
#######################################################
#                                                     #
#                        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 (  471),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  471),  selected   63 , 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:    63       1_A - 63_A        1.84     1.84
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.84     1.84
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      13_A - 38_A        0.98     2.35
  LONGEST_CONTINUOUS_SEGMENT:    26      14_A - 39_A        0.99     2.42
  LCS_AVERAGE:     32.33

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     A     1_A     A     1_A     10   63   63      3    6   22   42   56   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     13   63   63      4   13   29   53   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     21   63   63      5   21   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     22   63   63      7   21   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     22   63   63      7   19   43   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     22   63   63      7   18   43   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     23   63   63      7   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     23   63   63     10   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     23   63   63      7   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     23   63   63     10   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     23   63   63      9   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     23   63   63      6   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     26   63   63      3   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     26   63   63      6   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     26   63   63      3    6   28   49   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     26   63   63      6   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     26   63   63      7   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     26   63   63      4   20   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     26   63   63      4   22   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     26   63   63     10   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     26   63   63     10   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     26   63   63     10   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     26   63   63     10   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     26   63   63      6   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     26   63   63      7   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     26   63   63      5   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     26   63   63      5   21   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     26   63   63      6   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     26   63   63      6   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     26   63   63      5   20   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     26   63   63      4   15   41   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     26   63   63      4   21   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     26   63   63      7   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     26   63   63      5   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     26   63   63      7   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     26   63   63     10   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     26   63   63     10   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     26   63   63      9   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     26   63   63      4   23   43   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   63   63      3    6   13   31   44   54   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   63   63      3    6   13   23   41   51   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   63   63      4    4   15   28   41   51   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   63   63      5   21   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   63   63      8   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   63   63      7   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   63   63      6   21   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   63   63      8   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     14   63   63     10   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     15   63   63      3   23   42   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     15   63   63      5   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     15   63   63     10   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     15   63   63      4   21   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     15   63   63      5   21   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     15   63   63      3   15   43   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     15   63   63      5   16   31   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     15   63   63      5   10   22   40   56   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     15   63   63      5   15   31   44   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     15   63   63      5   15   31   44   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     15   63   63      5   15   36   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     15   63   63      5   19   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     15   63   63      4   20   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     15   63   63      5   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     15   63   63      7   23   45   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.44  (  32.33  100.00  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     10     23     45     54     58     60     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  36.51  71.43  85.71  92.06  95.24  95.24 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.62   1.07   1.28   1.45   1.57   1.57   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84
GDT RMS_ALL_AT   2.30   2.62   2.04   1.92   1.88   1.87   1.87   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84

# Checking swapping
#   possible swapping detected:  D     6_A      D     6_A
#   possible swapping detected:  E     8_A      E     8_A
#   possible swapping detected:  D    20_A      D    20_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    44_A      E    44_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     3.308     0    0.119   0.163     4.305   65.238   59.619
LGA    H     2_A      H     2_A     2.030     0    0.036   0.855     5.010   69.048   54.810
LGA    I     3_A      I     3_A     0.469     0    0.064   0.970     2.862   90.714   84.167
LGA    D     4_A      D     4_A     1.088     0    0.028   1.246     4.749   83.690   72.143
LGA    C     5_A      C     5_A     1.800     0    0.090   0.210     2.316   72.857   71.508
LGA    D     6_A      D     6_A     1.408     0    0.018   0.426     3.030   83.810   76.548
LGA    K     7_A      K     7_A     0.403     0    0.076   0.539     2.144   92.857   84.762
LGA    E     8_A      E     8_A     1.138     0    0.060   0.386     1.666   81.548   84.497
LGA    C     9_A      C     9_A     1.387     0    0.034   0.042     1.920   81.429   78.571
LGA    N    10_A      N    10_A     0.715     0    0.096   0.258     1.350   88.214   88.214
LGA    R    11_A      R    11_A     1.350     0    0.009   1.415     5.121   79.286   65.974
LGA    R    12_A      R    12_A     1.478     0    0.036   1.467     6.700   79.286   61.472
LGA    C    13_A      C    13_A     1.258     0    0.133   0.192     3.004   83.690   77.698
LGA    S    14_A      S    14_A     1.137     0    0.010   0.664     3.395   77.381   75.000
LGA    K    15_A      K    15_A     2.963     0    0.110   1.008     4.352   59.048   55.926
LGA    A    16_A      A    16_A     1.783     0    0.019   0.023     2.082   70.833   72.952
LGA    S    17_A      S    17_A     2.124     0    0.031   0.488     4.187   68.810   62.857
LGA    A    18_A      A    18_A     2.006     0    0.081   0.081     2.138   68.810   68.000
LGA    H    19_A      H    19_A     1.812     0    0.132   1.000     3.528   70.833   66.810
LGA    D    20_A      D    20_A     1.552     0    0.170   0.221     2.148   77.143   73.988
LGA    R    21_A      R    21_A     1.527     0    0.069   1.268     8.188   79.405   51.429
LGA    C    22_A      C    22_A     1.052     0    0.120   0.192     1.355   83.690   85.952
LGA    L    23_A      L    23_A     1.098     0    0.123   0.205     1.719   85.952   81.548
LGA    K    24_A      K    24_A     2.184     0    0.060   0.486     5.547   66.786   52.487
LGA    Y    25_A      Y    25_A     1.995     0    0.019   0.655     3.001   70.833   66.270
LGA    C    26_A      C    26_A     1.574     0    0.055   0.179     1.820   72.857   74.286
LGA    G    27_A      G    27_A     1.692     0    0.116   0.116     2.369   70.833   70.833
LGA    I    28_A      I    28_A     1.702     0    0.040   0.688     4.644   75.000   65.714
LGA    C    29_A      C    29_A     1.505     0    0.049   0.689     1.600   77.143   77.143
LGA    C    30_A      C    30_A     1.420     0    0.025   0.040     1.832   79.286   77.143
LGA    E    31_A      E    31_A     1.438     0    0.016   0.702     4.302   81.429   69.206
LGA    K    32_A      K    32_A     1.184     0    0.014   0.941     5.675   81.429   62.434
LGA    C    33_A      C    33_A     0.701     0    0.609   0.531     3.517   76.429   74.048
LGA    N    34_A      N    34_A     0.928     0    0.200   0.614     2.744   88.333   77.679
LGA    C    35_A      C    35_A     1.177     0    0.095   0.859     1.819   85.952   83.016
LGA    V    36_A      V    36_A     0.605     0    0.136   0.167     1.526   90.476   87.959
LGA    P    37_A      P    37_A     0.465     0    0.051   0.238     0.809   92.857   95.918
LGA    P    38_A      P    38_A     1.689     0    0.029   0.083     2.003   75.000   74.150
LGA    G    39_A      G    39_A     2.132     0    0.155   0.155     2.819   62.976   62.976
LGA    T    40_A      T    40_A     4.526     0    0.557   0.515     5.616   34.762   31.973
LGA    Y    41_A      Y    41_A     4.565     0    0.135   1.279     5.180   34.286   31.587
LGA    G    42_A      G    42_A     4.318     0    0.597   0.597     5.280   34.524   34.524
LGA    N    43_A      N    43_A     0.988     0    0.348   0.387     1.718   81.667   82.679
LGA    E    44_A      E    44_A     0.426     0    0.156   0.657     3.004  100.000   81.005
LGA    D    45_A      D    45_A     1.071     0    0.158   0.881     3.869   81.429   72.500
LGA    S    46_A      S    46_A     1.336     0    0.144   0.237     1.681   79.286   80.000
LGA    C    47_A      C    47_A     0.739     0    0.056   0.422     2.638   92.857   85.000
LGA    P    48_A      P    48_A     0.365     0    0.066   0.290     1.158   92.976   94.626
LGA    C    49_A      C    49_A     1.723     0    0.028   0.231     3.178   75.119   69.206
LGA    Y    50_A      Y    50_A     0.828     0    0.073   0.175     1.799   88.214   85.238
LGA    A    51_A      A    51_A     0.793     0    0.152   0.168     1.415   88.214   88.667
LGA    N    52_A      N    52_A     1.131     0    0.126   0.350     2.515   88.214   78.571
LGA    L    53_A      L    53_A     1.065     0    0.122   0.811     2.790   81.429   80.714
LGA    K    54_A      K    54_A     1.328     0    0.105   1.216     4.744   81.429   70.476
LGA    N    55_A      N    55_A     1.815     0    0.024   0.219     2.600   69.048   70.952
LGA    S    56_A      S    56_A     3.643     0    0.105   0.441     5.903   45.238   39.921
LGA    K    57_A      K    57_A     2.824     0    0.143   0.561     5.553   57.143   49.365
LGA    G    58_A      G    58_A     2.551     0    0.102   0.102     2.551   60.952   60.952
LGA    G    59_A      G    59_A     1.514     0    0.053   0.053     1.908   79.405   79.405
LGA    H    60_A      H    60_A     1.071     0    0.102   1.218     6.018   85.952   63.476
LGA    K    61_A      K    61_A     1.262     0    0.038   0.746     1.728   79.405   81.587
LGA    C    62_A      C    62_A     1.822     0    0.065   0.096     2.104   72.857   70.159
LGA    P    63_A      P    63_A     1.565     0    0.266   0.376     1.985   72.857   72.857

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     471    471  100.00                63
SUMMARY(RMSD_GDC):     1.842          1.850                  2.343           76.166   71.129

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.84    80.556    90.769     3.244

LGA_LOCAL      RMSD:   1.842  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.842  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.842  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.903328 * X  +   0.194875 * Y  +   0.382128 * Z  + -10.756006
  Y_new =   0.300036 * X  +  -0.923709 * Y  +  -0.238202 * Z  +  -0.792154
  Z_new =   0.306556 * X  +   0.329827 * Y  +  -0.892882 * Z  + -11.715488 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.320681 -0.311572  2.787744   [DEG:   18.3737  -17.8518  159.7260 ]
ZXZ:  1.013380  2.674501  0.748846   [DEG:   58.0624  153.2376   42.9057 ]
 
# END of job
