
#######################################################
#                                                     #
#                        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   63 (  525),  selected   63 , name one
# Molecule2: number of CA atoms  108 (  908),  selected   63 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       8_C - 39_C        4.96    17.83
  LCS_AVERAGE:     26.10

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22       8_C - 29_C        1.90    20.10
  LCS_AVERAGE:     13.90

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20       8_C - 27_C        0.75    21.22
  LCS_AVERAGE:     11.33

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     L     8_C     L     8_C     20   22   32     15   19   19   20   21   22   22   23   24   25   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     K     9_C     K     9_C     20   22   32     15   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     L    10_C     L    10_C     20   22   32     15   19   19   20   21   22   22   23   24   25   25   27   27   29   31   37   40   42   46   48 
LCS_GDT     L    11_C     L    11_C     20   22   32     15   19   19   20   21   22   22   23   24   25   25   27   31   35   38   42   45   46   47   48 
LCS_GDT     D    12_C     D    12_C     20   22   32     15   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     T    13_C     T    13_C     20   22   32     15   19   19   20   21   22   22   23   25   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     L    14_C     L    14_C     20   22   32     15   19   19   20   21   22   22   23   24   25   25   30   31   35   38   42   45   46   47   48 
LCS_GDT     L    15_C     L    15_C     20   22   32     15   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     T    16_C     T    16_C     20   22   32     15   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     M    17_C     M    17_C     20   22   32     15   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     V    18_C     V    18_C     20   22   32     15   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     E    19_C     E    19_C     20   22   32     15   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     W    20_C     W    20_C     20   22   32     15   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     V    21_C     V    21_C     20   22   32     14   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     K    22_C     K    22_C     20   22   32     15   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     E    23_C     E    23_C     20   22   32     15   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     L    24_C     L    24_C     20   22   32     14   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     L    25_C     L    25_C     20   22   32     14   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     E    26_C     E    26_C     20   22   32      9   19   19   20   21   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     E    27_C     E    27_C     20   22   32      0    4   18   20   21   22   22   23   24   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     S    28_C     S    28_C      5   22   32      5    5    5    6   13   22   22   23   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     V    29_C     V    29_C      5   22   32      5    5    5    5    7   14   20   23   24   25   25   27   31   35   38   42   45   46   47   48 
LCS_GDT     E    30_C     E    30_C      5    5   32      5    5    5    5    5    5    7    8   12   16   21   27   27   28   29   31   32   36   42   48 
LCS_GDT     K    31_C     K    31_C      5    5   32      5    5    5    5    6    8   11   14   24   25   25   27   27   28   29   31   32   36   42   45 
LCS_GDT     N    32_C     N    32_C      5    5   32      5    5    5    5    6    7    8    9   10   11   12   14   15   16   20   26   28   29   31   35 
LCS_GDT     S    33_C     S    33_C      4    5   32      3    4    4    5    6    7   11   11   13   17   23   27   27   28   28   29   31   40   47   48 
LCS_GDT     R    34_C     R    34_C      4    5   32      3    4    4    5    6    8   13   16   24   25   25   27   27   31   38   42   45   46   47   48 
LCS_GDT     M    35_C     M    35_C      4    5   32      3    4   15   18   21   22   22   23   24   25   25   27   27   34   38   42   45   46   47   48 
LCS_GDT     R    36_C     R    36_C      4    5   32      3    4    4    4    4    6    8   13   16   19   21   25   28   30   33   39   41   45   47   48 
LCS_GDT     H    37_C     H    37_C      4    5   32      3    4    4    4    8    9   12   14   16   19   21   25   30   35   38   42   45   46   47   48 
LCS_GDT     I    38_C     I    38_C      4    5   32      3    4    4    5    7    9   12   14   16   21   24   26   30   35   38   42   45   46   47   48 
LCS_GDT     R    39_C     R    39_C      3    5   32      3    3    4    4    6    7   10   11   15   19   21   22   23   27   33   38   40   41   43   46 
LCS_GDT     A    40_C     A    40_C      3    6   26      3    3    4    4    7    8   10   11   15   19   21   22   23   24   25   26   32   35   36   39 
LCS_GDT     V    41_C     V    41_C      4    6   26      3    4    4    5    7    9   11   14   16   19   21   25   28   34   38   42   45   46   47   48 
LCS_GDT     M    42_C     M    42_C      4    6   26      3    4    4    5    7    8   10   11   16   21   24   26   30   35   38   42   45   46   47   48 
LCS_GDT     W    43_C     W    43_C      4    6   26      3    4    4    5    7    8   10   11   15   19   21   25   30   35   38   42   45   46   47   48 
LCS_GDT     A    44_C     A    44_C      4   12   26      3    4    4    5    7    9   12   13   15   19   21   25   30   35   38   42   45   46   47   48 
LCS_GDT     E    45_C     E    45_C     11   12   26      8   10   11   11   14   16   18   19   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     Y    46_C     Y    46_C     11   12   26      8   10   11   11   14   16   18   19   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     M    47_C     M    47_C     11   12   26      8   10   11   11   14   16   18   19   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     L    48_C     L    48_C     11   12   26      8   10   11   11   14   16   18   19   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     E    49_C     E    49_C     11   12   26      8   10   11   11   14   16   18   19   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     I    50_C     I    50_C     11   12   26      8   10   11   11   14   16   18   19   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     A    51_C     A    51_C     11   12   26      8   10   11   11   14   16   18   19   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     R    52_C     R    52_C     11   12   26      8   10   11   11   14   16   18   19   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     S    53_C     S    53_C     11   12   26      8   10   11   11   14   16   18   19   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     L    54_C     L    54_C     11   12   26      3   10   11   11   14   16   18   19   26   28   29   30   31   35   38   42   45   46   47   48 
LCS_GDT     E    55_C     E    55_C     11   16   26      3    4   11   11   14   16   18   19   26   28   29   30   31   35   37   42   45   46   47   48 
LCS_GDT     D    56_C     D    56_C     13   16   26      9   12   12   13   15   15   15   17   18   19   23   25   28   35   38   42   45   46   47   48 
LCS_GDT     E    57_C     E    57_C     13   16   26      9   12   12   13   15   15   15   15   16   19   21   25   28   35   38   42   45   46   47   48 
LCS_GDT     K    58_C     K    58_C     13   16   26      9   12   12   13   15   15   15   15   16   19   22   26   30   35   38   42   45   46   47   48 
LCS_GDT     I    59_C     I    59_C     13   16   26      9   12   12   13   15   15   15   15   16   19   21   25   28   34   38   42   45   46   47   48 
LCS_GDT     L    60_C     L    60_C     13   16   26      9   12   12   13   15   15   15   15   16   18   21   25   28   34   38   42   45   46   47   48 
LCS_GDT     E    61_C     E    61_C     13   16   26      9   12   12   13   15   15   15   15   16   18   18   20   24   31   37   40   43   46   47   48 
LCS_GDT     I    62_C     I    62_C     13   16   20      9   12   12   13   15   15   15   15   16   18   18   18   21   24   30   34   38   43   47   48 
LCS_GDT     A    63_C     A    63_C     13   16   20      9   12   12   13   15   15   15   15   16   18   18   18   18   18   19   19   23   28   33   42 
LCS_GDT     E    64_C     E    64_C     13   16   20      9   12   12   13   15   15   15   15   16   18   18   18   18   18   19   19   23   28   36   42 
LCS_GDT     K    65_C     K    65_C     13   16   20      4   12   12   13   15   15   15   15   16   18   18   18   18   18   19   19   20   24   28   34 
LCS_GDT     L    66_C     L    66_C     13   16   20      5   12   12   13   15   15   15   15   16   18   18   18   18   18   19   19   20   21   25   25 
LCS_GDT     E    67_C     E    67_C     13   16   20      5   12   12   13   15   15   15   15   16   18   18   18   18   18   19   19   20   20   25   25 
LCS_GDT     K    68_C     K    68_C     13   16   20      5    5    8   13   15   15   15   15   16   18   18   18   18   18   19   19   20   21   25   25 
LCS_GDT     A    69_C     A    69_C      5   16   20      5    5    8   12   15   15   15   15   16   18   18   18   18   18   19   19   20   21   25   25 
LCS_GDT     L    70_C     L    70_C      5   16   20      5    5    9   12   15   15   15   15   16   18   18   18   18   18   19   19   20   20   21   22 
LCS_AVERAGE  LCS_A:  17.11  (  11.33   13.90   26.10 )

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     19     19     20     21     22     22     23     26     28     29     30     31     35     38     42     45     46     47     48 
GDT PERCENT_AT  13.89  17.59  17.59  18.52  19.44  20.37  20.37  21.30  24.07  25.93  26.85  27.78  28.70  32.41  35.19  38.89  41.67  42.59  43.52  44.44
GDT RMS_LOCAL    0.29   0.47   0.47   0.75   1.17   1.38   1.38   1.90   3.55   3.70   3.83   3.92   4.03   4.71   5.43   5.79   6.10   6.26   6.38   6.48
GDT RMS_ALL_AT  21.20  21.49  21.49  21.22  19.79  19.69  19.69  19.48  14.72  14.63  14.44  14.43  14.35  13.73  12.91  12.51  12.17  11.98  11.87  11.87

# Checking swapping
#   possible swapping detected:  E    30_C      E    30_C
#   possible swapping detected:  E    55_C      E    55_C
#   possible swapping detected:  E    57_C      E    57_C
#   possible swapping detected:  E    61_C      E    61_C
#   possible swapping detected:  E    64_C      E    64_C
#   possible swapping detected:  E    67_C      E    67_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_C      L     8_C     1.168     0    0.007   1.392     3.448   85.952   78.690
LGA    K     9_C      K     9_C     0.243     0    0.055   0.656     3.217  100.000   78.307
LGA    L    10_C      L    10_C     0.566     0    0.045   1.275     3.878   97.619   84.821
LGA    L    11_C      L    11_C     0.876     0    0.022   0.149     2.125   90.476   82.798
LGA    D    12_C      D    12_C     0.978     0    0.075   0.202     1.989   90.476   83.810
LGA    T    13_C      T    13_C     0.787     0    0.000   0.000     1.350   90.476   86.599
LGA    L    14_C      L    14_C     0.497     0    0.000   0.107     1.753  100.000   89.702
LGA    L    15_C      L    15_C     0.931     0    0.016   0.158     2.074   90.476   81.726
LGA    T    16_C      T    16_C     1.283     0    0.045   0.960     2.376   83.690   77.891
LGA    M    17_C      M    17_C     0.948     0    0.049   1.020     3.441   90.476   80.952
LGA    V    18_C      V    18_C     0.363     0    0.041   0.073     1.161  100.000   94.626
LGA    E    19_C      E    19_C     0.993     0    0.065   0.777     2.794   90.476   76.296
LGA    W    20_C      W    20_C     1.690     0    0.000   1.618     9.828   75.000   46.293
LGA    V    21_C      V    21_C     1.699     0    0.012   0.061     2.632   77.143   69.660
LGA    K    22_C      K    22_C     0.708     0    0.041   0.819     2.045   92.857   82.804
LGA    E    23_C      E    23_C     1.106     0    0.007   0.797     2.966   81.548   72.328
LGA    L    24_C      L    24_C     2.492     0    0.082   1.343     7.113   64.881   46.488
LGA    L    25_C      L    25_C     2.341     0    0.166   0.177     3.242   61.071   61.071
LGA    E    26_C      E    26_C     1.689     0    0.000   0.278     2.092   72.857   72.910
LGA    E    27_C      E    27_C     2.161     0    0.566   0.886     5.523   66.905   52.963
LGA    S    28_C      S    28_C     3.192     0    0.637   0.746     6.953   45.833   36.349
LGA    V    29_C      V    29_C     5.975     0    0.040   0.119     9.968   18.333   14.422
LGA    E    30_C      E    30_C     8.950     0    0.000   0.867    12.453    3.929    2.063
LGA    K    31_C      K    31_C     7.797     0    0.143   0.903    11.520    5.238    9.894
LGA    N    32_C      N    32_C    11.462     0    0.419   1.309    13.573    0.119    0.060
LGA    S    33_C      S    33_C     8.863     0    0.127   0.788     9.117    6.190    5.794
LGA    R    34_C      R    34_C     8.449     0    0.037   1.022    10.707   11.548    4.632
LGA    M    35_C      M    35_C     1.239     0    0.584   0.803     6.551   54.762   48.333
LGA    R    36_C      R    36_C     7.126     0    0.126   1.743    15.020   12.500    4.805
LGA    H    37_C      H    37_C    10.489     0    0.062   0.829    13.689    1.190    0.714
LGA    I    38_C      I    38_C    11.148     0    0.568   0.991    12.896    0.119    0.298
LGA    R    39_C      R    39_C    14.110     0    0.576   1.112    18.777    0.000    0.000
LGA    A    40_C      A    40_C    18.339     0    0.193   0.224    20.119    0.000    0.000
LGA    V    41_C      V    41_C    17.857     0    0.522   1.352    21.354    0.000    0.000
LGA    M    42_C      M    42_C    12.799     0    0.124   1.230    14.449    0.000    0.357
LGA    W    43_C      W    43_C    13.358     0    0.179   0.408    15.151    0.000    0.000
LGA    A    44_C      A    44_C    17.710     0    0.466   0.446    19.404    0.000    0.000
LGA    E    45_C      E    45_C    16.489     0    0.609   0.938    17.447    0.000    0.000
LGA    Y    46_C      Y    46_C    14.119     0    0.000   1.316    21.194    0.000    0.000
LGA    M    47_C      M    47_C    11.203     0    0.000   0.500    13.423    0.000    0.000
LGA    L    48_C      L    48_C    16.852     0    0.072   0.081    19.094    0.000    0.000
LGA    E    49_C      E    49_C    18.736     0    0.033   0.894    21.807    0.000    0.000
LGA    I    50_C      I    50_C    14.264     0    0.077   0.137    15.466    0.000    0.000
LGA    A    51_C      A    51_C    16.239     0    0.050   0.049    19.213    0.000    0.000
LGA    R    52_C      R    52_C    21.885     0    0.168   1.574    28.187    0.000    0.000
LGA    S    53_C      S    53_C    20.330     0    0.164   0.203    20.424    0.000    0.000
LGA    L    54_C      L    54_C    18.344     0    0.118   0.206    20.553    0.000    0.000
LGA    E    55_C      E    55_C    23.694     0    0.346   0.790    28.176    0.000    0.000
LGA    D    56_C      D    56_C    27.698     0    0.604   0.933    31.024    0.000    0.000
LGA    E    57_C      E    57_C    28.044     0    0.067   1.307    29.394    0.000    0.000
LGA    K    58_C      K    58_C    27.306     0    0.033   0.844    27.875    0.000    0.000
LGA    I    59_C      I    59_C    27.420     0    0.000   0.646    28.361    0.000    0.000
LGA    L    60_C      L    60_C    28.615     0    0.000   0.045    30.143    0.000    0.000
LGA    E    61_C      E    61_C    29.728     0    0.050   0.887    31.369    0.000    0.000
LGA    I    62_C      I    62_C    30.715     0    0.041   0.211    32.264    0.000    0.000
LGA    A    63_C      A    63_C    31.094     0    0.073   0.086    33.447    0.000    0.000
LGA    E    64_C      E    64_C    33.590     0    0.059   0.748    36.422    0.000    0.000
LGA    K    65_C      K    65_C    36.453     0    0.019   0.062    39.132    0.000    0.000
LGA    L    66_C      L    66_C    37.708     0    0.182   1.346    40.167    0.000    0.000
LGA    E    67_C      E    67_C    38.265     0    0.077   0.639    42.361    0.000    0.000
LGA    K    68_C      K    68_C    44.183     0    0.027   1.190    47.952    0.000    0.000
LGA    A    69_C      A    69_C    46.707     0    0.176   0.177    47.172    0.000    0.000
LGA    L    70_C      L    70_C    44.503     0    0.087   0.142    47.513    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     525    525  100.00               108
SUMMARY(RMSD_GDC):    10.647         10.774                 11.365           17.242   15.078

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63  108    4.0     23    1.90    24.074    20.922     1.151

LGA_LOCAL      RMSD:   1.899  Number of atoms:   23  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  19.482  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:  10.647  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.866302 * X  +  -0.203536 * Y  +  -0.456174 * Z  + 508.758331
  Y_new =  -0.073853 * X  +   0.955374 * Y  +  -0.286018 * Z  + -113.483131
  Z_new =   0.494031 * X  +  -0.214088 * Y  +  -0.842674 * Z  + 270.850708 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.056547 -0.516720 -2.892799   [DEG: -175.1272  -29.6059 -165.7451 ]
ZXZ: -1.010765  2.573027  1.979717   [DEG:  -57.9126  147.4236  113.4294 ]
 
# END of job
