
#######################################################
#                                                     #
#                        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   65 (  561),  selected   65 , name one
# Molecule2: number of CA atoms  104 (  843),  selected   65 , 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:    37      24_A - 60_A        4.11    24.54
  LONGEST_CONTINUOUS_SEGMENT:    37      25_A - 61_A        4.98    23.67
  LONGEST_CONTINUOUS_SEGMENT:    37      51_A - 87_A        4.94    19.27
  LONGEST_CONTINUOUS_SEGMENT:    37      52_A - 88_A        4.64    20.82
  LCS_AVERAGE:     35.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31      57_A - 87_A        1.89    24.03
  LCS_AVERAGE:     22.50

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27      60_A - 86_A        0.82    22.82
  LCS_AVERAGE:     15.46

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   65
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     H    24_A     H    24_A      3   18   37      3    4    5    7   13   18   24   29   31   32   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     N    25_A     N    25_A      9   18   37      5   10   17   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     I    26_A     I    26_A      9   18   37      5   10   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     K    27_A     K    27_A      9   18   37      5   11   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     C    28_A     C    28_A      9   18   37      5   11   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     H    29_A     H    29_A      9   18   37      5   11   18   22   26   28   29   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     F    30_A     F    30_A      9   18   37      5   11   18   22   26   28   29   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     D    31_A     D    31_A      9   18   37      5   10   17   22   26   28   29   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     N    32_A     N    32_A      9   18   37      3    9   14   20   26   28   29   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     C    33_A     C    33_A      9   18   37      5   11   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   37   40   41 
LCS_GDT     N    34_A     N    34_A      6   18   37      3    9   16   23   26   28   29   30   32   33   33   34   34   35   35   36   37   37   40   41 
LCS_GDT     R    35_A     R    35_A      6   18   37      4   11   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   37   40   42 
LCS_GDT     K    36_A     K    36_A      6   18   37      4   11   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     I    37_A     I    37_A      6   18   37      3   10   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     H    38_A     H    38_A      6   18   37      3    7   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     W    39_A     W    39_A      6   18   37      3   11   15   23   26   28   29   30   32   33   33   34   34   35   35   36   37   37   38   40 
LCS_GDT     K    40_A     K    40_A      4   18   37      3    4    9   21   25   28   29   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     I    41_A     I    41_A      4   18   37      3    8   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     R    42_A     R    42_A      3    6   37      3    3    7   10   15   23   26   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     Y    43_A     Y    43_A      3    6   37      3    3    4    6    9   11   11   18   24   27   30   32   34   35   35   36   37   37   38   38 
LCS_GDT     G    44_A     G    44_A      3   15   37      3    5    8   14   21   23   27   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     K    45_A     K    45_A     12   15   37      5   12   12   13   19   24   28   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     L    46_A     L    46_A     12   15   37      7   12   12   13   21   28   29   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     R    47_A     R    47_A     12   15   37      7   12   16   23   26   28   29   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     L    48_A     L    48_A     12   15   37      7   12   12   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     V    49_A     V    49_A     12   15   37      7   12   12   23   26   28   29   30   32   33   33   34   34   35   35   36   37   37   38   40 
LCS_GDT     D    50_A     D    50_A     12   15   37      7   12   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   37   38   38 
LCS_GDT     H    51_A     H    51_A     12   15   37      7   12   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     A    52_A     A    52_A     12   15   37      7   12   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     L    53_A     L    53_A     12   15   37      7   12   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     S    54_A     S    54_A     12   15   37      7   12   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     H    55_A     H    55_A     12   15   37      7   12   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     Q    56_A     Q    56_A     12   15   37      7   12   18   23   26   28   29   30   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     E    57_A     E    57_A     11   31   37      0    6   11   23   25   29   29   31   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     E    58_A     E    58_A      4   31   37      4    4    6    8   18   25   29   31   32   33   33   34   34   35   35   36   37   39   40   42 
LCS_GDT     K    59_A     K    59_A      4   31   37      4    4    6    8    9   12   26   31   31   31   31   32   33   35   35   36   37   39   40   42 
LCS_GDT     S    60_A     S    60_A     27   31   37      4   22   26   27   27   29   29   31   31   31   31   32   32   34   35   36   37   39   40   42 
LCS_GDT     I    61_A     I    61_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     D    62_A     D    62_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   34   35   39   40   42 
LCS_GDT     C    63_A     C    63_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   34   35   39   40   42 
LCS_GDT     Q    64_A     Q    64_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   34   35   37   40   42 
LCS_GDT     K    65_A     K    65_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   34   35   37   40   42 
LCS_GDT     C    66_A     C    66_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   34   35   37   40   42 
LCS_GDT     E    67_A     E    67_A     27   31   37     11   22   26   27   27   29   29   31   31   31   31   32   32   33   34   34   35   37   40   41 
LCS_GDT     Y    68_A     Y    68_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   34   35   38   40   42 
LCS_GDT     S    69_A     S    69_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     C    70_A     C    70_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     Q    71_A     Q    71_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   36   37   39   40   42 
LCS_GDT     T    72_A     T    72_A     27   31   37     10   18   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     T    73_A     T    73_A     27   31   37      6   16   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     R    74_A     R    74_A     27   31   37      5   22   26   27   27   29   29   31   31   31   31   32   32   33   34   34   35   37   40   41 
LCS_GDT     Q    75_A     Q    75_A     27   31   37      7   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   35   39   40   42 
LCS_GDT     M    76_A     M    76_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     R    77_A     R    77_A     27   31   37      9   20   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     Y    78_A     Y    78_A     27   31   37      9   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     H    79_A     H    79_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     Y    80_A     Y    80_A     27   31   37     11   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     K    81_A     K    81_A     27   31   37      9   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     K    82_A     K    82_A     27   31   37     10   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     I    83_A     I    83_A     27   31   37     12   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     H    84_A     H    84_A     27   31   37     11   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     A    85_A     A    85_A     27   31   37     11   22   26   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     N    86_A     N    86_A     27   31   37      3   18   25   27   27   29   29   31   31   31   31   32   32   33   34   35   36   39   40   42 
LCS_GDT     L    87_A     L    87_A     11   31   37      3    4   12   19   25   29   29   31   31   31   31   32   32   33   34   34   35   37   40   42 
LCS_GDT     K    88_A     K    88_A      5   29   37      3    3    5    6    6    8   11   14   18   25   28   32   32   33   33   34   34   34   35   35 
LCS_AVERAGE  LCS_A:  24.51  (  15.46   22.50   35.58 )

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     22     26     27     27     29     29     31     32     33     33     34     34     35     35     36     37     39     40     42 
GDT PERCENT_AT  11.54  21.15  25.00  25.96  25.96  27.88  27.88  29.81  30.77  31.73  31.73  32.69  32.69  33.65  33.65  34.62  35.58  37.50  38.46  40.38
GDT RMS_LOCAL    0.29   0.57   0.73   0.82   0.82   1.36   1.36   1.89   2.31   2.49   2.49   2.67   2.67   3.02   3.02   3.57   4.11   6.07   6.18   6.49
GDT RMS_ALL_AT  22.39  22.91  22.73  22.82  22.82  23.35  23.35  24.03  26.20  25.87  25.87  25.82  25.82  25.87  25.87  25.19  24.54  11.82  11.93  11.91

# Checking swapping
#   possible swapping detected:  F    30_A      F    30_A
#   possible swapping detected:  D    50_A      D    50_A
#   possible swapping detected:  Y    68_A      Y    68_A
#   possible swapping detected:  Y    80_A      Y    80_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    H    24_A      H    24_A    44.983     0    0.331   0.328    47.242    0.000    0.000
LGA    N    25_A      N    25_A    43.612     0    0.610   0.552    47.743    0.000    0.000
LGA    I    26_A      I    26_A    39.089     0    0.049   0.087    43.270    0.000    0.000
LGA    K    27_A      K    27_A    34.061     0    0.098   1.329    37.620    0.000    0.000
LGA    C    28_A      C    28_A    27.667     0    0.087   0.193    29.663    0.000    0.000
LGA    H    29_A      H    29_A    28.911     0    0.027   1.159    37.203    0.000    0.000
LGA    F    30_A      F    30_A    22.322     0    0.137   1.301    24.335    0.000    0.000
LGA    D    31_A      D    31_A    21.767     0    0.393   0.580    23.576    0.000    0.000
LGA    N    32_A      N    32_A    22.378     0    0.068   0.393    26.153    0.000    0.000
LGA    C    33_A      C    33_A    19.708     0    0.492   0.847    23.192    0.000    0.000
LGA    N    34_A      N    34_A    24.587     0    0.110   0.111    27.372    0.000    0.000
LGA    R    35_A      R    35_A    24.687     0    0.028   1.247    28.419    0.000    0.000
LGA    K    36_A      K    36_A    31.474     0    0.144   0.859    34.095    0.000    0.000
LGA    I    37_A      I    37_A    34.719     0    0.145   1.008    38.965    0.000    0.000
LGA    H    38_A      H    38_A    41.974     0    0.541   1.029    44.615    0.000    0.000
LGA    W    39_A      W    39_A    43.882     0    0.102   1.075    47.491    0.000    0.000
LGA    K    40_A      K    40_A    49.402     0    0.122   0.833    54.250    0.000    0.000
LGA    I    41_A      I    41_A    52.807     0    0.626   0.581    55.418    0.000    0.000
LGA    R    42_A      R    42_A    54.929     0    0.478   1.352    63.288    0.000    0.000
LGA    Y    43_A      Y    43_A    48.542     0    0.139   0.614    55.115    0.000    0.000
LGA    G    44_A      G    44_A    44.577     0    0.226   0.226    46.655    0.000    0.000
LGA    K    45_A      K    45_A    39.648     0    0.262   1.003    42.872    0.000    0.000
LGA    L    46_A      L    46_A    36.226     0    0.060   1.418    38.458    0.000    0.000
LGA    R    47_A      R    47_A    32.723     0    0.079   1.496    35.105    0.000    0.000
LGA    L    48_A      L    48_A    29.954     0    0.058   1.475    32.928    0.000    0.000
LGA    V    49_A      V    49_A    27.496     0    0.079   0.101    31.094    0.000    0.000
LGA    D    50_A      D    50_A    24.623     0    0.025   1.096    28.980    0.000    0.000
LGA    H    51_A      H    51_A    21.532     0    0.039   0.336    23.260    0.000    0.000
LGA    A    52_A      A    52_A    19.163     0    0.050   0.053    21.135    0.000    0.000
LGA    L    53_A      L    53_A    15.615     0    0.049   0.050    21.038    0.000    0.000
LGA    S    54_A      S    54_A    12.334     0    0.085   0.679    15.067    1.190    0.794
LGA    H    55_A      H    55_A     9.779     0    0.043   0.075    15.668    1.548    0.619
LGA    Q    56_A      Q    56_A     7.284     0    0.338   1.114    11.362   15.595    7.778
LGA    E    57_A      E    57_A     3.002     4    0.653   0.594     4.599   42.024   23.492
LGA    E    58_A      E    58_A     4.274     4    0.613   0.578     5.688   35.000   19.683
LGA    K    59_A      K    59_A     5.207     0    0.423   0.542    13.078   31.786   15.397
LGA    S    60_A      S    60_A     1.952     0    0.539   0.792     5.144   72.857   61.270
LGA    I    61_A      I    61_A     1.295     0    0.062   0.185     1.475   81.429   85.952
LGA    D    62_A      D    62_A     1.407     0    0.058   0.115     1.969   79.286   76.071
LGA    C    63_A      C    63_A     0.769     0    0.043   0.044     0.956   90.476   90.476
LGA    Q    64_A      Q    64_A     0.756     0    0.173   0.621     3.806   86.071   79.312
LGA    K    65_A      K    65_A     0.714     0    0.061   0.236     1.048   88.214   89.471
LGA    C    66_A      C    66_A     0.366     0    0.091   0.156     0.671   97.619   96.825
LGA    E    67_A      E    67_A     0.506     4    0.234   0.222     1.848   86.071   47.302
LGA    Y    68_A      Y    68_A     0.791     0    0.065   0.062     1.596   92.857   86.786
LGA    S    69_A      S    69_A     1.262     0    0.043   0.602     1.725   79.286   80.079
LGA    C    70_A      C    70_A     1.354     0    0.117   0.764     3.770   79.286   75.159
LGA    Q    71_A      Q    71_A     2.074     0    0.025   1.026     4.404   66.786   56.190
LGA    T    72_A      T    72_A     2.847     0    0.171   1.160     3.754   60.952   57.415
LGA    T    73_A      T    73_A     2.486     0    0.073   1.122     4.657   66.905   61.497
LGA    R    74_A      R    74_A     0.960     0    0.024   1.248     6.577   90.595   63.939
LGA    Q    75_A      Q    75_A     0.805     0    0.036   0.246     3.456   92.857   74.921
LGA    M    76_A      M    76_A     1.134     0    0.030   1.259     3.681   88.214   76.845
LGA    R    77_A      R    77_A     1.333     0    0.011   0.748     2.884   79.286   73.074
LGA    Y    78_A      Y    78_A     1.072     0    0.023   1.264     9.920   85.952   48.175
LGA    H    79_A      H    79_A     0.456     0    0.021   0.139     0.654   97.619   93.333
LGA    Y    80_A      Y    80_A     0.604     0    0.038   1.037     6.375   90.476   64.325
LGA    K    81_A      K    81_A     1.360     0    0.240   1.039     5.860   81.548   58.466
LGA    K    82_A      K    82_A     1.436     0    0.009   1.147     9.852   81.429   51.640
LGA    I    83_A      I    83_A     0.868     0    0.139   0.145     1.344   88.214   89.345
LGA    H    84_A      H    84_A     0.572     0    0.132   0.226     1.187   88.214   89.571
LGA    A    85_A      A    85_A     1.015     0    0.651   0.609     2.891   79.881   78.476
LGA    N    86_A      N    86_A     1.105     3    0.137   0.141     2.995   73.214   44.702
LGA    L    87_A      L    87_A     3.172     0    0.126   0.819     6.149   39.524   51.310
LGA    K    88_A      K    88_A     8.198     0    0.099   1.061    16.544   10.000    4.603

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       65     260    260  100.00     546    546  100.00               104
SUMMARY(RMSD_GDC):    11.286         11.158                 12.829           23.291   19.945

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65  104    4.0     31    1.89    27.885    27.036     1.561

LGA_LOCAL      RMSD:   1.886  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  24.029  Number of assigned atoms:   65 
Std_ASGN_ATOMS RMSD:  11.286  Standard rmsd on all 65 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.121536 * X  +  -0.653327 * Y  +   0.747257 * Z  +  32.603893
  Y_new =   0.096226 * X  +  -0.757047 * Y  +  -0.646236 * Z  + -16.757587
  Z_new =   0.987912 * X  +  -0.006636 * Y  +   0.154875 * Z  +  10.722468 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.471907 -1.415151 -0.042820   [DEG:  141.6298  -81.0822   -2.4534 ]
ZXZ:  0.857766  1.415295  1.577513   [DEG:   49.1464   81.0904   90.3849 ]
 
# END of job
