
#######################################################
#                                                     #
#                        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   80 (  669),  selected   72 , name one
# Molecule2: number of CA atoms  127 ( 1099),  selected   72 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      58_C - 81_C        4.67    35.80
  LCS_AVERAGE:     15.96

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      12_C - 26_C        1.57    22.32
  LCS_AVERAGE:      7.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      12_C - 25_C        0.59    20.79
  LCS_AVERAGE:      5.37

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     R    12_B     R    12_C     14   15   17      8   14   14   14   16   16   16   17   17   18   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     E    13_B     E    13_C     14   15   17      8   14   14   14   16   16   16   17   17   18   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     L    14_B     L    14_C     14   15   17      9   14   14   14   16   16   16   17   17   18   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     L    15_B     L    15_C     14   15   17      9   14   14   14   16   16   16   17   17   20   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     E    16_B     E    16_C     14   15   17      9   14   14   14   16   16   16   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     K    17_B     K    17_C     14   15   17      9   14   14   14   16   16   16   17   17   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     L    18_B     L    18_C     14   15   17      9   14   14   14   16   16   16   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     I    19_B     I    19_C     14   15   17      9   14   14   14   16   16   16   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     E    20_B     E    20_C     14   15   17      8   14   14   14   16   16   16   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     Y    21_B     Y    21_C     14   15   17      9   14   14   14   16   16   16   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     L    22_B     L    22_C     14   15   17      9   14   14   14   16   16   16   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     E    23_B     E    23_C     14   15   17      9   14   14   14   16   16   16   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     E    24_B     E    24_C     14   15   17      9   14   14   14   16   16   16   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     L    25_B     L    25_C     14   15   17      9   14   14   14   16   16   16   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     K    26_B     K    26_C      4   15   17      3    3    4    4    6   12   15   16   16   21   22   26   28   30   33   35   38   40   41   44 
LCS_GDT     E    27_B     E    27_C      4    5   17      0    3    4    4    4    6    8    8   10   14   18   19   19   20   24   27   32   38   41   44 
LCS_GDT     K    34_B     K    34_C      3    3   17      0    3    3    3    3    4    6    6    8    9   11   13   16   19   21   23   26   28   29   30 
LCS_GDT     E    35_B     E    35_C      3    4   12      3    3    3    4    5    5    7    8    8   10   11   13   16   19   22   24   26   28   29   32 
LCS_GDT     K    36_B     K    36_C      3    4   12      3    3    3    4    5    5    6    7    8   10   11   13   16   19   22   24   26   29   29   32 
LCS_GDT     L    37_B     L    37_C      3    4   21      3    3    3    4    5    5    6    7    8   10   10   14   16   19   22   24   26   29   29   32 
LCS_GDT     E    38_B     E    38_C      4    4   21      4    4    4    4    5    5    6    9   10   13   15   17   19   20   22   24   26   29   31   32 
LCS_GDT     E    39_B     E    39_C      4    4   21      4    4    4    4    4    5    6    9   12   14   16   18   19   20   21   22   22   29   29   32 
LCS_GDT     V    40_B     V    40_C      4    4   21      4    4    4    4    4    5    9   11   12   14   16   18   19   20   21   22   22   24   26   28 
LCS_GDT     I    41_B     I    41_C      4    4   21      4    4    4    4    5    5    9   11   12   14   16   18   19   20   22   24   26   29   30   32 
LCS_GDT     E    42_B     E    42_C      3    4   21      3    3    3    4    5    6    9   11   12   13   15   18   19   20   22   24   26   29   31   32 
LCS_GDT     G    43_B     G    43_C      3    4   21      3    3    3    4    5    7    8    8   10   13   15   18   19   20   22   24   28   31   35   40 
LCS_GDT     L    44_B     L    44_C      3    6   21      3    3    4    6    7    9   11   12   13   14   18   19   19   21   27   30   34   37   40   44 
LCS_GDT     E    45_B     E    45_C      5    8   21      5    5    5    6    7   11   15   15   15   18   20   23   27   30   33   35   38   40   41   44 
LCS_GDT     R    46_B     R    46_C      5    8   21      5    5    5    6    7    9   11   12   17   18   20   24   28   30   33   35   38   40   41   44 
LCS_GDT     L    47_B     L    47_C      5    8   21      5    5    5    6    7    9   11   11   13   18   20   26   28   30   33   35   38   40   41   44 
LCS_GDT     K    48_B     K    48_C      5    8   21      5    5    5    6    7   14   15   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     E    49_B     E    49_C      5    8   21      5    5    5    6    7    9   11   12   13   16   18   21   26   29   33   35   38   40   41   44 
LCS_GDT     E    50_B     E    50_C      3    8   21      3    3    3    6    7    9   11   12   13   16   16   20   24   27   31   35   38   40   41   44 
LCS_GDT     V    51_B     V    51_C      3    8   21      3    3    3    6    7    9   11   12   13   16   16   18   20   20   25   27   36   36   40   42 
LCS_GDT     D    52_B     D    52_C      6    8   21      4    6    7    8    8    9   11   12   13   14   16   18   20   20   21   22   22   22   25   26 
LCS_GDT     Q    55_B     Q    55_C      6    8   21      3    5    7    8    8    8   10   12   13   16   16   18   24   27   31   34   38   40   41   44 
LCS_GDT     L    56_B     L    56_C      6    8   21      4    6    7    8    8    9   11   12   13   16   16   18   24   27   31   34   38   40   41   44 
LCS_GDT     N    57_B     N    57_C      6    8   22      4    6    7    8    8    8   10   12   13   16   21   23   27   30   33   35   38   40   41   44 
LCS_GDT     M    58_B     M    58_C      6    8   24      4    6    7    8    8    9   11   12   14   19   21   24   27   30   33   35   38   40   41   44 
LCS_GDT     N    59_B     N    59_C      6    8   24      4    6    7    8    8    8   12   14   14   17   20   23   27   30   33   35   38   40   41   44 
LCS_GDT     L    60_B     L    60_C      6    8   24      3    5    6    8    8   10   12   14   15   18   20   22   22   23   24   28   32   36   40   44 
LCS_GDT     I    61_B     I    61_C      6    8   24      1    6    7    8    8    8    8   10   13   16   18   22   22   23   24   27   31   35   38   42 
LCS_GDT     V    62_B     V    62_C      4    9   24      3    4    4    6    9   10   12   14   14   17   20   22   22   23   24   27   32   35   38   42 
LCS_GDT     F    63_B     F    63_C      4    9   24      3    4    4    6    9   10   11   14   14   17   20   22   22   23   24   27   32   35   40   44 
LCS_GDT     E    64_B     E    64_C      4    9   24      3    4    4    6    9   10   12   14   16   18   20   22   22   23   24   26   32   35   38   42 
LCS_GDT     G    65_B     G    65_C      6    9   24      3    4    5    6    9   10   12   14   16   18   20   22   22   23   24   27   32   35   38   42 
LCS_GDT     L    66_B     L    66_C      6    9   24      3    5    5    6    9   10   12   14   16   18   20   22   22   23   24   27   32   35   40   44 
LCS_GDT     E    67_B     E    67_C      6    9   24      4    5    5    6    9   10   12   14   16   18   20   22   22   23   32   34   36   40   41   44 
LCS_GDT     V    68_B     V    68_C      6    9   24      4    5    5    6   15   15   15   16   16   18   20   22   23   26   32   35   37   40   41   44 
LCS_GDT     D    69_B     D    69_C      6    9   24      4    5    5    6   12   14   15   16   16   18   20   26   28   30   33   35   38   40   41   44 
LCS_GDT     E    70_B     E    70_C      6    9   24      4    5    5    6    9   10   12   14   16   18   20   22   22   23   24   25   31   36   40   44 
LCS_GDT     E    71_B     E    71_C      5    9   24      3    5    5    6    9   10   12   14   16   18   20   22   22   23   30   33   38   40   41   44 
LCS_GDT     G    72_B     G    72_C      5    7   24      4    5    5   13   16   16   16   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     R    73_B     R    73_C      5    7   24      4    5   10   14   16   16   16   17   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     V    74_B     V    74_C      5    8   24      4    5    5    8    8    9   11   15   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     W    75_B     W    75_C      6    8   24      4    5    6    8    8   10   10   15   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     F    76_B     F    76_C      6    8   24      4    5    6    8    8    8   11   14   17   20   22   24   28   30   33   35   38   40   41   44 
LCS_GDT     I    77_B     I    77_C      6    8   24      4    5    6    8    8   10   12   15   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     V    78_B     V    78_C      6    8   24      4    5    6    8    9   11   13   15   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     K    79_B     K    79_C      8   10   24      3    6    8    8    9   11   14   15   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     E    80_B     E    80_C      8   10   24      4    6    8    8    9   11   14   15   18   21   23   26   28   30   33   35   38   40   41   44 
LCS_GDT     M    81_B     M    81_C      8   10   24      4    6    8    8    8   10   12   15   18   21   22   23   25   29   33   35   38   40   41   44 
LCS_GDT     L    82_B     L    82_C      8   10   17      4    6    8    8    9   10   11   13   13   14   14   15   19   26   26   28   31   34   38   42 
LCS_GDT     H    83_B     H    83_C      8   10   17      4    6    8    8    9   10   11   13   13   14   14   15   15   16   17   19   20   29   31   32 
LCS_GDT     A    84_B     A    84_C      8   10   17      3    6    8    8    9   10   11   13   13   14   14   15   15   16   17   17   18   20   23   24 
LCS_GDT     T    85_B     T    85_C      8   10   17      3    5    8    8    9   10   11   13   13   14   14   15   15   16   17   17   17   18   18   20 
LCS_GDT     T    86_B     T    86_C      8   10   17      3    6    8    8    9   10   11   13   13   14   14   15   15   16   17   17   17   18   18   20 
LCS_GDT     E    87_B     E    87_C      3   10   17      3    3    3    4    7   10   11   13   13   14   14   15   15   16   17   17   17   18   23   24 
LCS_GDT     E    88_B     E    88_C      3   10   17      3    3    3    7    9   10   11   13   13   14   14   15   15   16   17   19   20   22   23   24 
LCS_GDT     E    89_B     E    89_C      3    5   17      3    3    3    3    4    6    6    7    7   11   14   15   15   16   17   19   20   22   23   24 
LCS_GDT     A    90_B     A    90_C      3    4   17      3    3    3    3    5    6    9   13   13   14   14   16   17   17   17   19   20   22   23   24 
LCS_GDT     L    91_B     L    91_C      3    3   17      3    3    3    5    9   10   11   13   13   14   14   16   17   17   17   18   20   22   23   24 
LCS_AVERAGE  LCS_A:   9.48  (   5.37    7.12   15.96 )

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     14     14     16     16     16     17     18     21     23     26     28     30     33     35     38     40     41     44 
GDT PERCENT_AT   7.09  11.02  11.02  11.02  12.60  12.60  12.60  13.39  14.17  16.54  18.11  20.47  22.05  23.62  25.98  27.56  29.92  31.50  32.28  34.65
GDT RMS_LOCAL    0.31   0.59   0.59   0.59   1.52   1.52   1.52   1.87   3.24   3.64   4.03   4.35   4.55   4.82   5.19   5.40   5.71   5.98   6.15   6.62
GDT RMS_ALL_AT  20.21  20.79  20.79  20.79  17.84  17.84  17.84  17.67  15.32  15.16  15.32  15.32  15.31  15.23  15.13  15.05  15.00  14.96  14.94  14.92

# Checking swapping
#   possible swapping detected:  E    16_B      E    16_C
#   possible swapping detected:  E    24_B      E    24_C
#   possible swapping detected:  E    35_B      E    35_C
#   possible swapping detected:  E    45_B      E    45_C
#   possible swapping detected:  D    52_B      D    52_C
#   possible swapping detected:  E    70_B      E    70_C
#   possible swapping detected:  E    80_B      E    80_C
#   possible swapping detected:  E    88_B      E    88_C
#   possible swapping detected:  E    89_B      E    89_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    R    12_B      R    12_C     2.139     0    0.350   1.727     5.609   72.976   49.567
LGA    E    13_B      E    13_C     2.374     0    0.125   0.913     3.693   66.786   56.720
LGA    L    14_B      L    14_C     1.981     0    0.091   1.024     6.669   70.833   53.036
LGA    L    15_B      L    15_C     1.271     0    0.102   0.957     3.430   79.286   73.393
LGA    E    16_B      E    16_C     0.765     0    0.056   1.111     4.281   90.476   75.132
LGA    K    17_B      K    17_C     0.949     0    0.035   1.355     7.473   90.476   65.503
LGA    L    18_B      L    18_C     1.140     0    0.080   1.430     3.354   85.952   78.750
LGA    I    19_B      I    19_C     1.472     0    0.079   1.421     4.357   81.548   71.964
LGA    E    20_B      E    20_C     1.574     0    0.047   0.943     3.358   79.286   74.127
LGA    Y    21_B      Y    21_C     0.729     0    0.041   0.873     2.665   88.214   79.683
LGA    L    22_B      L    22_C     1.542     0    0.048   0.254     2.642   72.976   70.952
LGA    E    23_B      E    23_C     1.848     0    0.025   0.343     2.606   70.833   67.513
LGA    E    24_B      E    24_C     1.185     0    0.138   1.528     6.765   81.429   57.884
LGA    L    25_B      L    25_C     1.279     0    0.421   1.337     4.930   59.405   53.393
LGA    K    26_B      K    26_C     8.038     0    0.175   1.192    17.257    7.976    3.598
LGA    E    27_B      E    27_C    13.172     0    0.157   1.188    15.736    0.000    0.000
LGA    K    34_B      K    34_C    20.620     0    0.655   1.106    22.026    0.000    0.000
LGA    E    35_B      E    35_C    22.399     0    0.630   1.335    26.659    0.000    0.000
LGA    K    36_B      K    36_C    21.252     0    0.382   0.943    29.626    0.000    0.000
LGA    L    37_B      L    37_C    22.573     0    0.620   1.153    27.517    0.000    0.000
LGA    E    38_B      E    38_C    22.628     0    0.660   0.726    28.923    0.000    0.000
LGA    E    39_B      E    39_C    24.373     0    0.038   1.479    27.803    0.000    0.000
LGA    V    40_B      V    40_C    24.352     0    0.048   0.102    26.220    0.000    0.000
LGA    I    41_B      I    41_C    21.760     0    0.605   1.594    28.175    0.000    0.000
LGA    E    42_B      E    42_C    19.991     0    0.595   0.710    23.434    0.000    0.000
LGA    G    43_B      G    43_C    15.098     0    0.647   0.647    17.357    0.000    0.000
LGA    L    44_B      L    44_C    10.255     0    0.569   1.022    12.148    6.071    3.214
LGA    E    45_B      E    45_C     5.734     0    0.111   1.153     7.823   34.167   22.063
LGA    R    46_B      R    46_C     5.647     0    0.047   1.621    15.767   23.810    9.091
LGA    L    47_B      L    47_C     5.488     0    0.097   1.280     6.691   25.595   28.571
LGA    K    48_B      K    48_C     4.434     0    0.553   0.913    12.603   32.262   18.677
LGA    E    49_B      E    49_C     8.358     0    0.282   1.093     9.581    5.000    7.302
LGA    E    50_B      E    50_C    10.416     0    0.599   1.023    13.940    0.119    0.053
LGA    V    51_B      V    51_C    13.325     0    0.563   0.650    14.936    0.000    0.000
LGA    D    52_B      D    52_C    18.284     0    0.701   1.251    23.684    0.000    0.000
LGA    Q    55_B      Q    55_C    14.109     0    0.092   1.124    16.192    0.000    1.481
LGA    L    56_B      L    56_C    15.276     0    0.180   1.402    18.717    0.000    0.000
LGA    N    57_B      N    57_C    14.261     0    0.028   1.369    15.410    0.000    0.000
LGA    M    58_B      M    58_C    13.826     0    0.057   0.932    15.128    0.000    0.000
LGA    N    59_B      N    59_C    15.286     0    0.059   1.082    16.349    0.000    0.000
LGA    L    60_B      L    60_C    17.575     0    0.604   0.593    20.783    0.000    0.000
LGA    I    61_B      I    61_C    20.030     0    0.614   1.080    21.908    0.000    0.000
LGA    V    62_B      V    62_C    22.456     0    0.626   0.541    24.413    0.000    0.000
LGA    F    63_B      F    63_C    19.726     0    0.020   1.080    23.433    0.000    0.000
LGA    E    64_B      E    64_C    23.463     0    0.621   1.224    27.362    0.000    0.000
LGA    G    65_B      G    65_C    21.405     0    0.241   0.241    22.099    0.000    0.000
LGA    L    66_B      L    66_C    18.326     0    0.090   1.153    20.281    0.000    0.000
LGA    E    67_B      E    67_C    16.459     0    0.045   0.681    20.272    0.000    0.000
LGA    V    68_B      V    68_C    12.840     0    0.032   0.158    14.050    0.000    0.000
LGA    D    69_B      D    69_C    11.905     0    0.117   0.674    13.469    0.000    0.000
LGA    E    70_B      E    70_C    13.014     0    0.692   1.545    15.366    0.000    0.000
LGA    E    71_B      E    71_C     9.316     0    0.259   1.182    16.633    7.024    3.122
LGA    G    72_B      G    72_C     2.170     0    0.319   0.319     4.582   60.595   60.595
LGA    R    73_B      R    73_C     1.653     0    0.098   1.104    10.850   47.976   33.117
LGA    V    74_B      V    74_C     7.944     0    0.072   1.023    11.489   12.024    6.939
LGA    W    75_B      W    75_C    10.618     0    0.384   0.875    13.513    0.119    0.034
LGA    F    76_B      F    76_C    10.271     0    0.196   1.202    11.128    0.119    2.468
LGA    I    77_B      I    77_C    12.542     0    0.023   0.630    14.861    0.000    0.000
LGA    V    78_B      V    78_C    12.218     0    0.079   1.066    15.532    0.000    0.000
LGA    K    79_B      K    79_C    15.925     0    0.524   1.322    23.416    0.000    0.000
LGA    E    80_B      E    80_C    16.623     0    0.060   0.898    18.199    0.000    0.000
LGA    M    81_B      M    81_C    18.014     0    0.059   0.964    19.023    0.000    0.000
LGA    L    82_B      L    82_C    21.411     0    0.307   0.323    23.662    0.000    0.000
LGA    H    83_B      H    83_C    23.570     0    0.140   1.429    26.863    0.000    0.000
LGA    A    84_B      A    84_C    28.881     0    0.121   0.140    29.628    0.000    0.000
LGA    T    85_B      T    85_C    32.086     0    0.600   0.998    34.594    0.000    0.000
LGA    T    86_B      T    86_C    36.217     0    0.045   1.077    39.338    0.000    0.000
LGA    E    87_B      E    87_C    36.154     0    0.519   1.448    36.774    0.000    0.000
LGA    E    88_B      E    88_C    36.137     0    0.595   1.140    37.119    0.000    0.000
LGA    E    89_B      E    89_C    36.512     0    0.684   0.927    39.557    0.000    0.000
LGA    A    90_B      A    90_C    34.227     0    0.590   0.595    35.830    0.000    0.000
LGA    L    91_B      L    91_C    31.921     0    0.615   0.959    32.846    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     605    605  100.00               127
SUMMARY(RMSD_GDC):    14.396         14.234                 14.901           10.656    8.881

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   80  127    4.0     17    1.87    15.748    13.277     0.862

LGA_LOCAL      RMSD:   1.873  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.672  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  14.396  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.023355 * X  +  -0.928868 * Y  +  -0.369675 * Z  + -26.820728
  Y_new =  -0.395374 * X  +   0.348211 * Y  +  -0.849958 * Z  +   4.285908
  Z_new =   0.918223 * X  +   0.126309 * Y  +  -0.375382 * Z  +  77.747078 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.629798 -1.163571  2.817012   [DEG:  -93.3806  -66.6677  161.4029 ]
ZXZ: -0.410254  1.955606  1.434096   [DEG:  -23.5058  112.0480   82.1677 ]
 
# END of job
