
#######################################################
#                                                     #
#                        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 (  525),  selected   64 , name one
# Molecule2: number of CA atoms  285 ( 2384),  selected   64 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51     224_B - 274_B       5.00     9.28
  LONGEST_CONTINUOUS_SEGMENT:    51     225_B - 275_B       4.71     9.48
  LCS_AVERAGE:     16.51

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37     238_B - 274_B       1.99    12.11
  LONGEST_CONTINUOUS_SEGMENT:    37     239_B - 275_B       1.48    12.52
  LCS_AVERAGE:      9.88

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31     243_B - 273_B       0.98    12.98
  LCS_AVERAGE:      7.70

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     E   212_B     E   212_B     16   19   30     10   12   15   16   17   18   18   19   20   22   24   24   24   26   27   27   29   30   33   35 
LCS_GDT     E   213_B     E   213_B     16   19   30     10   12   15   16   17   18   18   19   21   23   24   24   24   26   27   28   31   35   38   39 
LCS_GDT     L   214_B     L   214_B     16   19   30     10   12   15   16   17   18   18   19   21   23   24   24   24   26   27   29   38   42   47   50 
LCS_GDT     R   215_B     R   215_B     16   19   30     10   12   15   16   17   18   18   19   20   23   24   24   24   26   27   28   31   35   40   45 
LCS_GDT     Q   216_B     Q   216_B     16   19   30     10   12   15   16   17   18   18   19   21   23   24   24   24   26   27   28   31   35   38   39 
LCS_GDT     M   217_B     M   217_B     16   19   30     10   12   15   16   17   18   18   19   21   23   24   24   24   26   27   31   38   42   47   55 
LCS_GDT     R   218_B     R   218_B     16   19   30     10   12   15   16   17   18   18   19   21   23   24   24   24   26   30   37   46   52   54   56 
LCS_GDT     T   219_B     T   219_B     16   19   30     10   12   15   16   17   18   18   19   21   23   24   24   24   26   27   29   34   40   43   49 
LCS_GDT     A   220_B     A   220_B     16   19   30     10   12   15   16   17   18   18   19   21   23   24   24   24   26   27   29   34   38   42   48 
LCS_GDT     L   221_B     L   221_B     16   19   30     10   12   15   16   17   18   18   19   21   23   24   24   24   27   31   37   41   47   53   56 
LCS_GDT     V   222_B     V   222_B     16   19   30      4   12   15   16   17   18   18   19   21   23   24   24   24   29   37   44   50   52   54   56 
LCS_GDT     G   223_B     G   223_B     16   19   30      8   12   15   16   17   18   18   19   21   23   24   24   24   26   28   37   43   47   54   56 
LCS_GDT     A   224_B     A   224_B     16   19   51      3    8   12   16   17   18   18   19   21   23   24   24   24   26   35   44   50   52   54   56 
LCS_GDT     E   225_B     E   225_B     16   19   51      4   12   15   16   17   18   18   19   21   23   24   24   31   41   46   48   50   52   54   56 
LCS_GDT     A   226_B     A   226_B     16   19   51      6   12   15   16   17   18   18   19   21   23   24   34   43   44   46   48   50   52   54   56 
LCS_GDT     T   227_B     T   227_B     16   19   51      4   12   15   16   17   18   18   19   21   23   24   24   31   41   46   48   50   52   54   56 
LCS_GDT     Q   228_B     Q   228_B     14   19   51      3   10   15   16   17   18   18   19   21   23   24   24   25   36   46   48   50   52   54   56 
LCS_GDT     R   229_B     R   229_B      4   19   51      3    4    4    6   16   18   18   19   21   39   41   42   43   45   47   48   50   52   54   56 
LCS_GDT     L   230_B     L   230_B      4   19   51      3    4    4    5    8   18   32   37   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     E   231_B     E   231_B      4    6   51      3    4    4    4    7    9   11   17   39   40   42   43   44   45   47   47   48   51   52   56 
LCS_GDT     T   232_B     T   232_B      4    5   51      3    4    4    4    5    7    9   17   38   40   41   43   44   45   47   47   49   51   54   56 
LCS_GDT     L   233_B     L   233_B      4    5   51      3    5    5    5    5   10   16   37   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     D   234_B     D   234_B      4    5   51      3    5    5    5    5   10   19   35   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     I   235_B     I   235_B      4    4   51      3    5    5    5    5   29   36   37   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     Q   236_B     Q   236_B      4    5   51      3    7   23   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     R   237_B     R   237_B      4    5   51      3    3    4    5    5    8   11   12   19   28   34   41   43   45   47   48   49   52   54   56 
LCS_GDT     N   238_B     N   238_B      4   37   51      3    3    4    5    5    9   11   15   19   28   32   41   43   45   47   48   50   52   54   56 
LCS_GDT     A   239_B     A   239_B      4   37   51      3    5   20   25   26   29   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     W   240_B     W   240_B     22   37   51      9   20   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     Q   241_B     Q   241_B     22   37   51      9   20   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     Q   242_B     Q   242_B     26   37   51      9   20   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     R   243_B     R   243_B     31   37   51      4   20   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     V   244_B     V   244_B     31   37   51      9   20   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     T   245_B     T   245_B     31   37   51      9   23   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     G   246_B     G   246_B     31   37   51      9   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     Y   247_B     Y   247_B     31   37   51      9   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     L   248_B     L   248_B     31   37   51      9   23   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     N   249_B     N   249_B     31   37   51     12   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     Q   250_B     Q   250_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     R   251_B     R   251_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     D   252_B     D   252_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     E   253_B     E   253_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     V   254_B     V   254_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     L   255_B     L   255_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     H   256_B     H   256_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     S   257_B     S   257_B     31   37   51      6   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     N   258_B     N   258_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     M   259_B     M   259_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     S   260_B     S   260_B     31   37   51     13   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     D   261_B     D   261_B     31   37   51     13   24   28   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     S   262_B     S   262_B     31   37   51     13   21   27   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     A   263_B     A   263_B     31   37   51     13   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     K   264_B     K   264_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     K   265_B     K   265_B     31   37   51     13   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     Q   266_B     Q   266_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     A   267_B     A   267_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     I   268_B     I   268_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     Q   269_B     Q   269_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     Q   270_B     Q   270_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     L   271_B     L   271_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     R   272_B     R   272_B     31   37   51     15   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     Q   273_B     Q   273_B     31   37   51      9   25   30   33   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     Q   274_B     Q   274_B     30   37   51      3    5    9   29   35   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_GDT     Q   275_B     Q   275_B     30   37   51      3    3   25   29   32   36   37   38   39   40   42   43   44   45   47   48   50   52   54   56 
LCS_AVERAGE  LCS_A:  11.37  (   7.70    9.88   16.51 )

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     15     25     30     33     35     36     37     38     39     40     42     43     44     45     47     48     50     52     54     56 
GDT PERCENT_AT   5.26   8.77  10.53  11.58  12.28  12.63  12.98  13.33  13.68  14.04  14.74  15.09  15.44  15.79  16.49  16.84  17.54  18.25  18.95  19.65
GDT RMS_LOCAL    0.35   0.68   1.00   1.10   1.23   1.33   1.44   1.58   1.73   1.92   2.46   2.51   2.73   2.98   3.43   4.35   5.21   5.55   5.88   6.23
GDT RMS_ALL_AT  14.29  13.64  12.15  12.17  12.34  12.49  12.15  12.21  12.18  11.91  11.20  11.24  10.97  10.86  10.56   9.47   8.77   8.58   8.44   8.28

# Checking swapping
#   possible swapping detected:  E   225_B      E   225_B
#   possible swapping detected:  E   231_B      E   231_B
#   possible swapping detected:  Y   247_B      Y   247_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E   212_B      E   212_B    26.403     0    0.072   0.919    29.814    0.000    0.000
LGA    E   213_B      E   213_B    26.272     0    0.055   1.040    27.573    0.000    0.000
LGA    L   214_B      L   214_B    21.495     0    0.029   1.365    23.052    0.000    0.000
LGA    R   215_B      R   215_B    22.540     0    0.025   1.144    28.465    0.000    0.000
LGA    Q   216_B      Q   216_B    27.002     0    0.037   0.185    32.156    0.000    0.000
LGA    M   217_B      M   217_B    24.977     0    0.036   1.129    25.554    0.000    0.000
LGA    R   218_B      R   218_B    21.754     0    0.032   1.050    23.192    0.000    0.000
LGA    T   219_B      T   219_B    24.780     0    0.050   0.056    26.754    0.000    0.000
LGA    A   220_B      A   220_B    28.318     0    0.063   0.062    29.205    0.000    0.000
LGA    L   221_B      L   221_B    26.274     0    0.065   1.417    28.293    0.000    0.000
LGA    V   222_B      V   222_B    22.802     0    0.077   1.024    23.874    0.000    0.000
LGA    G   223_B      G   223_B    23.445     0    0.047   0.047    23.445    0.000    0.000
LGA    A   224_B      A   224_B    19.860     0    0.547   0.574    21.769    0.000    0.000
LGA    E   225_B      E   225_B    17.109     0    0.139   1.277    19.003    0.000    0.000
LGA    A   226_B      A   226_B    16.221     0    0.240   0.239    17.278    0.000    0.000
LGA    T   227_B      T   227_B    16.692     0    0.137   1.107    20.035    0.000    0.000
LGA    Q   228_B      Q   228_B    15.403     0    0.264   0.502    22.676    0.000    0.000
LGA    R   229_B      R   229_B    12.104     0    0.099   1.296    22.965    0.357    0.130
LGA    L   230_B      L   230_B     9.068     0    0.512   1.343    11.285    5.357    2.738
LGA    E   231_B      E   231_B     4.855     0    0.120   1.057     8.934   34.881   19.841
LGA    T   232_B      T   232_B     5.834     0    0.131   1.055     7.956   21.429   15.306
LGA    L   233_B      L   233_B     8.241     0    0.531   0.976    11.047   12.381    6.369
LGA    D   234_B      D   234_B     7.751     0    0.258   0.277    11.015    9.643    5.238
LGA    I   235_B      I   235_B     5.777     0    0.524   0.624     9.969   29.762   18.036
LGA    Q   236_B      Q   236_B     3.397     0    0.556   0.466     6.832   38.929   36.772
LGA    R   237_B      R   237_B     9.443     0    0.447   0.457    17.074    2.976    1.082
LGA    N   238_B      N   238_B     9.149     0    0.385   0.447    12.873    3.690    1.845
LGA    A   239_B      A   239_B     4.011     0    0.438   0.454     5.412   44.524   43.048
LGA    W   240_B      W   240_B     1.986     0    0.372   0.505    10.167   70.952   27.687
LGA    Q   241_B      Q   241_B     1.910     0    0.108   0.959     2.485   70.833   71.111
LGA    Q   242_B      Q   242_B     1.690     0    0.054   1.415     5.384   72.857   58.677
LGA    R   243_B      R   243_B     1.499     0    0.082   1.388     8.063   81.548   55.065
LGA    V   244_B      V   244_B     1.433     0    0.095   0.101     2.370   81.429   74.286
LGA    T   245_B      T   245_B     0.374     0    0.094   0.125     1.205   97.619   93.265
LGA    G   246_B      G   246_B     0.167     0    0.137   0.137     0.420  100.000  100.000
LGA    Y   247_B      Y   247_B     0.499     0    0.023   0.220     3.004   95.238   77.937
LGA    L   248_B      L   248_B     1.106     0    0.099   0.094     1.888   83.690   79.345
LGA    N   249_B      N   249_B     0.924     0    0.030   0.169     1.021   88.214   89.345
LGA    Q   250_B      Q   250_B     0.891     0    0.081   0.931     3.598   88.214   78.519
LGA    R   251_B      R   251_B     0.905     0    0.050   0.836     4.067   90.476   70.693
LGA    D   252_B      D   252_B     1.103     0    0.070   0.139     1.265   81.429   81.429
LGA    E   253_B      E   253_B     1.045     0    0.044   0.098     1.566   85.952   82.487
LGA    V   254_B      V   254_B     0.730     0    0.045   0.049     0.792   92.857   91.837
LGA    L   255_B      L   255_B     0.700     0    0.017   0.047     1.096   90.476   89.345
LGA    H   256_B      H   256_B     0.840     0    0.295   0.238     1.763   86.071   80.714
LGA    S   257_B      S   257_B     0.906     0    0.195   0.627     2.527   86.071   81.984
LGA    N   258_B      N   258_B     0.503     0    0.252   1.190     5.288   97.619   73.929
LGA    M   259_B      M   259_B     0.775     0    0.163   0.721     1.746   90.476   84.940
LGA    S   260_B      S   260_B     1.504     0    0.044   0.095     1.865   81.548   78.651
LGA    D   261_B      D   261_B     1.923     0    0.051   0.259     2.360   72.857   71.905
LGA    S   262_B      S   262_B     2.432     0    0.034   0.600     3.014   68.810   66.349
LGA    A   263_B      A   263_B     1.333     0    0.038   0.040     1.748   83.810   83.333
LGA    K   264_B      K   264_B     0.753     0    0.016   0.870     3.334   90.476   83.333
LGA    K   265_B      K   265_B     1.422     0    0.039   0.878     6.707   81.429   56.455
LGA    Q   266_B      Q   266_B     0.968     0    0.032   1.325     3.791   88.214   79.259
LGA    A   267_B      A   267_B     0.063     0    0.031   0.030     0.542   97.619   98.095
LGA    I   268_B      I   268_B     0.917     0    0.099   0.138     1.453   85.952   84.821
LGA    Q   269_B      Q   269_B     1.055     0    0.029   1.052     3.666   85.952   77.302
LGA    Q   270_B      Q   270_B     0.552     0    0.037   0.208     0.941   90.476   92.593
LGA    L   271_B      L   271_B     1.065     0    0.038   0.918     4.006   83.690   70.952
LGA    R   272_B      R   272_B     1.221     0    0.184   0.204     1.898   79.286   80.649
LGA    Q   273_B      Q   273_B     0.713     0    0.158   1.079     3.719   85.952   78.413
LGA    Q   274_B      Q   274_B     2.810     0    0.118   0.884     4.193   53.810   48.783
LGA    Q   275_B      Q   275_B     3.441     0    0.610   0.489     9.239   57.262   31.270

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     525    525  100.00               285
SUMMARY(RMSD_GDC):     7.882          7.740                  8.402           11.309   10.088

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64  285    4.0     38    1.58    12.632    12.193     2.266

LGA_LOCAL      RMSD:   1.577  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  12.210  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   7.882  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.385328 * X  +   0.759888 * Y  +  -0.523538 * Z  +  63.034882
  Y_new =   0.799297 * X  +   0.558366 * Y  +   0.222150 * Z  + -100.100159
  Z_new =   0.461136 * X  +  -0.332862 * Y  +  -0.822531 * Z  + -59.504391 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.020009 -0.479275 -2.757058   [DEG:  115.7380  -27.4604 -157.9678 ]
ZXZ: -1.972095  2.536643  2.196024   [DEG: -112.9927  145.3390  125.8229 ]
 
# END of job
