
#######################################################
#                                                     #
#                        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   64 (  532),  selected   64 , name one
# Molecule2: number of CA atoms  157 ( 1259),  selected   64 , 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:    45      21_A - 65_A        4.93    13.98
  LONGEST_CONTINUOUS_SEGMENT:    45      22_A - 66_A        4.99    13.81
  LONGEST_CONTINUOUS_SEGMENT:    45      23_A - 67_A        4.93    13.63
  LCS_AVERAGE:     26.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      40_A - 57_A        1.86    17.72
  LCS_AVERAGE:      8.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      61_A - 75_A        1.00    19.65
  LCS_AVERAGE:      6.02

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
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     V    21_A     V    21_A      6    6   45      3    5    6    6    6    6    6   17   21   23   27   33   41   43   45   46   46   47   49   49 
LCS_GDT     H    22_A     H    22_A      6    6   45      3    5    7   12   12   16   18   20   23   25   29   30   35   43   45   46   46   47   49   49 
LCS_GDT     R    23_A     R    23_A      6    6   45      3    5    6    6    6    6    6   19   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     L    24_A     L    24_A      6    7   45      3    5    6    8    9   12   15   18   24   27   32   38   41   43   45   46   46   47   49   49 
LCS_GDT     A    25_A     A    25_A      6    7   45      3    5    6    7    8   10   15   18   23   27   31   38   41   43   45   46   46   47   49   49 
LCS_GDT     G    26_A     G    26_A      6    7   45      3    4    6    8    9   12   15   22   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     I    27_A     I    27_A      5    7   45      3    4    6    8    8   10   12   16   21   23   29   38   41   43   45   46   46   47   49   49 
LCS_GDT     E    28_A     E    28_A      5    7   45      3    4    6    8    9   11   14   19   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     P    29_A     P    29_A      5   10   45      3    4    6    8    9   15   20   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     D    30_A     D    30_A      8   10   45      4    7    8    8    9   14   20   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     P    31_A     P    31_A      8   10   45      4    7    8    8    9   10   12   20   23   26   33   37   41   43   45   46   46   47   49   49 
LCS_GDT     R    32_A     R    32_A      8   10   45      4    7    8    8    9   10   21   22   23   30   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     F    33_A     F    33_A      8   10   45      5    7    8    8   10   16   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     E    34_A     E    34_A      8   10   45      5    7    8    8    9   18   19   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     I    35_A     I    35_A      8   10   45      5    7    8    8    9   10   11   14   23   26   33   38   41   43   45   46   46   47   49   49 
LCS_GDT     L    36_A     L    36_A      8   10   45      5    7    8    8    9   10   11   13   25   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     D    37_A     D    37_A      8   10   45      5    7    8    8    9   14   19   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     K    38_A     K    38_A      4   10   45      4    4    6    7    9   12   15   21   26   29   32   38   41   43   45   46   46   47   49   49 
LCS_GDT     Y    39_A     Y    39_A      4   16   45      4    4    6    8    9   13   18   22   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     I    40_A     I    40_A      7   18   45      5    5    9   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     F    41_A     F    41_A      7   18   45      5    5   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     R    42_A     R    42_A      7   18   45      5    5   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     Q    43_A     Q    43_A      7   18   45      5    5   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     I    44_A     I    44_A      9   18   45      5    5   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     V    45_A     V    45_A      9   18   45      3    8   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     A    46_A     A    46_A      9   18   45      5    8   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     D    47_A     D    47_A      9   18   45      5    8   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     N    48_A     N    48_A      9   18   45      5    8   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     P    49_A     P    49_A      9   18   45      4    8   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     E    50_A     E    50_A      9   18   45      5    8   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     E    51_A     E    51_A      9   18   45      8    8   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     R    52_A     R    52_A      9   18   45      8    8   12   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     E    53_A     E    53_A      9   18   45      8    8    9   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     K    54_A     K    54_A      9   18   45      8    8    9   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     I    55_A     I    55_A      9   18   45      8    8    9   12   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     R    56_A     R    56_A      9   18   45      8    8    9   15   18   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     L    57_A     L    57_A      9   18   45      8    8    9   12   17   19   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     D    58_A     D    58_A      9   16   45      8    8    9   11   12   15   20   22   26   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     Y    59_A     Y    59_A      9   17   45      3    4    9   11   14   18   21   22   23   29   34   37   40   43   45   46   46   47   49   49 
LCS_GDT     G    60_A     G    60_A      4   17   45      3    4    9   15   18   19   21   24   27   31   34   37   40   43   45   46   46   47   49   49 
LCS_GDT     R    61_A     R    61_A     15   17   45     10   12   14   15   16   16   20   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     A    62_A     A    62_A     15   17   45     10   12   14   15   16   16   18   22   27   31   33   38   41   43   45   46   46   47   49   49 
LCS_GDT     A    63_A     A    63_A     15   17   45     10   12   14   15   16   17   21   24   27   31   34   38   41   43   45   46   46   47   49   49 
LCS_GDT     E    64_A     E    64_A     15   17   45     10   12   14   15   16   16   18   19   21   25   30   34   40   43   45   46   46   47   49   49 
LCS_GDT     I    65_A     I    65_A     15   17   45     10   12   14   15   16   16   18   19   21   22   24   26   29   35   40   44   46   47   49   49 
LCS_GDT     F    66_A     F    66_A     15   17   45     10   12   14   15   16   16   18   19   21   27   29   33   38   41   43   46   46   47   49   49 
LCS_GDT     R    67_A     R    67_A     15   17   45     10   12   14   15   16   16   18   21   24   29   31   36   41   43   45   46   46   47   49   49 
LCS_GDT     D    68_A     D    68_A     15   17   33     10   12   14   15   16   16   18   19   21   22   24   26   28   28   29   32   37   39   46   49 
LCS_GDT     A    69_A     A    69_A     15   17   30     10   12   14   15   16   16   18   19   21   22   24   26   28   28   31   36   40   42   44   48 
LCS_GDT     L    70_A     L    70_A     15   17   30     10   12   14   15   16   16   18   19   21   22   24   26   31   36   40   44   45   46   49   49 
LCS_GDT     A    71_A     A    71_A     15   17   30      4   12   14   15   16   16   18   19   21   22   24   26   29   35   40   44   45   47   49   49 
LCS_GDT     R    72_A     R    72_A     15   17   30      3    8   14   15   16   16   18   19   21   22   24   26   28   28   29   29   30   35   37   40 
LCS_GDT     D    73_A     D    73_A     15   17   30      6   10   14   15   16   16   18   19   21   22   24   26   28   28   29   30   35   39   43   44 
LCS_GDT     I    74_A     I    74_A     15   17   30      9   12   14   15   16   16   18   19   21   22   24   26   28   28   29   29   30   35   39   42 
LCS_GDT     T    75_A     T    75_A     15   17   30      3    3   10   15   16   16   18   19   20   22   24   26   28   28   29   29   30   35   39   39 
LCS_GDT     T    76_A     T    76_A      9   17   30      5    9    9   11   13   16   18   19   21   22   24   26   28   28   29   29   30   35   39   39 
LCS_GDT     P    77_A     P    77_A      9   10   30      5    9    9    9   13   16   18   19   21   22   24   26   28   28   29   29   30   32   36   36 
LCS_GDT     E    78_A     E    78_A      9   10   30      5    9    9   11   13   16   18   19   21   22   24   26   28   28   29   29   30   33   36   36 
LCS_GDT     A    79_A     A    79_A      9   10   30      5    9    9    9    9    9   14   18   21   22   24   26   28   28   29   29   30   35   39   41 
LCS_GDT     F    80_A     F    80_A      9   10   30      5    9    9    9    9    9   11   18   20   22   24   26   28   28   29   29   32   36   39   42 
LCS_GDT     N    81_A     N    81_A      9   10   30      4    9    9    9    9   12   15   18   21   22   24   26   28   28   29   29   30   35   39   41 
LCS_GDT     A    82_A     A    82_A      9   10   30      4    9    9    9    9   10   14   18   20   22   24   25   26   28   29   29   30   35   39   41 
LCS_GDT     Y    83_A     Y    83_A      9   10   30      4    9    9    9    9    9   10   10   13   14   15   17   21   24   28   29   34   38   41   42 
LCS_GDT     L    84_A     L    84_A      9   10   29      4    9    9    9    9    9   10   12   13   14   16   17   21   24   26   29   32   36   41   42 
LCS_AVERAGE  LCS_A:  13.69  (   6.02    8.91   26.14 )

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     12     14     15     18     19     21     24     27     31     34     38     41     43     45     46     46     47     49     49 
GDT PERCENT_AT   6.37   7.64   8.92   9.55  11.46  12.10  13.38  15.29  17.20  19.75  21.66  24.20  26.11  27.39  28.66  29.30  29.30  29.94  31.21  31.21
GDT RMS_LOCAL    0.31   0.54   0.79   1.00   1.72   1.84   2.11   2.72   3.03   3.52   3.72   4.26   4.54   4.59   4.79   4.93   4.93   5.10   5.59   5.59
GDT RMS_ALL_AT  19.91  19.73  19.61  19.65  17.92  17.70  17.96  16.09  15.72  15.06  15.41  14.09  13.67  14.13  14.00  13.72  13.72  13.54  12.84  12.84

# Checking swapping
#   possible swapping detected:  E    28_A      E    28_A
#   possible swapping detected:  D    37_A      D    37_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  D    73_A      D    73_A
#   possible swapping detected:  E    78_A      E    78_A
#   possible swapping detected:  F    80_A      F    80_A
#   possible swapping detected:  Y    83_A      Y    83_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    V    21_A      V    21_A    11.629     0    0.037   0.055    14.825    0.000    0.000
LGA    H    22_A      H    22_A    10.992     0    0.022   1.001    16.617    0.714    0.286
LGA    R    23_A      R    23_A     7.550     0    0.045   1.327    16.205    6.548    3.463
LGA    L    24_A      L    24_A     9.990     0    0.219   0.218    12.053    0.833    0.417
LGA    A    25_A      A    25_A    11.052     0    0.318   0.308    12.220    0.119    0.095
LGA    G    26_A      G    26_A     7.015     0    0.062   0.062     7.911    8.571    8.571
LGA    I    27_A      I    27_A     7.451     0    0.162   1.104    10.436   16.667    8.929
LGA    E    28_A      E    28_A     5.062     0    0.040   1.137     8.580   26.310   17.460
LGA    P    29_A      P    29_A     3.871     0    0.632   0.693     6.398   32.262   36.122
LGA    D    30_A      D    30_A     3.954     0    0.567   1.252     4.763   40.476   57.976
LGA    P    31_A      P    31_A     7.890     0    0.060   0.116    10.798   10.952    6.939
LGA    R    32_A      R    32_A     6.839     0    0.111   1.007    14.019   19.524    7.532
LGA    F    33_A      F    33_A     3.139     0    0.053   1.438    10.673   57.381   26.320
LGA    E    34_A      E    34_A     4.947     0    0.122   0.192    13.900   33.452   16.032
LGA    I    35_A      I    35_A     7.473     0    0.030   0.072    13.176   15.357    7.738
LGA    L    36_A      L    36_A     5.228     0    0.258   0.245    11.258   36.429   20.238
LGA    D    37_A      D    37_A     3.792     0    0.449   1.000     8.744   45.238   30.060
LGA    K    38_A      K    38_A     6.992     0    0.192   0.260    14.749   13.810    6.508
LGA    Y    39_A      Y    39_A     6.520     0    0.170   1.250     7.575   18.571   14.365
LGA    I    40_A      I    40_A     2.572     0    0.323   0.636     3.296   65.357   61.310
LGA    F    41_A      F    41_A     0.904     0    0.042   1.143     6.431   83.690   57.879
LGA    R    42_A      R    42_A     1.662     0    0.055   1.250     3.635   77.143   70.563
LGA    Q    43_A      Q    43_A     1.202     0    0.023   0.234     2.600   85.952   77.884
LGA    I    44_A      I    44_A     0.695     0    0.062   0.094     1.697   83.810   86.012
LGA    V    45_A      V    45_A     2.515     0    0.055   1.148     4.278   59.286   54.490
LGA    A    46_A      A    46_A     3.005     0    0.052   0.060     3.623   53.690   51.619
LGA    D    47_A      D    47_A     3.262     0    0.018   0.186     4.934   53.571   45.417
LGA    N    48_A      N    48_A     2.350     0    0.043   0.234     3.286   64.762   59.167
LGA    P    49_A      P    49_A     2.809     0    0.148   0.173     3.655   60.952   55.374
LGA    E    50_A      E    50_A     2.191     0    0.188   1.153     3.090   66.786   63.175
LGA    E    51_A      E    51_A     2.032     0    0.169   1.213     3.610   68.810   63.386
LGA    R    52_A      R    52_A     2.643     0    0.040   1.294    11.184   65.000   31.515
LGA    E    53_A      E    53_A     1.416     0    0.040   0.253     4.189   77.143   62.222
LGA    K    54_A      K    54_A     1.613     0    0.025   1.549     9.554   71.310   48.624
LGA    I    55_A      I    55_A     2.871     0    0.019   0.154     4.514   57.619   49.048
LGA    R    56_A      R    56_A     2.046     0    0.048   0.305     4.590   57.500   60.346
LGA    L    57_A      L    57_A     3.814     0    0.123   1.058     7.188   39.524   33.631
LGA    D    58_A      D    58_A     6.132     0    0.122   0.377     8.265   19.762   13.512
LGA    Y    59_A      Y    59_A     6.276     0    0.060   0.249    12.232   22.738    9.484
LGA    G    60_A      G    60_A     2.741     0    0.427   0.427     4.552   49.167   49.167
LGA    R    61_A      R    61_A     3.956     0    0.322   1.408    11.450   37.738   20.996
LGA    A    62_A      A    62_A     8.127     0    0.056   0.057     9.553    7.381    6.190
LGA    A    63_A      A    63_A     5.424     0    0.110   0.110     6.007   22.738   26.857
LGA    E    64_A      E    64_A     7.258     0    0.048   0.720    10.798    8.214    4.868
LGA    I    65_A      I    65_A    12.632     0    0.026   0.093    15.900    0.000    0.000
LGA    F    66_A      F    66_A    12.980     0    0.031   1.648    17.763    0.000    0.000
LGA    R    67_A      R    67_A    10.107     0    0.025   1.393    13.539    0.000    1.126
LGA    D    68_A      D    68_A    15.840     0    0.021   0.151    19.283    0.000    0.000
LGA    A    69_A      A    69_A    19.269     0    0.412   0.405    21.521    0.000    0.000
LGA    L    70_A      L    70_A    17.951     0    0.077   1.382    19.259    0.000    0.000
LGA    A    71_A      A    71_A    17.259     0    0.029   0.026    20.138    0.000    0.000
LGA    R    72_A      R    72_A    22.450     0    0.305   1.158    30.280    0.000    0.000
LGA    D    73_A      D    73_A    24.284     0    0.315   1.062    28.115    0.000    0.000
LGA    I    74_A      I    74_A    27.101     0    0.532   0.742    27.792    0.000    0.000
LGA    T    75_A      T    75_A    29.682     0    0.684   0.606    31.748    0.000    0.000
LGA    T    76_A      T    76_A    33.248     0    0.486   1.404    36.032    0.000    0.000
LGA    P    77_A      P    77_A    36.375     0    0.141   0.438    38.259    0.000    0.000
LGA    E    78_A      E    78_A    38.255     0    0.024   1.134    40.084    0.000    0.000
LGA    A    79_A      A    79_A    33.907     0    0.111   0.105    35.334    0.000    0.000
LGA    F    80_A      F    80_A    32.868     0    0.055   1.638    34.106    0.000    0.000
LGA    N    81_A      N    81_A    36.461     0    0.148   0.198    39.916    0.000    0.000
LGA    A    82_A      A    82_A    35.017     0    0.066   0.067    35.465    0.000    0.000
LGA    Y    83_A      Y    83_A    31.674     0    0.085   0.334    32.916    0.000    0.000
LGA    L    84_A      L    84_A    33.544     0    0.623   0.509    36.351    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     532    532  100.00               157
SUMMARY(RMSD_GDC):     9.539          9.359                 10.732           11.101    9.127

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64  157    4.0     24    2.72    15.446    14.080     0.852

LGA_LOCAL      RMSD:   2.716  Number of atoms:   24  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  16.087  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   9.539  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.131917 * X  +   0.554896 * Y  +   0.821394 * Z  +   6.929252
  Y_new =  -0.989167 * X  +  -0.127523 * Y  +  -0.072713 * Z  + 183.741272
  Z_new =   0.064398 * X  +  -0.822088 * Y  +   0.565707 * Z  +  10.960225 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.703376 -0.064443 -0.968078   [DEG:  -97.5962   -3.6923  -55.4668 ]
ZXZ:  1.482503  0.969506  3.063417   [DEG:   84.9412   55.5486  175.5209 ]
 
# END of job
