
#######################################################
#                                                     #
#                        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        1.27     1.27
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.27     1.27
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    65       1_B - 65_B        0.98     1.37
  LONGEST_CONTINUOUS_SEGMENT:    65       2_B - 66_B        0.99     1.36
  LCS_AVERAGE:     88.91

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     65   71   71      4    9   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     65   71   71      4   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     65   71   71     18   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     65   71   71     18   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     65   71   71     18   44   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     65   71   71     18   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     65   71   71     18   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     65   71   71     20   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     65   71   71     18   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     65   71   71     14   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     65   71   71      9   45   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     65   71   71     11   45   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     65   71   71     12   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     65   71   71     12   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     65   71   71     11   44   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     65   71   71      9   22   56   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     65   71   71      9   22   53   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     65   71   71     20   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     65   71   71     13   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     65   71   71     11   45   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     65   71   71     11   40   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     65   71   71     13   32   62   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     65   71   71     13   32   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     65   71   71     13   45   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     65   71   71     13   43   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     65   71   71     13   32   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     65   71   71     13   36   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     65   71   71     22   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     65   71   71     13   46   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     65   71   71     13   32   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     65   71   71     13   36   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     65   71   71     18   44   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     65   71   71     13   36   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     47   71   71     13   31   60   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     46   71   71     13   24   52   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     33   71   71      7   20   34   58   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     33   71   71      9   20   34   53   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     33   71   71      3   16   27   43   57   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  96.30  (  88.91  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     46     63     68     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  30.99  64.79  88.73  95.77  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
GDT RMS_LOCAL    0.31   0.63   0.94   1.07   1.19   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27
GDT RMS_ALL_AT   1.56   1.45   1.34   1.31   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27   1.27

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    23_B      E    23_B
#   possible swapping detected:  D    34_B      D    34_B
#   possible swapping detected:  F    67_B      F    67_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     1.436     0    0.414   0.414     2.534   73.452   73.452
LGA    S     2_B      S     2_B     1.271     0    0.101   0.160     2.570   83.690   76.111
LGA    V     3_B      V     3_B     1.050     0    0.062   0.122     1.574   85.952   82.789
LGA    S     4_B      S     4_B     1.028     0    0.082   0.560     2.500   85.952   81.667
LGA    K     5_B      K     5_B     0.822     0    0.158   0.898     3.362   81.548   74.497
LGA    W     6_B      W     6_B     1.064     0    0.024   0.089     1.690   83.690   80.884
LGA    S     7_B      S     7_B     1.138     0    0.082   0.096     1.426   85.952   84.444
LGA    T     8_B      T     8_B     0.382     0    0.036   0.963     2.657   97.619   87.483
LGA    D     9_B      D     9_B     0.929     0    0.039   0.814     4.125   88.214   73.214
LGA    E    10_B      E    10_B     1.109     0    0.028   0.226     1.876   83.690   78.624
LGA    V    11_B      V    11_B     0.602     0    0.033   0.110     0.824   90.476   90.476
LGA    S    12_B      S    12_B     1.091     0    0.030   0.726     2.199   83.690   80.159
LGA    E    13_B      E    13_B     1.529     0    0.047   0.647     3.411   79.286   66.349
LGA    F    14_B      F    14_B     1.209     0    0.040   0.153     1.909   81.429   78.312
LGA    I    15_B      I    15_B     0.896     0    0.034   0.956     2.625   85.952   79.643
LGA    Q    16_B      Q    16_B     1.276     0    0.074   1.077     5.026   81.429   63.333
LGA    S    17_B      S    17_B     1.417     0    0.099   0.676     2.036   83.690   78.730
LGA    L    18_B      L    18_B     0.939     0    0.020   0.962     2.807   83.690   80.714
LGA    P    19_B      P    19_B     1.195     0    0.495   0.787     3.801   69.762   76.054
LGA    G    20_B      G    20_B     1.097     0    0.131   0.131     2.231   77.262   77.262
LGA    C    21_B      C    21_B     0.912     0    0.094   0.148     1.124   85.952   87.460
LGA    E    22_B      E    22_B     1.030     0    0.075   0.491     2.602   85.952   79.788
LGA    E    23_B      E    23_B     0.739     0    0.167   0.595     2.019   88.214   83.651
LGA    H    24_B      H    24_B     0.495     0    0.134   0.919     3.262  100.000   86.000
LGA    G    25_B      G    25_B     0.530     0    0.030   0.030     0.576   90.476   90.476
LGA    K    26_B      K    26_B     0.783     0    0.027   1.366     5.711   90.476   76.349
LGA    V    27_B      V    27_B     1.022     0    0.024   1.148     3.371   88.214   77.347
LGA    F    28_B      F    28_B     0.661     0    0.029   0.143     1.122   90.476   89.697
LGA    K    29_B      K    29_B     0.670     0    0.033   0.598     2.226   88.214   85.714
LGA    D    30_B      D    30_B     1.244     0    0.076   1.130     4.470   83.690   71.905
LGA    E    31_B      E    31_B     1.258     0    0.110   0.299     2.853   81.429   74.074
LGA    Q    32_B      Q    32_B     1.261     0    0.075   0.826     2.971   81.429   76.931
LGA    I    33_B      I    33_B     0.655     0    0.110   0.112     1.004   90.476   90.536
LGA    D    34_B      D    34_B     0.750     0    0.031   0.677     2.783   90.476   85.179
LGA    G    35_B      G    35_B     0.744     0    0.025   0.025     0.810   90.476   90.476
LGA    E    36_B      E    36_B     1.122     0    0.035   0.367     2.652   85.952   77.884
LGA    A    37_B      A    37_B     0.960     0    0.037   0.041     1.116   90.476   88.667
LGA    F    38_B      F    38_B     0.272     0    0.042   0.414     1.886  100.000   88.355
LGA    L    39_B      L    39_B     0.265     0    0.122   0.114     1.044   95.238   91.726
LGA    L    40_B      L    40_B     0.407     0    0.179   0.154     1.028   97.619   92.917
LGA    M    41_B      M    41_B     0.399     0    0.037   0.935     2.035   97.619   88.631
LGA    T    42_B      T    42_B     0.825     0    0.052   0.051     1.042   88.214   87.891
LGA    Q    43_B      Q    43_B     1.334     0    0.040   1.317     5.150   81.429   62.116
LGA    T    44_B      T    44_B     1.471     0    0.043   0.153     2.046   81.429   76.599
LGA    D    45_B      D    45_B     0.891     0    0.037   0.084     1.032   88.214   87.083
LGA    I    46_B      I    46_B     0.613     0    0.035   0.131     0.852   90.476   91.667
LGA    V    47_B      V    47_B     1.226     0    0.043   1.162     4.056   83.690   73.946
LGA    K    48_B      K    48_B     1.975     0    0.081   1.759    11.962   70.833   41.693
LGA    I    49_B      I    49_B     1.919     0    0.028   1.255     5.483   72.857   63.036
LGA    M    50_B      M    50_B     1.072     0    0.750   1.081     2.325   81.905   76.429
LGA    S    51_B      S    51_B     0.945     0    0.230   0.745     3.789   86.071   78.175
LGA    I    52_B      I    52_B     0.494     0    0.049   0.575     1.348   95.238   88.333
LGA    K    53_B      K    53_B     0.799     0    0.058   0.745     2.523   88.214   82.063
LGA    E    54_B      E    54_B     1.294     0    0.029   0.945     3.129   81.429   74.180
LGA    G    55_B      G    55_B     1.813     0    0.047   0.047     1.813   72.857   72.857
LGA    P    56_B      P    56_B     1.529     0    0.044   0.293     1.650   77.143   76.531
LGA    A    57_B      A    57_B     1.023     0    0.046   0.047     1.252   83.690   83.238
LGA    E    58_B      E    58_B     1.394     0    0.029   0.985     5.333   81.429   61.005
LGA    K    59_B      K    59_B     1.663     0    0.040   0.077     2.730   75.000   68.519
LGA    I    60_B      I    60_B     1.086     0    0.039   0.610     1.989   85.952   81.548
LGA    F    61_B      F    61_B     0.594     0    0.031   1.141     5.195   90.476   70.909
LGA    N    62_B      N    62_B     0.740     0    0.059   0.203     1.018   90.476   89.345
LGA    S    63_B      S    63_B     1.332     0    0.030   0.065     1.543   81.429   80.000
LGA    I    64_B      I    64_B     1.234     0    0.024   0.167     1.518   81.429   80.357
LGA    L    65_B      L    65_B     0.821     0    0.041   0.904     2.363   88.214   85.000
LGA    M    66_B      M    66_B     1.171     0    0.043   0.793     2.134   81.548   79.405
LGA    F    67_B      F    67_B     1.683     0    0.029   0.892     3.540   72.976   67.403
LGA    K    68_B      K    68_B     1.963     0    0.044   1.107     3.511   66.905   61.746
LGA    A    69_B      A    69_B     2.525     0    0.129   0.126     2.823   59.048   58.667
LGA    A    70_B      A    70_B     3.032     0    0.494   0.457     4.777   45.476   46.381
LGA    E    71_B      E    71_B     3.842     0    0.258   1.074     4.923   40.476   50.000

# 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):     1.268          1.336                  1.893           83.434   77.945

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.27    90.141    95.991     5.189

LGA_LOCAL      RMSD:   1.268  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.268  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.268  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.748193 * X  +  -0.616382 * Y  +  -0.245522 * Z  +  21.324198
  Y_new =   0.166051 * X  +   0.532234 * Y  +  -0.830153 * Z  +  72.546776
  Z_new =   0.642366 * X  +   0.580345 * Y  +   0.500564 * Z  +   4.411146 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.218397 -0.697582  0.859074   [DEG:   12.5132  -39.9685   49.2213 ]
ZXZ: -0.287558  1.046546  0.836079   [DEG:  -16.4758   59.9627   47.9038 ]
 
# END of job
