
#######################################################
#                                                     #
#                        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   68 (  505),  selected   68 , name one
# Molecule2: number of CA atoms  124 (  971),  selected   68 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -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      35_A - 63_A        4.94    19.16
  LONGEST_CONTINUOUS_SEGMENT:    29      36_A - 64_A        4.47    18.47
  LCS_AVERAGE:     20.96

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      41_A - 62_A        1.99    17.83
  LCS_AVERAGE:      9.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      50_A - 62_A        1.00    16.81
  LCS_AVERAGE:      5.73

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   68
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     C    34_F     C    34_A      3    7   15      0    3    3    3    4    7    7    9   12   13   14   14   18   21   22   24   26   28   29   31 
LCS_GDT     V    35_F     V    35_A      6    8   29      2    5    7    7    8    8    8    9   10   13   14   14   18   19   22   24   26   28   29   31 
LCS_GDT     F    36_F     F    36_A      6    8   29      3    5    7    7    8    8    8    9   12   13   14   17   20   25   26   27   27   28   29   31 
LCS_GDT     T    37_F     T    37_A      6    8   29      3    5    7    7    8    8    8    9   12   13   14   17   20   25   26   27   27   28   29   31 
LCS_GDT     F    38_F     F    38_A      6    8   29      3    5    7    7    8    8    8   10   19   23   25   25   25   26   28   30   34   34   35   35 
LCS_GDT     T    39_F     T    39_A      6    8   29      3    5    7    7    8    8    8   17   22   24   25   25   27   29   31   32   34   34   35   35 
LCS_GDT     D    40_F     D    40_A      6   16   29      3    5    7    8   14   20   22   23   25   25   26   27   28   29   31   32   34   34   35   35 
LCS_GDT     P    41_F     P    41_A      5   22   29      3    4    7    8   15   20   22   23   25   25   26   27   28   29   31   32   34   34   35   35 
LCS_GDT     K    42_F     K    42_A      6   22   29      4    6    6    8   14   20   22   23   25   25   26   27   28   29   31   32   34   34   35   35 
LCS_GDT     G    43_F     G    43_A      9   22   29      4    6   15   16   19   20   22   23   25   25   26   27   28   29   31   32   34   34   35   35 
LCS_GDT     S    44_F     S    44_A      9   22   29      4    6    9   16   19   20   22   23   25   25   26   27   28   29   31   32   34   34   35   35 
LCS_GDT     L    45_F     L    45_A      9   22   29      4    7   15   16   19   20   22   23   25   25   26   27   28   29   31   32   34   34   35   35 
LCS_GDT     H    46_F     H    46_A      9   22   29      3    7   15   16   19   20   22   23   25   25   26   27   28   29   31   32   34   34   35   35 
LCS_GDT     S    47_F     S    47_A      9   22   29      4    7   15   16   19   20   22   23   25   25   26   27   28   29   31   32   34   34   35   35 
LCS_GDT     I    48_F     I    48_A      9   22   29      4    7   11   15   19   20   22   23   25   25   26   27   28   29   31   32   34   34   35   35 
LCS_GDT     D    49_F     D    49_A     12   22   29      4    7    9   16   19   20   22   23   25   25   26   27   28   29   31   32   34   34   35   35 
LCS_GDT     V    50_F     V    50_A     13   22   29      9   11   12   13   19   20   22   23   25   25   26   27   28   29   31   32   35   38   39   39 
LCS_GDT     T    51_F     T    51_A     13   22   29     10   11   15   16   19   20   22   23   25   25   26   27   28   29   31   33   36   38   39   39 
LCS_GDT     E    52_F     E    52_A     13   22   29     10   11   15   16   19   20   22   23   25   25   26   27   28   29   33   37   37   38   39   39 
LCS_GDT     V    53_F     V    53_A     13   22   29     10   11   15   16   19   20   22   23   25   25   26   27   28   30   33   37   37   38   39   39 
LCS_GDT     L    54_F     L    54_A     13   22   29     10   11   15   16   19   20   22   23   25   25   26   27   28   30   33   37   37   38   39   39 
LCS_GDT     N    55_F     N    55_A     13   22   29     10   11   15   16   19   20   22   23   25   25   26   27   28   30   33   37   37   38   39   39 
LCS_GDT     N    56_F     N    56_A     13   22   29     10   11   15   16   19   20   22   23   25   25   26   27   28   30   33   37   37   38   39   39 
LCS_GDT     M    57_F     M    57_A     13   22   29     10   11   15   16   19   20   22   23   25   25   26   27   28   30   33   37   37   38   39   39 
LCS_GDT     A    58_F     A    58_A     13   22   29     10   11   15   16   19   20   22   23   25   25   26   27   28   30   33   37   37   38   39   39 
LCS_GDT     K    59_F     K    59_A     13   22   29     10   11   15   16   19   20   22   23   25   25   26   27   28   30   33   37   37   38   39   39 
LCS_GDT     G    60_F     G    60_A     13   22   29     10   11   15   16   19   20   22   23   25   25   26   27   28   30   33   37   37   38   39   39 
LCS_GDT     F    61_F     F    61_A     13   22   29      3   11   15   16   19   20   22   23   25   25   26   27   28   30   33   37   37   38   39   39 
LCS_GDT     R    62_F     R    62_A     13   22   29      3    4    6   10   19   20   22   23   25   25   26   27   28   29   33   35   37   38   39   39 
LCS_GDT     D    63_F     D    63_A      4   19   29      3    4    4    6   12   16   20   22   25   25   26   27   28   29   31   32   34   34   35   36 
LCS_GDT     A    64_F     A    64_A      4    5   29      3    4    4    4    5    8   13   16   19   23   26   27   28   29   31   32   34   34   35   35 
LCS_GDT     Q    65_F     Q    65_A      5    5   13      3    4    5    5    5    5    5    5    6    6    6    7    7    7    7    8   11   13   15   18 
LCS_GDT     N    66_F     N    66_A      5    5   14      3    4    5    5    5    5    5    5    6    6    6   12   12   14   14   14   16   19   20   20 
LCS_GDT     P    67_F     P    67_A      5    5   14      3    4    5    5    5    5    5    6   11   11   11   13   15   16   17   18   20   21   23   26 
LCS_GDT     P    68_F     P    68_A      7    9   15      4    5    6    7    9    9   10   10   11   11   11   13   15   16   17   18   22   23   25   26 
LCS_GDT     S    69_F     S    69_A      7    9   15      4    5    6    7    9    9   10   10   11   11   12   13   15   16   17   18   20   21   25   26 
LCS_GDT     S    70_F     S    70_A      7    9   15      4    5    6    7    9    9   10   10   11   11   12   13   15   16   17   20   22   23   25   26 
LCS_GDT     F    71_F     F    71_A      7    9   15      4    5    6    7    9    9   10   10   11   11   12   13   17   17   19   21   22   23   25   26 
LCS_GDT     T    72_F     T    72_A      7    9   15      4    5    6    7    9    9   10   10   11   11   13   16   19   19   24   25   26   28   28   31 
LCS_GDT     L    73_F     L    73_A      7    9   15      4    5    6    7    9    9   10   13   20   22   24   25   28   28   28   29   33   35   35   38 
LCS_GDT     G    74_F     G    74_A      7    9   22      4    5    6   10   12   16   20   22   25   25   26   27   28   30   33   37   37   38   39   39 
LCS_GDT     G    75_F     G    75_A      4    9   27      4    4    5    6    9   10   14   17   20   23   25   27   28   30   33   37   37   38   39   39 
LCS_GDT     H    76_F     H    76_A      4    9   27      4    4    5    6    9   11   14   16   18   20   22   25   27   29   33   37   37   38   39   39 
LCS_GDT     C    77_F     C    77_A      3    7   27      3    3    4    7    8    9   12   14   16   18   19   20   23   24   26   29   30   33   36   36 
LCS_GDT     Q    78_F     Q    78_A      4    7   27      3    3    5    7    9   11   14   16   18   20   22   24   27   29   32   37   37   38   39   39 
LCS_GDT     A    79_F     A    79_A      4    7   27      3    3    5    7    9   11   14   16   18   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     P    80_F     P    80_A      4    7   27      3    4    6    8    8   13   15   17   20   21   24   25   28   30   33   37   37   38   39   39 
LCS_GDT     L    81_F     L    81_A      4    7   27      3    3    4    7    8   11   15   17   20   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     N    82_F     N    82_A      6    7   27      4    5    6    7    9   13   15   17   20   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     A    83_F     A    83_A      6    7   27      4    5    6    7    9   13   15   17   20   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     F    84_F     F    84_A      6    6   27      4    5    6    7    9   13   15   17   20   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     S    85_F     S    85_A      6    6   27      4    5    6    7    9   11   14   16   20   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     F    86_F     F    86_A      6    6   27      3    5    6    6    8   11   13   16   17   20   22   25   27   30   33   37   37   38   39   39 
LCS_GDT     V    87_F     V    87_A      6    7   27      3    5    6    6    9   11   14   16   18   20   22   25   27   30   33   37   37   38   39   39 
LCS_GDT     L    88_F     L    88_A      3    7   27      3    3    3    5    8   11   14   17   20   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     P    89_F     P    89_A      5    7   27      3    4    5    7    8    9   12   15   18   20   22   25   27   30   33   37   37   38   39   39 
LCS_GDT     G    90_F     G    90_A      5    7   27      3    4    5    6    7    8   11   12   15   19   21   24   27   29   32   37   37   38   39   39 
LCS_GDT     V    91_F     V    91_A      5    7   27      3    4    5    6    7    8    9    9   11   14   20   22   25   30   33   37   37   38   39   39 
LCS_GDT     N    92_F     N    92_A      5    7   27      3    4    5    6    7    8    9    9   11   14   20   22   26   30   33   37   37   38   39   39 
LCS_GDT     D    93_F     D    93_A      5    7   27      3    4    5    6    7    8    9   12   16   20   22   25   27   30   33   37   37   38   39   39 
LCS_GDT     R    94_F     R    94_A      4    6   27      1    4    4    6    7    8    9   14   16   20   22   25   27   30   33   37   37   38   39   39 
LCS_GDT     A    95_F     A    95_A      3    4   27      3    4    4    4    5   11   14   17   20   21   22   25   27   30   33   37   37   38   39   39 
LCS_GDT     T    96_F     T    96_A      5    6   27      3    4    6    8    9   13   15   17   20   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     V    97_F     V    97_A      5    6   27      3    4    6    8    8   13   15   17   20   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     A    98_F     A    98_A      5    6   27      3    4    5    5    6   13   15   17   20   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     T    99_F     T    99_A      5    6   27      3    4    6    8   10   14   16   17   20   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     A   100_F     A   100_A      5    6   27      3    3    5    9   12   14   16   17   20   21   24   25   27   30   33   37   37   38   39   39 
LCS_GDT     D   101_F     D   101_A      3    6   27      3    3    3    4    4    6   12   15   18   20   22   25   27   30   33   37   37   38   39   39 
LCS_AVERAGE  LCS_A:  12.17  (   5.73    9.83   20.96 )

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     10     11     15     16     19     20     22     23     25     25     26     27     28     30     33     37     37     38     39     39 
GDT PERCENT_AT   8.06   8.87  12.10  12.90  15.32  16.13  17.74  18.55  20.16  20.16  20.97  21.77  22.58  24.19  26.61  29.84  29.84  30.65  31.45  31.45
GDT RMS_LOCAL    0.25   0.31   1.10   1.23   1.54   1.61   1.97   2.11   2.54   2.54   2.82   3.02   3.35   4.53   4.96   5.34   5.33   5.46   5.61   5.61
GDT RMS_ALL_AT  16.87  16.80  18.26  18.26  18.33  18.35  18.01  17.85  17.54  17.54  17.40  17.29  17.23  17.18  17.08  17.35  17.47  17.37  17.27  17.27

# Checking swapping
#   possible swapping detected:  F    36_F      F    36_A
#   possible swapping detected:  F    61_F      F    61_A
#   possible swapping detected:  F    84_F      F    84_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    C    34_F      C    34_A    16.626     0    0.049   0.123    19.074    0.000    0.000
LGA    V    35_F      V    35_A    16.706     0    0.632   0.613    19.223    0.000    0.000
LGA    F    36_F      F    36_A    12.319     0    0.104   1.307    13.494    0.000    4.329
LGA    T    37_F      T    37_A    12.481     0    0.019   0.096    16.214    0.000    0.000
LGA    F    38_F      F    38_A     8.547     0    0.037   1.257     9.811    2.381    4.459
LGA    T    39_F      T    39_A     7.460     0    0.063   1.128    10.787   17.500   12.313
LGA    D    40_F      D    40_A     3.758     0    0.170   1.220     7.765   37.500   28.095
LGA    P    41_F      P    41_A     3.004     0    0.620   0.720     5.320   42.381   50.884
LGA    K    42_F      K    42_A     3.775     0    0.652   0.919    13.563   55.833   28.571
LGA    G    43_F      G    43_A     1.908     0    0.032   0.032     3.959   65.595   65.595
LGA    S    44_F      S    44_A     2.337     0    0.026   0.670     5.449   72.976   61.349
LGA    L    45_F      L    45_A     2.494     0    0.215   1.293     6.949   64.762   48.810
LGA    H    46_F      H    46_A     1.390     0    0.049   0.151     2.407   79.286   73.857
LGA    S    47_F      S    47_A     1.322     0    0.053   0.567     2.868   81.548   73.413
LGA    I    48_F      I    48_A     2.087     0    0.075   1.202     7.389   81.786   57.083
LGA    D    49_F      D    49_A     1.668     0    0.214   0.834     5.013   66.905   53.036
LGA    V    50_F      V    50_A     2.659     0    0.356   1.261     5.534   66.905   55.646
LGA    T    51_F      T    51_A     1.484     0    0.042   0.057     2.107   79.524   80.408
LGA    E    52_F      E    52_A     1.900     0    0.056   1.072     7.222   72.857   50.212
LGA    V    53_F      V    53_A     1.506     0    0.030   0.063     1.771   77.143   76.531
LGA    L    54_F      L    54_A     0.858     0    0.000   0.050     1.315   88.214   85.952
LGA    N    55_F      N    55_A     0.901     0    0.041   0.193     1.393   85.952   84.821
LGA    N    56_F      N    56_A     1.665     0    0.063   0.079     2.548   79.286   70.119
LGA    M    57_F      M    57_A     0.886     0    0.017   0.862     2.929   85.952   85.238
LGA    A    58_F      A    58_A     1.136     0    0.066   0.070     1.463   83.690   83.238
LGA    K    59_F      K    59_A     1.637     0    0.055   0.196     2.336   75.000   70.212
LGA    G    60_F      G    60_A     1.602     0    0.150   0.150     1.602   75.000   75.000
LGA    F    61_F      F    61_A     2.020     0    0.637   0.523     3.204   65.119   62.814
LGA    R    62_F      R    62_A     2.849     0    0.076   1.147    12.474   53.810   26.926
LGA    D    63_F      D    63_A     6.500     0    0.681   0.615    10.436   15.357    8.810
LGA    A    64_F      A    64_A     8.530     0    0.039   0.038     9.558    4.524    4.190
LGA    Q    65_F      Q    65_A    33.900     0    0.589   0.690    39.219    0.000    0.000
LGA    N    66_F      N    66_A    35.369     0    0.199   1.215    40.938    0.000    0.000
LGA    P    67_F      P    67_A    32.605     0    0.662   0.768    34.178    0.000    0.000
LGA    P    68_F      P    68_A    33.458     0    0.646   0.620    35.502    0.000    0.000
LGA    S    69_F      S    69_A    33.533     0    0.105   0.135    34.473    0.000    0.000
LGA    S    70_F      S    70_A    27.308     0    0.075   0.157    29.364    0.000    0.000
LGA    F    71_F      F    71_A    21.641     0    0.064   1.321    23.642    0.000    0.000
LGA    T    72_F      T    72_A    14.776     0    0.086   0.110    17.276    0.000    0.000
LGA    L    73_F      L    73_A     8.819     0    0.168   1.342    10.914    5.000    8.512
LGA    G    74_F      G    74_A     5.560     0    0.599   0.599     7.735   14.762   14.762
LGA    G    75_F      G    75_A     7.845     0    0.212   0.212     8.615    9.286    9.286
LGA    H    76_F      H    76_A    12.058     0    0.623   1.280    18.713    0.000    0.000
LGA    C    77_F      C    77_A    14.807     0    0.111   0.169    16.483    0.000    0.000
LGA    Q    78_F      Q    78_A    12.702     0    0.459   1.083    14.892    0.000    0.000
LGA    A    79_F      A    79_A    13.311     0    0.168   0.218    15.611    0.000    0.000
LGA    P    80_F      P    80_A     9.527     0    0.080   0.289    12.634    0.119    1.429
LGA    L    81_F      L    81_A    11.277     0    0.081   0.216    13.372    0.119    0.119
LGA    N    82_F      N    82_A    17.726     0    0.714   0.948    21.569    0.000    0.000
LGA    A    83_F      A    83_A    19.929     0    0.094   0.098    20.833    0.000    0.000
LGA    F    84_F      F    84_A    18.702     0    0.098   0.223    19.774    0.000    0.000
LGA    S    85_F      S    85_A    18.070     0    0.047   0.642    19.631    0.000    0.000
LGA    F    86_F      F    86_A    21.273     0    0.628   0.525    22.491    0.000    0.000
LGA    V    87_F      V    87_A    22.131     0    0.573   0.570    22.542    0.000    0.000
LGA    L    88_F      L    88_A    22.106     0    0.136   1.397    25.298    0.000    0.000
LGA    P    89_F      P    89_A    28.106     0    0.175   0.386    29.859    0.000    0.000
LGA    G    90_F      G    90_A    30.888     0    0.710   0.710    32.120    0.000    0.000
LGA    V    91_F      V    91_A    29.814     0    0.237   0.252    30.399    0.000    0.000
LGA    N    92_F      N    92_A    27.486     0    0.339   1.206    28.048    0.000    0.000
LGA    D    93_F      D    93_A    26.323     0    0.681   1.293    28.381    0.000    0.000
LGA    R    94_F      R    94_A    28.846     0    0.617   1.004    34.562    0.000    0.000
LGA    A    95_F      A    95_A    29.458     0    0.624   0.578    29.458    0.000    0.000
LGA    T    96_F      T    96_A    26.190     0    0.620   0.558    27.447    0.000    0.000
LGA    V    97_F      V    97_A    23.541     0    0.179   0.176    24.300    0.000    0.000
LGA    A    98_F      A    98_A    27.306     0    0.689   0.660    29.950    0.000    0.000
LGA    T    99_F      T    99_A    24.477     0    0.083   0.109    26.073    0.000    0.000
LGA    A   100_F      A   100_A    21.378     0    0.331   0.332    22.421    0.000    0.000
LGA    D   101_F      D   101_A    24.294     0    0.606   1.299    30.341    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       68     272    272  100.00     505    505  100.00               124
SUMMARY(RMSD_GDC):    15.305         15.284                 15.479           13.759   12.226

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68  124    4.0     23    2.11    17.540    15.637     1.040

LGA_LOCAL      RMSD:   2.111  Number of atoms:   23  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.852  Number of assigned atoms:   68 
Std_ASGN_ATOMS RMSD:  15.305  Standard rmsd on all 68 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.350379 * X  +   0.441946 * Y  +   0.825784 * Z  + -55.065922
  Y_new =   0.844246 * X  +  -0.232753 * Y  +   0.482778 * Z  + -107.007973
  Z_new =   0.405566 * X  +   0.866320 * Y  +  -0.291559 * Z  +   8.185218 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.964183 -0.417598  1.895439   [DEG:  112.5394  -23.9266  108.6006 ]
ZXZ:  2.099838  1.866653  0.437843   [DEG:  120.3118  106.9513   25.0865 ]
 
# END of job
