
#######################################################
#                                                     #
#                        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   97 (  681),  selected   64 , name one
# Molecule2: number of CA atoms   64 (  433),  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:    64      22_A - 85_A        3.12     3.12
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      60_A - 85_A        1.98     3.31
  LCS_AVERAGE:     35.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      69_A - 85_A        0.81     3.57
  LCS_AVERAGE:     21.04

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     A    22_A     A    22_A      4   18   64      3    4   14   25   35   42   50   54   58   59   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      9   18   64      3    5   15   25   35   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     14   18   64      3   13   22   32   39   47   51   57   58   60   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     15   18   64      3    4   15   29   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     15   18   64      8   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     15   18   64     11   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     15   18   64     11   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     15   18   64      8   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     15   18   64      6   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     15   18   64     10   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     15   18   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     15   18   64      6   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     15   18   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     15   18   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     15   18   64      3   25   29   31   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     15   18   64      3   16   29   31   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     15   18   64      3   14   29   31   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     15   18   64      3   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A      5   18   64      4    4    5    8   16   23   41   52   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A      5    7   64      4    4    5    6   15   23   30   51   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      5    7   64      4    4    5    5    8   12   18   29   33   49   56   61   63   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      5   24   64      4    4    5    9   18   23   32   51   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A      5   24   64      3    3    5    5   20   23   28   47   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A      4   24   64      3   10   14   29   38   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     14   24   64      3   12   16   17   20   38   49   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     14   24   64      3   12   16   17   20   23   42   51   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     14   24   64      3    7   11   29   38   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     15   24   64      5   12   16   17   34   43   50   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     15   24   64     10   12   16   17   20   41   49   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     15   24   64     10   12   16   17   30   41   50   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     15   24   64     10   12   22   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     15   24   64     10   12   20   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     15   24   64     10   12   16   23   36   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     15   24   64     10   12   16   17   36   46   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     15   24   64     10   12   21   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     15   24   64     10   12   22   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     15   24   64     10   12   16   17   27   43   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     15   24   64     10   12   16   17   20   37   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     15   26   64      5   12   16   17   20   38   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     15   26   64      3   12   19   29   38   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     15   26   64      5   19   27   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     15   26   64      3    5   21   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A      5   26   64      3   13   26   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A      5   26   64      3   10   21   29   35   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A      5   26   64      3    4    9   17   38   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A      3   26   64      0    3    3   16   19   26   49   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A      7   26   64      4    6    7   23   30   47   50   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     17   26   64      4    9   19   31   32   44   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     17   26   64      4   11   22   31   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     17   26   64      7   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     17   26   64     10   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     17   26   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     17   26   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     17   26   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     17   26   64     10   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     17   26   64     10   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     17   26   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     17   26   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     17   26   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     17   26   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     17   26   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     17   26   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     17   26   64     13   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     17   26   64      5   25   29   32   39   47   51   57   58   61   62   63   63   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  52.07  (  21.04   35.16  100.00 )

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     13     25     29     32     39     47     51     57     58     61     62     63     63     64     64     64     64     64     64     64 
GDT PERCENT_AT  20.31  39.06  45.31  50.00  60.94  73.44  79.69  89.06  90.62  95.31  96.88  98.44  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.59   0.73   1.22   1.48   1.83   2.09   2.36   2.40   2.91   2.86   2.95   2.95   3.12   3.12   3.12   3.12   3.12   3.12   3.12
GDT RMS_ALL_AT   3.84   3.72   3.84   3.35   3.39   3.34   3.33   3.27   3.28   3.13   3.13   3.13   3.13   3.12   3.12   3.12   3.12   3.12   3.12   3.12

# Checking swapping
#   possible swapping detected:  D    23_A      D    23_A
#   possible swapping detected:  D    25_A      D    25_A
#   possible swapping detected:  Y    30_A      Y    30_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     3.925     0    0.083   0.081     4.529   45.476   43.810
LGA    D    23_A      D    23_A     3.263     0    0.153   1.019     7.203   50.119   35.774
LGA    G    24_A      G    24_A     2.389     0    0.453   0.453     2.479   66.786   66.786
LGA    D    25_A      D    25_A     2.853     0    0.655   1.144     5.069   49.405   48.095
LGA    G    26_A      G    26_A     1.026     0    0.103   0.103     1.078   85.952   85.952
LGA    Q    27_A      Q    27_A     0.737     0    0.040   1.220     3.918   90.476   74.974
LGA    G    28_A      G    28_A     0.599     0    0.031   0.031     0.715   95.238   95.238
LGA    L    29_A      L    29_A     0.692     0    0.046   0.778     3.845   88.214   72.262
LGA    Y    30_A      Y    30_A     0.843     0    0.076   0.363     1.117   88.214   92.103
LGA    A    31_A      A    31_A     0.867     0    0.022   0.036     1.379   85.952   86.857
LGA    A    32_A      A    32_A     1.352     0    0.047   0.047     1.891   77.143   78.000
LGA    N    33_A      N    33_A     1.770     0    0.288   1.017     3.239   67.262   67.202
LGA    C    34_A      C    34_A     1.410     0    0.067   0.740     2.604   79.286   75.952
LGA    A    35_A      A    35_A     1.312     0    0.025   0.041     1.956   77.143   78.000
LGA    A    36_A      A    36_A     2.434     0    0.056   0.054     3.031   61.190   61.905
LGA    C    37_A      C    37_A     2.932     0    0.039   0.063     4.196   57.143   51.508
LGA    H    38_A      H    38_A     2.940     0    0.219   1.442     3.456   55.357   61.714
LGA    G    39_A      G    39_A     1.660     0    0.097   0.097     4.687   56.786   56.786
LGA    A    40_A      A    40_A     6.852     0    0.323   0.391     9.135   18.810   15.333
LGA    L    41_A      L    41_A     7.288     0    0.085   0.963     9.358    7.976    7.619
LGA    A    42_A      A    42_A    10.041     0    0.063   0.059    11.525    0.833    0.667
LGA    T    43_A      T    43_A     7.799     0    0.652   1.057    10.356   13.810    8.776
LGA    S    44_A      S    44_A     7.137     0    0.068   0.641    10.775   16.190   10.873
LGA    E    45_A      E    45_A     2.742     0    0.690   1.231     7.467   43.690   34.921
LGA    K    46_A      K    46_A     4.648     0    0.550   1.699     7.934   31.786   23.439
LGA    K    47_A      K    47_A     6.040     0    0.593   1.150    13.191   28.214   13.862
LGA    G    48_A      G    48_A     2.545     0    0.464   0.464     4.247   52.143   52.143
LGA    T    49_A      T    49_A     3.360     0    0.043   1.134     5.000   48.333   48.503
LGA    T    50_A      T    50_A     4.019     0    0.063   0.103     4.082   41.905   42.585
LGA    L    51_A      L    51_A     3.628     0    0.043   1.083     6.005   50.238   43.571
LGA    A    52_A      A    52_A     1.446     0    0.027   0.047     2.160   77.262   79.905
LGA    R    53_A      R    53_A     1.696     0    0.045   1.392     2.929   72.857   67.792
LGA    L    54_A      L    54_A     2.886     0    0.040   1.126     5.878   59.048   49.405
LGA    Q    55_A      Q    55_A     3.023     0    0.042   0.954     4.409   53.571   49.418
LGA    S    56_A      S    56_A     1.726     0    0.046   0.662     2.238   70.833   71.587
LGA    A    57_A      A    57_A     1.424     0    0.045   0.048     2.244   70.952   73.048
LGA    V    58_A      V    58_A     3.530     0    0.024   0.092     4.788   45.238   40.952
LGA    S    59_A      S    59_A     4.360     0    0.174   0.615     5.351   35.952   35.397
LGA    A    60_A      A    60_A     4.014     0    0.343   0.345     5.309   37.500   38.667
LGA    N    61_A      N    61_A     2.158     0    0.576   0.548     3.988   59.405   64.107
LGA    A    62_A      A    62_A     0.595     0    0.059   0.081     1.286   85.952   85.048
LGA    G    63_A      G    63_A     2.185     0    0.692   0.692     3.634   63.571   63.571
LGA    G    64_A      G    64_A     2.224     0    0.261   0.261     2.303   68.810   68.810
LGA    M    65_A      M    65_A     3.018     0    0.578   0.714     4.012   50.357   52.083
LGA    G    66_A      G    66_A     2.856     0    0.679   0.679     4.128   50.357   50.357
LGA    F    67_A      F    67_A     4.130     0    0.728   1.351     6.548   45.357   28.225
LGA    L    68_A      L    68_A     3.019     0    0.669   0.558     8.520   61.071   37.202
LGA    S    69_A      S    69_A     3.528     0    0.066   0.668     5.563   48.690   41.270
LGA    S    70_A      S    70_A     2.500     0    0.090   0.620     3.084   61.190   61.111
LGA    L    71_A      L    71_A     0.904     0    0.038   0.193     1.633   81.548   83.869
LGA    T    72_A      T    72_A     1.562     0    0.075   1.088     2.955   79.286   75.510
LGA    S    73_A      S    73_A     1.555     0    0.055   0.617     2.831   77.143   73.095
LGA    A    74_A      A    74_A     0.701     0    0.069   0.067     1.025   90.595   90.571
LGA    Q    75_A      Q    75_A     0.447     0    0.094   0.823     3.112   97.619   82.381
LGA    L    76_A      L    76_A     1.044     0    0.039   1.410     3.146   83.690   76.548
LGA    Q    77_A      Q    77_A     0.948     0    0.068   1.109     4.687   88.214   71.799
LGA    A    78_A      A    78_A     0.647     0    0.025   0.030     1.025   88.214   88.667
LGA    I    79_A      I    79_A     0.907     0    0.035   1.284     3.259   85.952   73.929
LGA    V    80_A      V    80_A     1.408     0    0.061   0.130     1.848   77.143   76.531
LGA    D    81_A      D    81_A     1.623     0    0.034   1.142     3.186   75.000   71.131
LGA    V    82_A      V    82_A     1.530     0    0.107   0.923     3.252   75.000   73.333
LGA    L    83_A      L    83_A     1.384     0    0.144   0.174     1.433   83.690   82.560
LGA    A    84_A      A    84_A     2.089     0    0.086   0.085     2.180   66.786   66.381
LGA    V    85_A      V    85_A     2.148     0    0.322   1.296     3.929   64.881   64.150

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     433    433  100.00                64
SUMMARY(RMSD_GDC):     3.117          3.071                  3.621           61.935   58.494

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     57    2.36    69.531    64.573     2.313

LGA_LOCAL      RMSD:   2.364  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.267  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.117  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.572682 * X  +   0.630068 * Y  +   0.524451 * Z  +  38.374477
  Y_new =   0.805422 * X  +  -0.313248 * Y  +  -0.503161 * Z  +  20.534609
  Z_new =  -0.152743 * X  +   0.710556 * Y  +  -0.686863 * Z  + -20.943642 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.952703  0.153343  2.339241   [DEG:   54.5859    8.7859  134.0286 ]
ZXZ:  0.806113  2.327960 -0.211740   [DEG:   46.1869  133.3823  -12.1318 ]
 
# END of job
