    64_A      K    64_A    33.778     0    0.583   1.158    36.862    0.000    0.000
LGA    E    65_A      E    65_A    40.963     0    0.724   1.418    43.743    0.000    0.000
LGA    P    66_A      P    66_A    44.339     0    0.676   0.584    46.777    0.000    0.000
LGA    I    67_A      I    67_A    45.199     0    0.077   0.959    47.191    0.000    0.000
LGA    N    68_A      N    68_A    51.095     0    0.488   0.875    56.531    0.000    0.000
LGA    E    69_A      E    69_A    51.559     0    0.312   0.519    53.755    0.000    0.000
LGA    R    70_A      R    70_A    50.016     0    0.337   1.473    55.229    0.000    0.000
LGA    R    71_A      R    71_A    46.486     0    0.069   1.358    52.242    0.000    0.000
LGA    V    72_A      V    72_A    41.814     0    0.020   0.152    43.997    0.000    0.000
LGA    I    73_A      I    73_A    40.583     0    0.120   1.239    43.154    0.000    0.000
LGA    R    74_A      R    74_A    39.963     0    0.033   1.179    45.197    0.000    0.000
LGA    I    75_A      I    75_A    36.026     0    0.051   0.112    40.077    0.000    0.000
LGA    I    76_A      I    76_A    33.038     0    0.021   0.841    34.583    0.000    0.000
LGA    N    77_A      N    77_A    33.362     0    0.039   1.351    38.174    0.000    0.000
LGA    K    78_A      K    78_A    30.750     0    0.091   0.924    32.095    0.000    0.000
LGA    L    79_A      L    79_A    27.125     0    0.057   1.430    28.808    0.000    0.000
LGA    T    80_A      T    80_A    26.922     0    0.017   1.150    31.175    0.000    0.000
LGA    K    81_A      K    81_A    26.589     0    0.044   0.908    29.913    0.000    0.000
LGA    K    82_A      K    82_A    22.351     0    0.480   1.161    23.919    0.000    0.000
LGA    F    83_A      F    83_A    21.945     0    0.559   1.258    25.283    0.000    0.000
LGA    T    84_A      T    84_A    21.101     0    0.308   0.983    24.352    0.000    0.000
LGA    W    85_A      W    85_A    18.311     0    0.279   0.949    19.411    0.000    0.000
LGA    L    86_A      L    86_A    17.789     0    0.607   1.452    19.829    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       69     276    276  100.00     597    597  100.00               106
SUMMARY(RMSD_GDC):    14.738         14.722                 15.328           14.433   12.374

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   69  106    4.0     22    2.58    20.283    18.505     0.821

LGA_LOCAL      RMSD:   2.578  Number of atoms:   22  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  23.268  Number of assigned atoms:   69 
Std_ASGN_ATOMS RMSD:  14.738  Standard rmsd on all 69 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.884672 * X  +  -0.298989 * Y  +   0.357715 * Z  +   2.401494
  Y_new =   0.236074 * X  +  -0.374351 * Y  +  -0.896733 * Z  + -42.474693
  Z_new =   0.402024 * X  +   0.877763 * Y  +  -0.260594 * Z  +  -0.510843 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.260773 -0.413727  1.859392   [DEG:   14.9412  -23.7048  106.5353 ]
ZXZ:  0.379566  1.834434  0.429495   [DEG:   21.7475  105.1053   24.6083 ]
 
# END of job
