
#######################################################
#                                                     #
#                        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        2.68     2.68
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       4_A - 63_A        1.97     2.78
  LCS_AVERAGE:     93.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      14_A - 38_A        1.00     3.16
  LCS_AVERAGE:     28.87

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      3    4   63      3    3    4    4    4    4    6    7    8   17   24   28   34   39   40   43   60   63   63   63 
LCS_GDT     H     2_A     H     2_A      3   40   63      3    3    4    5   14   31   43   54   58   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     I     3_A     I     3_A      3   53   63      3    6    9   16   25   30   43   46   56   59   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D     4_A     D     4_A     15   60   63      7   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C     5_A     C     5_A     19   60   63      7   13   31   49   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D     6_A     D     6_A     19   60   63      7   11   30   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K     7_A     K     7_A     19   60   63      7   18   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E     8_A     E     8_A     19   60   63     10   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C     9_A     C     9_A     19   60   63      7   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    10_A     N    10_A     19   60   63     10   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    11_A     R    11_A     19   60   63     10   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    12_A     R    12_A     19   60   63      4   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    13_A     C    13_A     19   60   63      5   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    14_A     S    14_A     25   60   63      5   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    15_A     K    15_A     25   60   63      3   11   20   43   54   56   57   58   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    16_A     A    16_A     25   60   63      4   20   38   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    17_A     S    17_A     25   60   63      5   20   34   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    18_A     A    18_A     25   60   63      3   14   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     H    19_A     H    19_A     25   60   63      4   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D    20_A     D    20_A     25   60   63      6   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    21_A     R    21_A     25   60   63      6   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    22_A     C    22_A     25   60   63     10   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     L    23_A     L    23_A     25   60   63     10   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    24_A     K    24_A     25   60   63      5   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     25   60   63      5   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    26_A     C    26_A     25   60   63      5   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    27_A     G    27_A     25   60   63      4   17   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     I    28_A     I    28_A     25   60   63      5   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    29_A     C    29_A     25   60   63      6   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    30_A     C    30_A     25   60   63      5   17   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E    31_A     E    31_A     25   60   63      3   12   33   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    32_A     K    32_A     25   60   63      3   17   34   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    33_A     C    33_A     25   60   63      6   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    34_A     N    34_A     25   60   63      4   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    35_A     C    35_A     25   60   63      5   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     V    36_A     V    36_A     25   60   63     10   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   60   63     10   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    38_A     P    38_A     25   60   63     10   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   60   63      6   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   60   63      3    6   13   29   42   50   55   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   60   63      3    6   17   24   38   48   55   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   60   63      4    4   17   24   38   48   55   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   60   63      5   18   38   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   60   63      6   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   60   63      5   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   60   63      5   18   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   60   63     10   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   60   63     10   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    49_A     C    49_A     13   60   63      9   21   35   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     13   60   63      4   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    51_A     A    51_A     13   60   63     10   21   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    52_A     N    52_A     13   60   63      6   21   38   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     L    53_A     L    53_A     13   60   63      6   20   38   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    54_A     K    54_A     13   60   63      5   12   31   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    55_A     N    55_A     13   60   63      6   14   30   49   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    56_A     S    56_A     13   60   63      6   10   20   33   48   53   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    57_A     K    57_A     13   60   63      6   12   28   38   48   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    58_A     G    58_A     13   60   63      6   12   24   38   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    59_A     G    59_A     13   60   63      6   12   30   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     H    60_A     H    60_A     13   60   63      6   14   38   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    61_A     K    61_A     13   60   63      4   14   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    62_A     C    62_A     13   60   63      6   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    63_A     P    63_A     13   60   63      6   20   39   50   54   56   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_AVERAGE  LCS_A:  74.01  (  28.87   93.15  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     21     39     50     54     56     57     59     60     61     62     62     62     62     62     62     62     63     63     63 
GDT PERCENT_AT  15.87  33.33  61.90  79.37  85.71  88.89  90.48  93.65  95.24  96.83  98.41  98.41  98.41  98.41  98.41  98.41  98.41 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.65   1.12   1.32   1.47   1.61   1.69   1.93   1.97   2.11   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.68   2.68   2.68
GDT RMS_ALL_AT   3.10   3.16   2.97   2.86   2.82   2.80   2.81   2.79   2.78   2.74   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.68   2.68   2.68

# Checking swapping
#   possible swapping detected:  D     6_A      D     6_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A    13.098     0    0.019   0.050    15.393    0.000    0.000
LGA    H     2_A      H     2_A     6.425     0    0.125   0.755     8.497   11.310   37.571
LGA    I     3_A      I     3_A     6.710     0    0.590   1.576    12.648   23.810   12.560
LGA    D     4_A      D     4_A     1.015     0    0.549   1.211     4.260   75.357   59.464
LGA    C     5_A      C     5_A     2.077     0    0.121   0.360     2.871   70.833   67.540
LGA    D     6_A      D     6_A     1.589     0    0.025   0.704     3.530   79.405   71.429
LGA    K     7_A      K     7_A     0.622     0    0.080   0.976     3.571   90.476   77.566
LGA    E     8_A      E     8_A     1.071     0    0.034   0.683     3.035   83.690   77.989
LGA    C     9_A      C     9_A     1.312     0    0.040   0.172     1.850   81.429   78.571
LGA    N    10_A      N    10_A     0.481     0    0.125   0.755     2.398   90.595   88.512
LGA    R    11_A      R    11_A     1.034     0    0.020   1.401     5.079   83.690   71.212
LGA    R    12_A      R    12_A     1.387     0    0.039   1.420     6.233   79.286   64.502
LGA    C    13_A      C    13_A     1.177     0    0.259   0.256     3.176   79.286   74.762
LGA    S    14_A      S    14_A     1.345     0    0.052   0.674     3.729   73.452   69.762
LGA    K    15_A      K    15_A     3.554     0    0.292   1.140     4.837   53.690   51.587
LGA    A    16_A      A    16_A     2.267     0    0.049   0.060     2.672   62.857   64.857
LGA    S    17_A      S    17_A     2.792     0    0.099   0.684     4.641   57.143   52.857
LGA    A    18_A      A    18_A     2.417     0    0.213   0.211     2.601   62.857   63.238
LGA    H    19_A      H    19_A     2.224     0    0.137   0.360     2.946   62.857   61.714
LGA    D    20_A      D    20_A     2.114     0    0.139   0.251     3.413   68.810   63.036
LGA    R    21_A      R    21_A     1.994     0    0.080   0.862     7.348   72.976   50.736
LGA    C    22_A      C    22_A     1.302     0    0.111   0.232     1.626   79.286   81.508
LGA    L    23_A      L    23_A     1.107     0    0.093   0.196     2.248   83.690   77.262
LGA    K    24_A      K    24_A     2.155     0    0.066   0.402     4.169   68.810   60.159
LGA    Y    25_A      Y    25_A     2.153     0    0.029   0.695     3.129   66.786   66.984
LGA    C    26_A      C    26_A     1.842     0    0.020   0.565     2.364   72.857   71.508
LGA    G    27_A      G    27_A     1.915     0    0.123   0.123     2.589   66.905   66.905
LGA    I    28_A      I    28_A     1.635     0    0.048   0.725     4.597   77.143   66.786
LGA    C    29_A      C    29_A     1.623     0    0.044   0.653     1.797   77.143   78.651
LGA    C    30_A      C    30_A     1.653     0    0.062   0.661     2.367   72.857   70.159
LGA    E    31_A      E    31_A     1.765     0    0.069   0.289     3.818   70.833   62.698
LGA    K    32_A      K    32_A     1.745     0    0.044   0.727     4.893   72.976   66.508
LGA    C    33_A      C    33_A     1.020     0    0.632   0.547     3.647   69.762   68.175
LGA    N    34_A      N    34_A     1.034     0    0.223   0.594     3.263   86.071   72.679
LGA    C    35_A      C    35_A     1.183     0    0.109   0.903     1.707   83.690   80.079
LGA    V    36_A      V    36_A     0.449     0    0.164   0.189     1.579  100.000   93.401
LGA    P    37_A      P    37_A     0.348     0    0.032   0.326     0.962   95.238   94.558
LGA    P    38_A      P    38_A     1.245     0    0.057   0.371     2.454   83.690   77.891
LGA    G    39_A      G    39_A     1.866     0    0.214   0.214     2.426   68.810   68.810
LGA    T    40_A      T    40_A     4.387     0    0.606   0.999     5.264   37.619   36.599
LGA    Y    41_A      Y    41_A     4.540     0    0.094   1.301     5.128   34.286   34.444
LGA    G    42_A      G    42_A     4.328     0    0.629   0.629     5.454   34.524   34.524
LGA    N    43_A      N    43_A     1.244     0    0.283   0.336     1.866   77.143   82.679
LGA    E    44_A      E    44_A     0.560     0    0.113   0.839     3.551   90.476   78.730
LGA    D    45_A      D    45_A     0.975     0    0.103   0.716     2.504   90.476   82.917
LGA    S    46_A      S    46_A     1.157     0    0.049   0.442     1.574   85.952   83.016
LGA    C    47_A      C    47_A     0.586     0    0.094   0.451     2.822   90.476   83.413
LGA    P    48_A      P    48_A     0.663     0    0.059   0.370     1.311   88.214   89.184
LGA    C    49_A      C    49_A     1.686     0    0.034   0.257     3.105   72.976   67.778
LGA    Y    50_A      Y    50_A     1.016     0    0.091   0.336     2.358   85.952   79.405
LGA    A    51_A      A    51_A     0.947     0    0.100   0.130     1.303   85.952   85.048
LGA    N    52_A      N    52_A     0.948     0    0.054   0.556     2.012   88.214   82.738
LGA    L    53_A      L    53_A     1.000     0    0.149   0.875     3.224   83.690   79.762
LGA    K    54_A      K    54_A     1.301     0    0.086   1.336     4.875   81.429   69.312
LGA    N    55_A      N    55_A     1.976     0    0.021   0.427     2.888   67.143   65.000
LGA    S    56_A      S    56_A     4.122     0    0.038   0.435     6.384   38.929   34.048
LGA    K    57_A      K    57_A     3.420     0    0.076   0.482     5.923   46.667   40.106
LGA    G    58_A      G    58_A     3.096     0    0.092   0.092     3.096   53.571   53.571
LGA    G    59_A      G    59_A     1.583     0    0.083   0.083     2.068   77.381   77.381
LGA    H    60_A      H    60_A     1.156     0    0.126   1.282     7.934   85.952   53.476
LGA    K    61_A      K    61_A     1.485     0    0.040   0.808     2.663   77.381   76.032
LGA    C    62_A      C    62_A     2.179     0    0.095   0.154     2.478   66.786   66.111
LGA    P    63_A      P    63_A     1.950     0    0.364   0.407     2.335   68.810   70.544

# 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):     2.683          2.687                  2.986           70.958   66.508

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     59    1.93    76.190    85.574     2.901

LGA_LOCAL      RMSD:   1.934  Number of atoms:   59  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.792  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.683  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.955956 * X  +  -0.263186 * Y  +  -0.129929 * Z  +   5.646205
  Y_new =  -0.276286 * X  +   0.956300 * Y  +   0.095692 * Z  +  -1.078469
  Z_new =   0.099066 * X  +   0.127375 * Y  +  -0.986895 * Z  +  -3.335197 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.860243 -0.099229  3.013236   [DEG: -163.8799   -5.6854  172.6457 ]
ZXZ: -2.205595  2.979520  0.661030   [DEG: -126.3713  170.7139   37.8742 ]
 
# END of job
