
#######################################################
#                                                     #
#                        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        1.10     1.10
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.10     1.10
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_B - 68_B        1.00     1.11
  LCS_AVERAGE:     93.45

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     66   71   71      4   29   52   66   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     67   71   71     20   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     67   71   71     20   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     67   71   71     13   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     67   71   71      8   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     67   71   71     21   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     67   71   71     19   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     67   71   71     19   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     67   71   71     14   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     67   71   71     14   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     67   71   71     14   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     67   71   71     20   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     67   71   71     21   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     67   71   71     13   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     67   71   71     19   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     67   71   71     21   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     67   71   71     13   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     67   71   71     21   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     67   71   71     20   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     67   71   71     21   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     67   71   71     19   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     67   71   71     13   46   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     67   71   71     14   46   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     67   71   71     13   46   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     67   71   71     14   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     67   71   71     14   44   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     67   71   71      8   25   58   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     67   71   71     14   26   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     67   71   71     22   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     67   71   71     20   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     67   71   71     14   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     67   71   71     14   46   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     67   71   71     14   36   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     67   71   71     14   28   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     67   71   71     14   36   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     67   71   71     14   46   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     67   71   71     14   46   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     67   71   71     14   28   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     67   71   71     14   38   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     67   71   71     14   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     67   71   71     14   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     67   71   71     14   31   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     67   71   71     14   34   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     67   71   71     20   42   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     67   71   71     11   30   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     67   71   71     14   24   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     67   71   71     13   24   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     52   71   71     11   24   38   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     52   71   71      5   24   60   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     52   71   71      5   19   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  97.82  (  93.45  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     22     47     63     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  30.99  66.20  88.73  98.59 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.63   0.91   1.07   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10
GDT RMS_ALL_AT   1.24   1.22   1.13   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    23_B      E    23_B
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  F    67_B      F    67_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.319     0    0.235   0.235     2.812   69.048   69.048
LGA    S     2_B      S     2_B     1.153     0    0.098   0.720     3.599   83.810   76.667
LGA    V     3_B      V     3_B     0.738     0    0.057   1.225     3.748   90.476   78.776
LGA    S     4_B      S     4_B     0.767     0    0.077   0.151     1.326   90.476   88.968
LGA    K     5_B      K     5_B     0.698     0    0.144   0.710     3.999   88.214   75.079
LGA    W     6_B      W     6_B     0.821     0    0.020   0.110     1.388   90.476   85.306
LGA    S     7_B      S     7_B     0.845     0    0.068   0.076     1.062   90.476   87.460
LGA    T     8_B      T     8_B     0.334     0    0.034   0.969     2.492  100.000   89.932
LGA    D     9_B      D     9_B     0.744     0    0.030   0.814     3.956   90.476   76.250
LGA    E    10_B      E    10_B     1.011     0    0.033   0.451     1.522   88.214   83.492
LGA    V    11_B      V    11_B     0.585     0    0.033   0.107     0.803   90.476   93.197
LGA    S    12_B      S    12_B     1.030     0    0.029   0.717     1.993   83.690   81.508
LGA    E    13_B      E    13_B     1.356     0    0.038   0.280     1.897   81.429   76.667
LGA    F    14_B      F    14_B     1.048     0    0.040   0.081     1.480   85.952   83.074
LGA    I    15_B      I    15_B     0.765     0    0.026   0.566     2.019   90.476   88.452
LGA    Q    16_B      Q    16_B     1.241     0    0.080   1.287     5.856   81.429   60.635
LGA    S    17_B      S    17_B     1.248     0    0.106   0.678     1.964   85.952   83.016
LGA    L    18_B      L    18_B     0.759     0    0.027   0.099     1.187   88.214   90.536
LGA    P    19_B      P    19_B     1.098     0    0.550   0.904     3.851   72.024   76.122
LGA    G    20_B      G    20_B     0.901     0    0.103   0.103     1.874   81.548   81.548
LGA    C    21_B      C    21_B     0.842     0    0.106   0.132     1.051   88.214   88.968
LGA    E    22_B      E    22_B     0.861     0    0.081   0.676     2.601   90.476   83.757
LGA    E    23_B      E    23_B     0.612     0    0.174   0.926     3.388   88.214   74.709
LGA    H    24_B      H    24_B     0.538     0    0.146   0.320     1.941   97.619   88.000
LGA    G    25_B      G    25_B     0.596     0    0.037   0.037     0.643   90.476   90.476
LGA    K    26_B      K    26_B     0.893     0    0.030   1.042     5.530   90.476   74.550
LGA    V    27_B      V    27_B     1.023     0    0.029   1.129     3.399   88.214   78.435
LGA    F    28_B      F    28_B     0.630     0    0.030   0.060     1.253   90.476   88.009
LGA    K    29_B      K    29_B     0.769     0    0.023   1.086     2.763   88.214   80.952
LGA    D    30_B      D    30_B     1.181     0    0.080   0.936     3.630   83.690   70.833
LGA    E    31_B      E    31_B     1.128     0    0.111   0.232     2.671   83.690   76.878
LGA    Q    32_B      Q    32_B     1.135     0    0.043   1.070     3.467   85.952   77.143
LGA    I    33_B      I    33_B     0.567     0    0.121   0.591     1.281   95.238   92.917
LGA    D    34_B      D    34_B     0.620     0    0.030   0.154     1.530   95.238   88.393
LGA    G    35_B      G    35_B     0.402     0    0.023   0.023     0.535   97.619   97.619
LGA    E    36_B      E    36_B     0.799     0    0.027   0.880     2.074   90.476   85.608
LGA    A    37_B      A    37_B     0.760     0    0.042   0.046     0.900   90.476   90.476
LGA    F    38_B      F    38_B     0.355     0    0.044   0.427     1.239  100.000   94.026
LGA    L    39_B      L    39_B     0.317     0    0.107   0.113     0.886   95.238   97.619
LGA    L    40_B      L    40_B     0.328     0    0.174   1.437     3.818   97.619   79.286
LGA    M    41_B      M    41_B     0.352     0    0.032   0.644     1.845  100.000   94.226
LGA    T    42_B      T    42_B     0.648     0    0.045   0.044     0.977   92.857   91.837
LGA    Q    43_B      Q    43_B     1.191     0    0.040   0.983     4.199   81.429   67.513
LGA    T    44_B      T    44_B     1.370     0    0.039   0.922     3.817   81.429   71.293
LGA    D    45_B      D    45_B     0.836     0    0.027   0.087     0.959   90.476   90.476
LGA    I    46_B      I    46_B     0.506     0    0.062   0.633     1.734   90.476   88.274
LGA    V    47_B      V    47_B     1.219     0    0.027   1.138     3.970   83.690   74.830
LGA    K    48_B      K    48_B     1.802     0    0.098   1.029     7.555   75.000   53.069
LGA    I    49_B      I    49_B     1.695     0    0.029   0.096     2.636   77.143   70.000
LGA    M    50_B      M    50_B     0.734     0    0.086   0.621     1.593   95.238   88.393
LGA    S    51_B      S    51_B     0.207     0    0.055   0.063     0.832  100.000   98.413
LGA    I    52_B      I    52_B     0.471     0    0.038   0.111     1.372   95.238   91.726
LGA    K    53_B      K    53_B     0.804     0    0.050   1.127     6.811   90.476   71.481
LGA    E    54_B      E    54_B     1.252     0    0.027   1.078     5.392   81.429   67.354
LGA    G    55_B      G    55_B     1.713     0    0.046   0.046     1.713   75.000   75.000
LGA    P    56_B      P    56_B     1.458     0    0.048   0.295     1.560   79.286   80.204
LGA    A    57_B      A    57_B     1.009     0    0.039   0.041     1.210   83.690   83.238
LGA    E    58_B      E    58_B     1.311     0    0.026   0.967     4.917   81.429   65.238
LGA    K    59_B      K    59_B     1.628     0    0.038   1.104     2.774   77.143   74.074
LGA    I    60_B      I    60_B     1.109     0    0.037   0.614     2.175   85.952   81.607
LGA    F    61_B      F    61_B     0.617     0    0.062   0.257     1.028   92.857   90.519
LGA    N    62_B      N    62_B     0.740     0    0.040   1.125     2.857   90.476   84.107
LGA    S    63_B      S    63_B     1.405     0    0.028   0.739     1.563   79.286   80.079
LGA    I    64_B      I    64_B     1.297     0    0.029   0.150     1.570   81.429   80.357
LGA    L    65_B      L    65_B     0.902     0    0.046   0.937     2.242   85.952   82.798
LGA    M    66_B      M    66_B     1.350     0    0.043   0.799     2.263   77.143   76.131
LGA    F    67_B      F    67_B     1.678     0    0.040   0.828     3.608   75.000   67.446
LGA    K    68_B      K    68_B     1.783     0    0.042   0.564     2.200   72.857   69.259
LGA    A    69_B      A    69_B     2.138     0    0.104   0.102     2.468   68.810   68.000
LGA    A    70_B      A    70_B     1.904     0    0.214   0.219     2.048   72.976   72.952
LGA    E    71_B      E    71_B     1.742     0    0.533   0.993     3.909   63.452   69.788

# 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):     1.096          1.123                  1.667           86.311   80.902

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.10    91.197    96.392     5.938

LGA_LOCAL      RMSD:   1.096  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.096  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.096  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.761194 * X  +  -0.590050 * Y  +  -0.269119 * Z  +  22.051788
  Y_new =   0.108511 * X  +   0.525001 * Y  +  -0.844156 * Z  +  73.202095
  Z_new =   0.639382 * X  +   0.613364 * Y  +   0.463655 * Z  +   6.114451 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.141600 -0.693694  0.923516   [DEG:    8.1131  -39.7457   52.9136 ]
ZXZ: -0.308617  1.088680  0.806164   [DEG:  -17.6824   62.3768   46.1898 ]
 
# END of job
