
#######################################################
#                                                     #
#                        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        1.81     1.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.81     1.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      13_A - 38_A        0.99     2.30
  LONGEST_CONTINUOUS_SEGMENT:    26      14_A - 39_A        0.98     2.38
  LCS_AVERAGE:     30.99

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     13   63   63      4    9   19   40   57   60   61   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   15   27   52   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     15   63   63      6   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     21   63   63      7   18   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     21   63   63      7   15   37   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     21   63   63      7   14   39   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     21   63   63      7   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     21   63   63      9   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     21   63   63      7   22   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     21   63   63     10   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     21   63   63      8   22   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     21   63   63      4   22   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     26   63   63      4   22   46   54   57   60   61   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   24   46   54   57   60   61   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    5   22   47   57   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      4   23   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     26   63   63      6   24   46   54   57   60   61   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   11   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     26   63   63      5   23   46   54   57   60   61   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   24   46   54   57   60   61   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   24   46   54   57   60   61   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   24   46   54   57   60   61   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   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     26   63   63      5   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     26   63   63      6   24   46   54   57   60   61   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   24   46   54   57   60   61   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   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     26   63   63      7   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     26   63   63      5   24   46   54   57   60   61   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   19   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     26   63   63      5   14   41   54   57   60   61   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   23   46   54   57   60   61   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   24   46   54   57   60   61   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   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     26   63   63      6   24   46   54   57   60   61   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   24   46   54   57   60   61   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   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     26   63   63      8   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     26   63   63      5   22   44   54   57   60   61   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   14   31   46   56   61   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    7   14   28   42   53   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     12   63   63      4    6   17   29   43   54   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   63   63      6   18   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   63   63     10   22   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   63   63     10   22   46   54   57   60   61   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   14   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   63   63      9   22   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   63   63     10   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     13   63   63      4   22   40   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     13   63   63     10   22   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     13   63   63     10   22   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     13   63   63      9   22   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     13   63   63      7   20   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     13   63   63      3   14   40   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     13   63   63      5   16   33   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     13   63   63      5    8   20   35   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     13   63   63      5   14   33   47   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     13   63   63      5   14   33   52   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     13   63   63      5   14   40   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     13   63   63      5   19   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     12   63   63      5   19   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     12   63   63      7   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   63   63      7   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.00  (  30.99  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     24     46     54     57     60     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  38.10  73.02  85.71  90.48  95.24  96.83 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.78   1.09   1.27   1.39   1.55   1.72   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81
GDT RMS_ALL_AT   2.24   2.28   1.98   1.89   1.87   1.84   1.82   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81

# Checking swapping
#   possible swapping detected:  E     8_A      E     8_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  D    45_A      D    45_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     3.018     0    0.114   0.168     3.714   63.095   59.143
LGA    H     2_A      H     2_A     2.103     0    0.031   0.777     4.947   68.810   55.238
LGA    I     3_A      I     3_A     0.417     0    0.073   0.931     2.649   88.333   84.107
LGA    D     4_A      D     4_A     1.147     0    0.058   1.064     3.685   83.690   71.786
LGA    C     5_A      C     5_A     1.894     0    0.087   0.231     2.468   72.857   71.508
LGA    D     6_A      D     6_A     1.528     0    0.012   0.573     3.435   79.405   73.333
LGA    K     7_A      K     7_A     0.354     0    0.078   0.539     2.433   95.238   84.021
LGA    E     8_A      E     8_A     0.982     0    0.055   0.461     1.577   83.810   85.503
LGA    C     9_A      C     9_A     1.407     0    0.078   0.086     1.837   81.429   78.571
LGA    N    10_A      N    10_A     0.642     0    0.117   0.390     1.604   85.952   86.012
LGA    R    11_A      R    11_A     1.336     0    0.023   1.480     5.704   81.429   63.550
LGA    R    12_A      R    12_A     1.373     0    0.022   1.392     6.337   81.429   64.459
LGA    C    13_A      C    13_A     1.174     0    0.272   0.281     3.033   81.548   76.270
LGA    S    14_A      S    14_A     1.115     0    0.069   0.666     3.305   73.452   72.381
LGA    K    15_A      K    15_A     3.145     0    0.153   1.019     4.620   57.262   52.169
LGA    A    16_A      A    16_A     1.909     0    0.055   0.063     2.282   70.833   72.952
LGA    S    17_A      S    17_A     2.130     0    0.025   0.686     3.983   66.786   62.540
LGA    A    18_A      A    18_A     2.080     0    0.060   0.065     2.260   66.786   66.381
LGA    H    19_A      H    19_A     1.831     0    0.191   1.187     3.620   68.929   65.238
LGA    D    20_A      D    20_A     1.458     0    0.194   0.220     2.169   79.286   74.048
LGA    R    21_A      R    21_A     1.549     0    0.065   0.943     4.512   77.143   59.740
LGA    C    22_A      C    22_A     1.041     0    0.087   0.127     1.358   85.952   87.460
LGA    L    23_A      L    23_A     1.010     0    0.066   0.177     1.780   85.952   82.619
LGA    K    24_A      K    24_A     2.070     0    0.099   0.428     4.767   68.810   57.513
LGA    Y    25_A      Y    25_A     1.946     0    0.020   0.753     3.078   72.857   68.968
LGA    C    26_A      C    26_A     1.503     0    0.094   0.203     1.744   72.857   74.286
LGA    G    27_A      G    27_A     1.591     0    0.184   0.184     2.550   71.071   71.071
LGA    I    28_A      I    28_A     1.525     0    0.100   0.697     4.303   77.143   68.512
LGA    C    29_A      C    29_A     1.446     0    0.047   0.646     1.471   81.429   81.429
LGA    C    30_A      C    30_A     1.354     0    0.029   0.062     1.978   81.429   78.571
LGA    E    31_A      E    31_A     1.416     0    0.032   0.673     3.876   79.286   68.148
LGA    K    32_A      K    32_A     1.170     0    0.049   1.054     6.217   81.429   60.688
LGA    C    33_A      C    33_A     0.737     0    0.604   0.525     3.563   74.286   72.619
LGA    N    34_A      N    34_A     1.075     0    0.220   0.309     3.049   86.071   73.810
LGA    C    35_A      C    35_A     1.096     0    0.016   0.373     1.587   83.690   80.079
LGA    V    36_A      V    36_A     0.744     0    0.151   0.177     1.646   90.476   85.374
LGA    P    37_A      P    37_A     0.470     0    0.064   0.280     0.786   95.238   97.279
LGA    P    38_A      P    38_A     1.512     0    0.030   0.087     1.820   77.143   77.755
LGA    G    39_A      G    39_A     2.077     0    0.155   0.155     2.766   62.976   62.976
LGA    T    40_A      T    40_A     4.349     0    0.581   0.584     5.403   37.619   34.218
LGA    Y    41_A      Y    41_A     4.388     0    0.163   1.083     5.246   35.714   34.563
LGA    G    42_A      G    42_A     4.199     0    0.597   0.597     5.304   35.952   35.952
LGA    N    43_A      N    43_A     1.067     0    0.290   0.307     1.766   81.548   80.417
LGA    E    44_A      E    44_A     0.314     0    0.111   0.724     2.725  100.000   82.646
LGA    D    45_A      D    45_A     1.038     0    0.103   1.113     5.693   83.690   65.536
LGA    S    46_A      S    46_A     1.418     0    0.129   0.229     1.791   79.286   78.571
LGA    C    47_A      C    47_A     0.828     0    0.081   0.327     1.475   90.476   87.460
LGA    P    48_A      P    48_A     0.403     0    0.064   0.324     1.190   92.976   93.265
LGA    C    49_A      C    49_A     1.759     0    0.030   0.235     3.078   72.976   67.778
LGA    Y    50_A      Y    50_A     0.806     0    0.100   0.286     2.243   90.476   83.889
LGA    A    51_A      A    51_A     0.848     0    0.120   0.121     1.353   85.952   86.857
LGA    N    52_A      N    52_A     1.113     0    0.095   0.277     2.417   88.214   80.595
LGA    L    53_A      L    53_A     1.201     0    0.073   0.518     2.151   79.286   79.405
LGA    K    54_A      K    54_A     1.488     0    0.105   1.321     5.383   81.429   68.254
LGA    N    55_A      N    55_A     1.823     0    0.050   0.123     2.711   67.143   70.060
LGA    S    56_A      S    56_A     3.804     0    0.170   0.676     6.565   42.024   36.429
LGA    K    57_A      K    57_A     2.711     0    0.173   0.555     5.263   57.143   52.222
LGA    G    58_A      G    58_A     2.427     0    0.139   0.139     2.427   64.762   64.762
LGA    G    59_A      G    59_A     1.293     0    0.046   0.046     1.655   81.548   81.548
LGA    H    60_A      H    60_A     1.199     0    0.177   1.024     6.121   83.690   57.810
LGA    K    61_A      K    61_A     1.325     0    0.036   0.739     1.776   79.286   82.540
LGA    C    62_A      C    62_A     1.671     0    0.029   0.063     2.159   77.143   74.365
LGA    P    63_A      P    63_A     1.376     0    0.328   0.458     2.001   75.119   76.599

# 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):     1.812          1.841                  2.320           76.175   71.172

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.81    80.952    90.998     3.296

LGA_LOCAL      RMSD:   1.812  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.812  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.812  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.905260 * X  +   0.293059 * Y  +  -0.307604 * Z  +  -9.665771
  Y_new =  -0.327656 * X  +  -0.942463 * Y  +   0.066371 * Z  +  -0.639953
  Z_new =  -0.270455 * X  +   0.160872 * Y  +   0.949197 * Z  + -13.105336 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.794315  0.273866  0.167886   [DEG: -160.1025   15.6913    9.6192 ]
ZXZ: -1.783307  0.320123 -1.034196   [DEG: -102.1760   18.3417  -59.2550 ]
 
# END of job
