
#######################################################
#                                                     #
#                        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   73 (  570),  selected   71 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   71 , 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:    71       1_B - 71_B        0.72     0.72
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        0.72     0.72
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        0.72     0.72
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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     71   71   71      7   44   67   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     71   71   71     35   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     71   71   71     28   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     71   71   71     29   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     71   71   71     30   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     71   71   71     14   56   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     71   71   71     14   40   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     71   71   71     14   40   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     71   71   71     29   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     71   71   71     41   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     71   71   71     39   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     71   71   71     36   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     71   71   71     29   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     71   71   71     29   63   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     71   71   71     26   61   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     71   71   71     16   54   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     71   71   71     13   44   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     71   71   71     13   44   67   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     41     63     69     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  57.75  88.73  97.18 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.51   0.66   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72
GDT RMS_ALL_AT   0.79   0.74   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72

# 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:  F    14_B      F    14_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  F    28_B      F    28_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  F    38_B      F    38_B
#   possible swapping detected:  F    61_B      F    61_B
#   possible swapping detected:  E    71_B      E    71_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     1.693     0    0.354   0.354     2.838   80.119   80.119
LGA    S     2_B      S     2_B     0.712     0    0.041   0.698     2.754   92.857   86.508
LGA    V     3_B      V     3_B     0.187     0    0.068   0.067     0.418  100.000  100.000
LGA    S     4_B      S     4_B     0.678     0    0.019   0.132     0.898   90.476   90.476
LGA    K     5_B      K     5_B     0.623     0    0.038   0.836     4.941   92.857   71.852
LGA    W     6_B      W     6_B     0.712     0    0.034   0.128     0.804   90.476   90.476
LGA    S     7_B      S     7_B     0.639     0    0.013   0.042     0.686   90.476   92.063
LGA    T     8_B      T     8_B     0.575     0    0.042   1.091     2.521   90.476   82.041
LGA    D     9_B      D     9_B     0.322     0    0.047   0.744     3.395  100.000   84.940
LGA    E    10_B      E    10_B     0.326     0    0.021   0.281     1.657  100.000   91.799
LGA    V    11_B      V    11_B     0.403     0    0.013   0.034     0.503  100.000   98.639
LGA    S    12_B      S    12_B     0.480     0    0.020   0.105     0.561   97.619   95.238
LGA    E    13_B      E    13_B     0.290     0    0.042   1.063     5.072  100.000   76.772
LGA    F    14_B      F    14_B     0.407     0    0.021   0.222     1.622  100.000   89.091
LGA    I    15_B      I    15_B     0.428     0    0.009   0.625     1.640  100.000   93.036
LGA    Q    16_B      Q    16_B     0.526     0    0.031   0.162     0.704   92.857   93.651
LGA    S    17_B      S    17_B     0.654     0    0.028   0.036     0.791   90.476   90.476
LGA    L    18_B      L    18_B     0.532     0    0.099   0.148     0.532   92.857   95.238
LGA    P    19_B      P    19_B     0.812     0    0.073   0.390     2.337   90.476   84.218
LGA    G    20_B      G    20_B     0.709     0    0.107   0.107     0.913   90.476   90.476
LGA    C    21_B      C    21_B     0.257     0    0.011   0.091     0.599  100.000   98.413
LGA    E    22_B      E    22_B     0.484     0    0.079   0.163     1.019   95.238   91.587
LGA    E    23_B      E    23_B     0.482     0    0.062   1.110     5.383   97.619   73.175
LGA    H    24_B      H    24_B     0.199     0    0.099   0.151     0.876  100.000   96.190
LGA    G    25_B      G    25_B     0.290     0    0.011   0.011     0.454  100.000  100.000
LGA    K    26_B      K    26_B     0.377     0    0.017   0.620     2.733  100.000   94.180
LGA    V    27_B      V    27_B     0.732     0    0.060   1.122     3.377   90.476   82.109
LGA    F    28_B      F    28_B     0.282     0    0.025   0.028     0.491  100.000  100.000
LGA    K    29_B      K    29_B     0.407     0    0.020   0.787     2.553   95.238   85.291
LGA    D    30_B      D    30_B     0.898     0    0.087   0.106     1.226   90.476   85.952
LGA    E    31_B      E    31_B     0.871     0    0.022   0.083     1.250   90.476   87.460
LGA    Q    32_B      Q    32_B     0.835     0    0.051   0.095     1.552   90.476   85.503
LGA    I    33_B      I    33_B     0.442     0    0.045   0.624     1.635   97.619   94.226
LGA    D    34_B      D    34_B     0.522     0    0.033   0.120     1.049   97.619   92.917
LGA    G    35_B      G    35_B     0.388     0    0.026   0.026     0.480  100.000  100.000
LGA    E    36_B      E    36_B     0.751     0    0.038   0.902     2.503   90.476   83.757
LGA    A    37_B      A    37_B     0.637     0    0.054   0.066     0.656   90.476   92.381
LGA    F    38_B      F    38_B     0.375     0    0.033   0.249     0.932  100.000   96.537
LGA    L    39_B      L    39_B     0.449     0    0.075   0.176     0.671   97.619   95.238
LGA    L    40_B      L    40_B     0.267     0    0.110   0.196     0.745   97.619   95.238
LGA    M    41_B      M    41_B     0.178     0    0.086   0.362     1.241  100.000   95.298
LGA    T    42_B      T    42_B     0.653     0    0.036   0.044     0.828   92.857   91.837
LGA    Q    43_B      Q    43_B     0.616     0    0.013   0.583     2.464   95.238   88.730
LGA    T    44_B      T    44_B     0.565     0    0.012   0.132     0.956   95.238   93.197
LGA    D    45_B      D    45_B     0.442     0    0.031   0.160     0.704   95.238   95.238
LGA    I    46_B      I    46_B     0.564     0    0.035   0.077     0.962   90.476   90.476
LGA    V    47_B      V    47_B     0.564     0    0.040   0.056     0.762   90.476   90.476
LGA    K    48_B      K    48_B     1.414     0    0.032   0.920     5.526   77.143   63.968
LGA    I    49_B      I    49_B     1.592     0    0.080   0.121     1.777   75.000   73.929
LGA    M    50_B      M    50_B     1.312     0    0.014   0.719     1.510   81.429   81.488
LGA    S    51_B      S    51_B     0.934     0    0.028   0.028     1.352   90.595   87.540
LGA    I    52_B      I    52_B     0.377     0    0.028   0.033     0.724   97.619   96.429
LGA    K    53_B      K    53_B     0.433     0    0.024   0.667     2.962  100.000   87.302
LGA    E    54_B      E    54_B     0.477     0    0.034   0.746     3.490   97.619   83.651
LGA    G    55_B      G    55_B     0.474     0    0.019   0.019     0.481  100.000  100.000
LGA    P    56_B      P    56_B     0.321     0    0.016   0.286     0.845  100.000   98.639
LGA    A    57_B      A    57_B     0.294     0    0.023   0.028     0.411  100.000  100.000
LGA    E    58_B      E    58_B     0.518     0    0.036   0.145     0.604   90.476   93.651
LGA    K    59_B      K    59_B     0.497     0    0.053   0.126     0.659   95.238   97.884
LGA    I    60_B      I    60_B     0.279     0    0.014   0.032     0.331  100.000  100.000
LGA    F    61_B      F    61_B     0.299     0    0.036   0.056     0.496  100.000  100.000
LGA    N    62_B      N    62_B     0.455     0    0.030   0.071     0.723  100.000   95.238
LGA    S    63_B      S    63_B     0.421     0    0.022   0.036     0.454  100.000  100.000
LGA    I    64_B      I    64_B     0.418     0    0.010   0.042     0.503   97.619   98.810
LGA    L    65_B      L    65_B     0.474     0    0.015   0.153     0.770   95.238   96.429
LGA    M    66_B      M    66_B     0.708     0    0.024   0.630     3.655   88.214   74.226
LGA    F    67_B      F    67_B     0.883     0    0.047   0.322     1.349   85.952   88.009
LGA    K    68_B      K    68_B     1.087     0    0.048   0.955     2.652   83.690   80.741
LGA    A    69_B      A    69_B     1.282     0    0.065   0.076     1.467   81.429   81.429
LGA    A    70_B      A    70_B     1.753     0    0.153   0.172     2.261   70.833   71.238
LGA    E    71_B      E    71_B     1.848     0    0.128   0.665     2.364   72.857   74.868

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     553    553  100.00                71
SUMMARY(RMSD_GDC):     0.719          0.718                  1.128           93.583   89.831

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    0.72    97.183    98.900     8.672

LGA_LOCAL      RMSD:   0.719  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.719  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   0.719  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.539229 * X  +  -0.461096 * Y  +  -0.704715 * Z  +  18.691750
  Y_new =  -0.105913 * X  +  -0.793021 * Y  +   0.599917 * Z  +  38.410820
  Z_new =  -0.835473 * X  +   0.398131 * Y  +   0.378783 * Z  +   5.785376 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.947646  0.988993  0.810296   [DEG: -168.8877   56.6651   46.4266 ]
ZXZ: -2.276039  1.182315 -1.126097   [DEG: -130.4075   67.7417  -64.5206 ]
 
# END of job
