
#######################################################
#                                                     #
#                        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   69 (  539),  selected   69 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   69 , 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:    69       1_B - 69_B        1.02     1.02
  LCS_AVERAGE:     97.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    69       1_B - 69_B        1.02     1.02
  LCS_AVERAGE:     97.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    68       1_B - 68_B        0.96     1.02
  LONGEST_CONTINUOUS_SEGMENT:    68       2_B - 69_B        0.98     1.02
  LCS_AVERAGE:     95.77

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   69
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     G     1_B     G     1_B     68   69   69      3    7   16   61   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S     2_B     S     2_B     68   69   69     17   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     V     3_B     V     3_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S     4_B     S     4_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K     5_B     K     5_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     W     6_B     W     6_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S     7_B     S     7_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     T     8_B     T     8_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     D     9_B     D     9_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    10_B     E    10_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     V    11_B     V    11_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S    12_B     S    12_B     68   69   69     18   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    13_B     E    13_B     68   69   69     18   49   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     F    14_B     F    14_B     68   69   69     18   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    15_B     I    15_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     Q    16_B     Q    16_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S    17_B     S    17_B     68   69   69     13   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     L    18_B     L    18_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     P    19_B     P    19_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     G    20_B     G    20_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     C    21_B     C    21_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    22_B     E    22_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    23_B     E    23_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     H    24_B     H    24_B     68   69   69     21   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     G    25_B     G    25_B     68   69   69     21   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    26_B     K    26_B     68   69   69     21   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     V    27_B     V    27_B     68   69   69     18   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     F    28_B     F    28_B     68   69   69     21   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    29_B     K    29_B     68   69   69     21   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     D    30_B     D    30_B     68   69   69     18   37   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    31_B     E    31_B     68   69   69     21   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     Q    32_B     Q    32_B     68   69   69     21   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    33_B     I    33_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     D    34_B     D    34_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     G    35_B     G    35_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    36_B     E    36_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     A    37_B     A    37_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     F    38_B     F    38_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     L    39_B     L    39_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     L    40_B     L    40_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     M    41_B     M    41_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     T    42_B     T    42_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     Q    43_B     Q    43_B     68   69   69     10   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     T    44_B     T    44_B     68   69   69     16   48   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     D    45_B     D    45_B     68   69   69     16   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    46_B     I    46_B     68   69   69     21   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     V    47_B     V    47_B     68   69   69     10   48   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    48_B     K    48_B     68   69   69     11   33   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    49_B     I    49_B     68   69   69     12   38   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     M    50_B     M    50_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S    51_B     S    51_B     68   69   69     27   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    52_B     I    52_B     68   69   69     16   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    53_B     K    53_B     68   69   69     16   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    54_B     E    54_B     68   69   69     16   48   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     G    55_B     G    55_B     68   69   69     16   34   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     P    56_B     P    56_B     68   69   69     16   34   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     A    57_B     A    57_B     68   69   69     16   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     E    58_B     E    58_B     68   69   69     16   34   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    59_B     K    59_B     68   69   69     11   34   47   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    60_B     I    60_B     68   69   69     11   47   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     F    61_B     F    61_B     68   69   69     25   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     N    62_B     N    62_B     68   69   69     21   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     S    63_B     S    63_B     68   69   69     11   26   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     I    64_B     I    64_B     68   69   69     11   43   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     L    65_B     L    65_B     68   69   69     15   50   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     M    66_B     M    66_B     68   69   69     11   48   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     F    67_B     F    67_B     68   69   69     11   21   65   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     K    68_B     K    68_B     68   69   69      4   21   61   67   68   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_GDT     A    69_B     A    69_B     68   69   69      3   17   42   49   66   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69 
LCS_AVERAGE  LCS_A:  96.71  (  95.77   97.18   97.18 )

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     27     50     65     67     68     69     69     69     69     69     69     69     69     69     69     69     69     69     69     69 
GDT PERCENT_AT  38.03  70.42  91.55  94.37  95.77  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18  97.18
GDT RMS_LOCAL    0.35   0.64   0.88   0.93   0.96   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02
GDT RMS_ALL_AT   1.17   1.08   1.03   1.03   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02   1.02

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  E    54_B      E    54_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.391     0    0.054   0.054     2.646   71.190   71.190
LGA    S     2_B      S     2_B     0.617     0    0.259   0.833     2.825   90.595   82.063
LGA    V     3_B      V     3_B     0.378     0    0.006   0.062     0.506   97.619   98.639
LGA    S     4_B      S     4_B     0.341     0    0.020   0.144     0.679   95.238   95.238
LGA    K     5_B      K     5_B     0.816     0    0.074   0.992     8.980   90.476   60.741
LGA    W     6_B      W     6_B     0.768     0    0.034   0.149     1.262   90.476   87.245
LGA    S     7_B      S     7_B     0.784     0    0.036   0.079     1.009   90.476   88.968
LGA    T     8_B      T     8_B     0.558     0    0.009   0.047     0.729   90.476   90.476
LGA    D     9_B      D     9_B     0.763     0    0.013   0.771     3.680   90.476   76.250
LGA    E    10_B      E    10_B     0.945     0    0.030   0.143     2.014   90.476   80.741
LGA    V    11_B      V    11_B     0.622     0    0.023   0.048     0.685   90.476   90.476
LGA    S    12_B      S    12_B     0.952     0    0.012   0.069     1.195   88.214   85.952
LGA    E    13_B      E    13_B     1.198     0    0.022   0.821     5.240   83.690   64.286
LGA    F    14_B      F    14_B     0.936     0    0.029   0.325     2.233   90.476   80.130
LGA    I    15_B      I    15_B     0.738     0    0.018   0.651     1.859   90.476   88.274
LGA    Q    16_B      Q    16_B     1.133     0    0.039   0.716     2.919   83.690   79.735
LGA    S    17_B      S    17_B     1.098     0    0.015   0.052     1.139   85.952   84.444
LGA    L    18_B      L    18_B     0.833     0    0.018   0.036     0.898   90.476   90.476
LGA    P    19_B      P    19_B     0.843     0    0.026   0.394     1.569   88.214   85.374
LGA    G    20_B      G    20_B     1.108     0    0.016   0.016     1.292   83.690   83.690
LGA    C    21_B      C    21_B     1.003     0    0.031   0.035     1.058   85.952   84.444
LGA    E    22_B      E    22_B     1.069     0    0.049   0.762     4.249   83.690   69.788
LGA    E    23_B      E    23_B     0.843     0    0.168   0.872     2.230   88.214   84.603
LGA    H    24_B      H    24_B     0.529     0    0.142   1.061     2.959   97.619   87.476
LGA    G    25_B      G    25_B     0.670     0    0.019   0.019     0.670   90.476   90.476
LGA    K    26_B      K    26_B     0.692     0    0.081   1.019     5.506   90.476   68.254
LGA    V    27_B      V    27_B     1.005     0    0.015   1.017     3.245   85.952   79.524
LGA    F    28_B      F    28_B     0.626     0    0.005   0.113     1.362   90.476   88.874
LGA    K    29_B      K    29_B     0.613     0    0.015   0.858     3.049   88.214   81.376
LGA    D    30_B      D    30_B     1.298     0    0.023   0.040     1.787   81.429   78.214
LGA    E    31_B      E    31_B     0.992     0    0.021   0.117     1.723   88.214   84.497
LGA    Q    32_B      Q    32_B     0.939     0    0.003   0.806     3.796   90.476   75.026
LGA    I    33_B      I    33_B     0.462     0    0.112   0.114     0.937   95.238   95.238
LGA    D    34_B      D    34_B     0.416     0    0.041   0.141     0.939  100.000   96.429
LGA    G    35_B      G    35_B     0.404     0    0.013   0.013     0.446  100.000  100.000
LGA    E    36_B      E    36_B     0.701     0    0.014   0.826     2.474   90.476   85.608
LGA    A    37_B      A    37_B     0.662     0    0.025   0.025     0.762   92.857   92.381
LGA    F    38_B      F    38_B     0.280     0    0.022   0.220     1.548  100.000   91.558
LGA    L    39_B      L    39_B     0.214     0    0.028   0.086     0.381  100.000  100.000
LGA    L    40_B      L    40_B     0.443     0    0.075   0.072     0.662   97.619   95.238
LGA    M    41_B      M    41_B     0.440     0    0.030   0.645     1.948  100.000   91.905
LGA    T    42_B      T    42_B     0.365     0    0.024   0.045     0.825   95.238   95.918
LGA    Q    43_B      Q    43_B     1.012     0    0.014   0.580     3.663   88.214   77.407
LGA    T    44_B      T    44_B     1.130     0    0.067   0.101     1.627   85.952   82.789
LGA    D    45_B      D    45_B     0.788     0    0.031   0.095     1.351   90.476   87.083
LGA    I    46_B      I    46_B     0.431     0    0.039   0.078     0.650   92.857   94.048
LGA    V    47_B      V    47_B     1.079     0    0.027   0.044     1.573   83.690   81.497
LGA    K    48_B      K    48_B     1.515     0    0.086   1.242    10.117   77.143   48.942
LGA    I    49_B      I    49_B     1.334     0    0.088   0.127     1.874   81.429   78.214
LGA    M    50_B      M    50_B     0.632     0    0.088   0.868     2.518   90.476   85.179
LGA    S    51_B      S    51_B     0.448     0    0.037   0.048     1.433   95.238   92.143
LGA    I    52_B      I    52_B     0.467     0    0.015   0.627     1.547   95.238   89.524
LGA    K    53_B      K    53_B     0.795     0    0.053   0.683     2.205   90.476   84.762
LGA    E    54_B      E    54_B     1.145     0    0.011   0.738     3.707   83.690   72.011
LGA    G    55_B      G    55_B     1.653     0    0.012   0.012     1.653   75.000   75.000
LGA    P    56_B      P    56_B     1.312     0    0.031   0.282     1.424   81.429   81.429
LGA    A    57_B      A    57_B     0.907     0    0.028   0.026     1.073   88.214   88.667
LGA    E    58_B      E    58_B     1.330     0    0.033   0.838     4.373   81.429   66.720
LGA    K    59_B      K    59_B     1.762     0    0.023   0.111     3.708   77.143   64.550
LGA    I    60_B      I    60_B     1.137     0    0.021   0.089     1.256   85.952   83.690
LGA    F    61_B      F    61_B     0.363     0    0.057   0.210     0.917   97.619   96.537
LGA    N    62_B      N    62_B     0.636     0    0.012   0.037     1.279   90.476   88.214
LGA    S    63_B      S    63_B     1.339     0    0.039   0.655     1.697   79.286   78.571
LGA    I    64_B      I    64_B     1.301     0    0.011   0.033     1.561   81.429   80.357
LGA    L    65_B      L    65_B     0.766     0    0.084   0.136     1.243   90.476   90.536
LGA    M    66_B      M    66_B     0.965     0    0.070   1.263     4.305   83.810   70.119
LGA    F    67_B      F    67_B     1.404     0    0.015   0.257     1.888   77.143   79.870
LGA    K    68_B      K    68_B     1.727     0    0.187   0.637     2.072   72.857   71.958
LGA    A    69_B      A    69_B     2.817     0    0.571   0.517     4.609   50.833   52.095

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       69     276    276  100.00     539    539  100.00                71
SUMMARY(RMSD_GDC):     1.020          1.024                  1.633           85.542   80.607

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   69   71    4.0     69    1.02    89.789    94.360     6.161

LGA_LOCAL      RMSD:   1.020  Number of atoms:   69  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.020  Number of assigned atoms:   69 
Std_ASGN_ATOMS RMSD:   1.020  Standard rmsd on all 69 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.638237 * X  +  -0.356993 * Y  +  -0.682063 * Z  +  38.494926
  Y_new =  -0.371502 * X  +   0.633168 * Y  +  -0.679032 * Z  +  73.805992
  Z_new =   0.674270 * X  +   0.686771 * Y  +   0.271487 * Z  +  14.845531 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.527136 -0.739975  1.194340   [DEG:  -30.2027  -42.3975   68.4306 ]
ZXZ: -0.787625  1.295859  0.776213   [DEG:  -45.1276   74.2472   44.4737 ]
 
# END of job
