
#######################################################
#                                                     #
#                        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 (  519),  selected   65 , name one
# Molecule2: number of CA atoms  109 (  875),  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:    40      18_A - 57_A        4.95    11.44
  LCS_AVERAGE:     28.75

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30      18_A - 47_A        2.00    11.80
  LCS_AVERAGE:     16.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      18_A - 33_A        0.84    11.63
  LONGEST_CONTINUOUS_SEGMENT:    16      19_A - 34_A        0.99    11.64
  LCS_AVERAGE:      8.57

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     Y    18_A     Y    18_A     16   30   40      3   13   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     A    19_A     A    19_A     16   30   40      5   12   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     I    20_A     I    20_A     16   30   40      7   13   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     T    21_A     T    21_A     16   30   40      7   13   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     L    22_A     L    22_A     16   30   40      7   13   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     S    23_A     S    23_A     16   30   40      7   13   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     D    24_A     D    24_A     16   30   40      7   12   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     G    25_A     G    25_A     16   30   40      7   13   17   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     T    26_A     T    26_A     16   30   40      7   13   17   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     I    27_A     I    27_A     16   30   40      7   11   17   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     L    28_A     L    28_A     16   30   40      5   13   17   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     K    29_A     K    29_A     16   30   40      7   13   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     S    30_A     S    30_A     16   30   40      7   13   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     T    31_A     T    31_A     16   30   40      7   13   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     I    32_A     I    32_A     16   30   40      7   13   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     K    33_A     K    33_A     16   30   40      7   13   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     N    34_A     N    34_A     16   30   40      4   10   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     E    35_A     E    35_A     12   30   40      3   10   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     T    36_A     T    36_A     12   30   40      4   10   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     L    37_A     L    37_A     12   30   40      4   10   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     K    38_A     K    38_A     12   30   40      4   10   13   22   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     K    39_A     K    39_A     12   30   40      4   10   13   22   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     T    40_A     T    40_A     12   30   40      4   10   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     F    41_A     F    41_A     11   30   40      4    9   11   16   19   27   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     P    42_A     P    42_A     11   30   40      7    9   11   16   19   21   27   31   34   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     I    43_A     I    43_A     10   30   40      7    9   11   16   24   27   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     L    44_A     L    44_A     10   30   40      7   12   17   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     K    45_A     K    45_A     10   30   40      7    9   11   19   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     N    46_A     N    46_A     10   30   40      7    9   18   23   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     L    47_A     L    47_A     10   30   40      7   10   15   19   25   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     L    48_A     L    48_A     10   21   40      7    9   11   17   19   26   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     K    49_A     K    49_A     10   21   40      3    8   11   18   24   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     D    50_A     D    50_A      5   21   40      4   10   17   18   26   28   32   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     Q    51_A     Q    51_A      5   16   40      4    5    5    7    8   17   28   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     I    52_A     I    52_A      5    9   40      4    5    5    7    8    9    9   15   30   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     P    53_A     P    53_A      5    9   40      4    5    5    7    8    9    9   11   14   21   28   37   40   42   42   43   44   45   46   48 
LCS_GDT     T    54_A     T    54_A      5    9   40      3    5    5    7    8    9    9   11   11   12   15   18   20   24   28   36   41   45   46   48 
LCS_GDT     G    55_A     G    55_A      4    9   40      3    4    5    7    8    9    9   11   11   12   15   19   21   23   28   32   38   43   44   48 
LCS_GDT     S    56_A     S    56_A      4    9   40      3    4    5    7    8    9    9   11   12   17   26   34   40   42   42   43   44   45   46   48 
LCS_GDT     S    57_A     S    57_A      3    9   40      0    3    4    6    8    9    9   11   11   12   15   16   18   20   26   33   40   45   46   48 
LCS_GDT     F    58_A     F    58_A      4    6   17      0    4    4    4    5    8    9   11   11   12   14   16   16   18   19   25   26   31   35   39 
LCS_GDT     F    59_A     F    59_A      4    5   17      3    4    4    4    6    8    9   11   11   12   15   19   24   29   33   39   44   45   46   48 
LCS_GDT     K    60_A     K    60_A      5    5   17      3    4    5    5    6    7   10   12   12   16   17   20   23   24   25   33   36   40   43   44 
LCS_GDT     L    61_A     L    61_A      5    5   17      3    4    5    5    6    6   10   12   12   16   18   21   24   28   33   36   37   45   46   48 
LCS_GDT     P    62_A     P    62_A      5    5   16      2    4    5    5    6    7   10   12   13   16   18   20   22   24   30   35   37   42   46   48 
LCS_GDT     V    63_A     V    63_A      5    5   16      2    4    5    5    6    7   10   12   12   16   18   20   22   24   25   25   36   40   43   48 
LCS_GDT     V    64_A     V    64_A      6    7   18      4    4    6    6    6    9   10   12   13   16   20   26   33   40   42   43   44   45   46   48 
LCS_GDT     F    65_A     F    65_A      6    7   18      4    4    6    6    6    7    9   21   31   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     F    66_A     F    66_A      6    7   18      4    4    6    9   16   23   28   34   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     R    67_A     R    67_A      6    7   18      4    5   11   16   19   21   23   25   29   34   36   38   39   39   41   42   43   43   44   45 
LCS_GDT     V    68_A     V    68_A      6    7   18      3    4    6    6   13   19   20   23   23   25   26   27   28   39   39   41   41   42   43   44 
LCS_GDT     T    69_A     T    69_A      6    7   18      3    4    6    6    6    7    9    9   12   16   23   23   25   25   26   28   29   33   39   41 
LCS_GDT     D    70_A     D    70_A      3    7   18      3    3    3    4    6    7    9    9   12   16   18   21   23   24   25   25   26   27   28   30 
LCS_GDT     N    71_A     N    71_A      3    5   18      3    3    3    4    5    8   10   11   12   16   18   21   23   24   25   25   26   27   28   30 
LCS_GDT     V    72_A     V    72_A      7    8   18      3    6    8    8    9   10   10   11   12   16   18   21   23   24   25   25   26   27   28   30 
LCS_GDT     I    73_A     I    73_A      7    8   18      5    6    8    8    9   10   10   11   12   16   17   21   23   24   25   26   29   32   34   37 
LCS_GDT     V    74_A     V    74_A      7    8   18      5    6    8    8    9   19   22   23   23   25   27   27   37   39   40   41   43   43   43   45 
LCS_GDT     I    75_A     I    75_A      7    8   18      5    6    8   11   19   21   24   30   34   37   38   39   40   42   42   43   43   45   46   48 
LCS_GDT     L    76_A     L    76_A      7    8   18      5    6    8    8   11   23   28   32   35   37   38   39   40   42   42   43   44   45   46   48 
LCS_GDT     L    77_A     L    77_A      7    8   18      5    6    8    8    9   10   10   16   23   25   31   37   40   42   42   43   44   45   46   48 
LCS_GDT     T    78_A     T    78_A      7    8   18      3    6    8    8    9   10   10   11   14   18   25   28   31   33   35   39   44   45   46   48 
LCS_GDT     N    79_A     N    79_A      4    8   18      3    4    5    6    9   10   10   11   12   16   20   22   23   24   25   25   26   35   37   38 
LCS_GDT     E    80_A     E    80_A      4    6   18      3    4    5    6    6    8    9   11   12   16   20   22   23   24   25   25   26   34   37   38 
LCS_GDT     K    81_A     K    81_A      4    6   18      3    4    5    6    6    8    9   11   12   16   20   22   22   23   24   25   26   27   28   30 
LCS_GDT     E    82_A     E    82_A      4    6   13      0    4    5    6    6    8    9   11   11   12   20   22   22   22   24   25   26   26   26   27 
LCS_AVERAGE  LCS_A:  18.09  (   8.57   16.94   28.75 )

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      7     13     18     23     26     28     32     34     35     37     38     39     40     42     42     43     44     45     46     48 
GDT PERCENT_AT   6.42  11.93  16.51  21.10  23.85  25.69  29.36  31.19  32.11  33.94  34.86  35.78  36.70  38.53  38.53  39.45  40.37  41.28  42.20  44.04
GDT RMS_LOCAL    0.19   0.68   1.10   1.32   1.55   1.73   2.06   2.30   2.44   2.69   2.97   3.06   3.36   3.89   3.89   4.24   4.92   5.18   5.22   5.85
GDT RMS_ALL_AT  14.85  11.68  11.71  11.70  11.75  11.89  11.95  11.88  11.79  11.81  11.67  11.68  11.62  11.48  11.48  11.40  11.30  11.28  11.27  11.29

# Checking swapping
#   possible swapping detected:  F    65_A      F    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y    18_A      Y    18_A     1.473     0    0.122   1.463     6.100   85.952   65.397
LGA    A    19_A      A    19_A     1.126     0    0.248   0.297     1.822   83.929   81.714
LGA    I    20_A      I    20_A     1.111     0    0.063   0.127     1.617   81.429   80.357
LGA    T    21_A      T    21_A     1.209     0    0.016   1.010     2.799   81.429   75.578
LGA    L    22_A      L    22_A     1.334     0    0.024   0.076     2.306   81.429   76.131
LGA    S    23_A      S    23_A     1.285     0    0.040   0.099     1.837   81.429   78.571
LGA    D    24_A      D    24_A     1.196     0    0.109   1.219     3.616   81.429   76.726
LGA    G    25_A      G    25_A     1.530     0    0.239   0.239     2.602   71.071   71.071
LGA    T    26_A      T    26_A     2.260     0    0.062   0.070     3.141   68.810   62.789
LGA    I    27_A      I    27_A     2.318     0    0.074   1.113     3.485   57.262   55.417
LGA    L    28_A      L    28_A     2.663     0    0.068   0.166     3.395   57.262   55.417
LGA    K    29_A      K    29_A     1.307     0    0.063   1.197     6.537   81.548   60.265
LGA    S    30_A      S    30_A     0.650     0    0.015   0.606     2.307   88.214   84.683
LGA    T    31_A      T    31_A     1.201     0    0.061   0.068     1.875   81.548   81.497
LGA    I    32_A      I    32_A     1.202     0    0.167   0.237     1.885   79.286   84.881
LGA    K    33_A      K    33_A     1.972     0    0.050   1.158     7.356   79.405   56.032
LGA    N    34_A      N    34_A     1.699     0    0.099   0.192     3.888   75.000   61.726
LGA    E    35_A      E    35_A     0.766     0    0.055   1.374     7.149   81.786   57.725
LGA    T    36_A      T    36_A     1.286     0    0.019   0.034     1.751   79.286   78.980
LGA    L    37_A      L    37_A     1.451     0    0.017   1.386     4.009   75.119   67.619
LGA    K    38_A      K    38_A     2.081     0    0.102   0.822     6.502   64.881   48.571
LGA    K    39_A      K    39_A     2.240     0    0.243   0.833     4.956   61.071   54.021
LGA    T    40_A      T    40_A     1.533     0    0.157   0.250     2.134   70.833   79.320
LGA    F    41_A      F    41_A     3.685     0    0.109   0.122     5.006   41.905   37.965
LGA    P    42_A      P    42_A     5.356     0    0.022   0.273     7.333   32.976   25.238
LGA    I    43_A      I    43_A     3.793     0    0.012   0.169     6.145   54.048   40.417
LGA    L    44_A      L    44_A     1.082     0    0.033   1.398     6.165   79.286   58.810
LGA    K    45_A      K    45_A     2.609     0    0.011   0.037     7.121   64.881   43.069
LGA    N    46_A      N    46_A     2.268     0    0.043   0.833     8.112   68.810   44.226
LGA    L    47_A      L    47_A     2.783     0    0.015   0.050     5.463   59.286   46.250
LGA    L    48_A      L    48_A     3.218     0    0.015   0.072     5.146   52.024   44.762
LGA    K    49_A      K    49_A     3.435     0    0.414   0.782     6.713   55.476   43.016
LGA    D    50_A      D    50_A     3.148     0    0.627   0.534     5.707   51.905   41.131
LGA    Q    51_A      Q    51_A     4.124     0    0.240   0.816     6.028   32.024   37.831
LGA    I    52_A      I    52_A     7.138     0    0.022   1.085    10.483    8.690    7.202
LGA    P    53_A      P    53_A    10.185     0    0.626   0.561    13.060    0.714    1.020
LGA    T    54_A      T    54_A    14.513     0    0.644   0.979    17.395    0.000    0.000
LGA    G    55_A      G    55_A    16.127     0    0.034   0.034    16.127    0.000    0.000
LGA    S    56_A      S    56_A    11.284     0    0.659   0.862    12.861    0.000    0.317
LGA    S    57_A      S    57_A    15.685     0    0.552   0.917    18.359    0.000    0.000
LGA    F    58_A      F    58_A    17.294     0    0.648   0.945    24.828    0.000    0.000
LGA    F    59_A      F    59_A    16.339     0    0.438   0.393    16.774    0.000    0.000
LGA    K    60_A      K    60_A    19.880     0    0.480   1.110    29.781    0.000    0.000
LGA    L    61_A      L    61_A    19.665     0    0.637   0.530    19.852    0.000    0.000
LGA    P    62_A      P    62_A    18.580     0    0.154   0.412    22.156    0.000    0.000
LGA    V    63_A      V    63_A    17.158     0    0.581   0.635    20.304    0.000    0.000
LGA    V    64_A      V    64_A    13.723     0    0.591   0.704    17.416    0.000    0.000
LGA    F    65_A      F    65_A     7.613     0    0.036   0.202    15.075   12.619    5.022
LGA    F    66_A      F    66_A     4.822     0    0.135   0.246    12.810   27.619   11.948
LGA    R    67_A      R    67_A     8.135     0    0.107   0.919    16.180    5.476    2.381
LGA    V    68_A      V    68_A    13.677     0    0.626   1.368    16.576    0.000    0.000
LGA    T    69_A      T    69_A    19.465     0    0.129   1.134    21.703    0.000    0.000
LGA    D    70_A      D    70_A    24.011     0    0.566   0.645    27.921    0.000    0.000
LGA    N    71_A      N    71_A    27.530     0    0.333   1.252    33.109    0.000    0.000
LGA    V    72_A      V    72_A    23.940     0    0.607   0.600    26.875    0.000    0.000
LGA    I    73_A      I    73_A    16.940     0    0.168   1.065    19.392    0.000    0.000
LGA    V    74_A      V    74_A    11.189     0    0.079   1.126    13.026    2.500    1.429
LGA    I    75_A      I    75_A     5.689     0    0.153   0.182     8.863   15.476   15.774
LGA    L    76_A      L    76_A     5.587     0    0.090   0.123     6.703   24.881   28.929
LGA    L    77_A      L    77_A    10.800     0    0.056   0.079    14.396    0.357    0.536
LGA    T    78_A      T    78_A    15.513     0    0.147   1.020    17.635    0.000    0.000
LGA    N    79_A      N    79_A    21.698     0    0.553   1.257    27.516    0.000    0.000
LGA    E    80_A      E    80_A    23.067     0    0.044   1.425    24.248    0.000    0.000
LGA    K    81_A      K    81_A    27.060     0    0.525   1.420    36.805    0.000    0.000
LGA    E    82_A      E    82_A    25.147     0    0.090   1.260    29.055    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       65     260    260  100.00     519    519  100.00               109
SUMMARY(RMSD_GDC):    11.140         11.064                 11.992           22.389   19.557

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65  109    4.0     34    2.30    25.917    24.776     1.417

LGA_LOCAL      RMSD:   2.300  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.885  Number of assigned atoms:   65 
Std_ASGN_ATOMS RMSD:  11.140  Standard rmsd on all 65 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.608326 * X  +   0.689800 * Y  +   0.392576 * Z  +   7.089102
  Y_new =   0.454510 * X  +  -0.708253 * Y  +   0.540184 * Z  +  -1.814319
  Z_new =   0.650662 * X  +  -0.150178 * Y  +  -0.744369 * Z  +   7.497651 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.641674 -0.708456 -2.942513   [DEG:   36.7652  -40.5915 -168.5936 ]
ZXZ:  2.513141  2.410386  1.797632   [DEG:  143.9924  138.1049  102.9967 ]
 
# END of job
