
#######################################################
#                                                     #
#                        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   97 (  681),  selected   64 , name one
# Molecule2: number of CA atoms   64 (  433),  selected   64 , 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:    64      22_A - 85_A        1.11     1.11
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.11     1.11
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63      22_A - 84_A        0.97     1.12
  LCS_AVERAGE:     98.41

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
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    22_A     A    22_A     63   64   64      4   12   28   53   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     63   64   64      4    4    4   53   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     63   64   64      4    4   24   55   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     63   64   64      4    4   24   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     63   64   64     34   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     63   64   64     34   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     63   64   64     29   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     63   64   64     17   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     63   64   64     17   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     63   64   64      6   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     63   64   64     27   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     63   64   64     27   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     63   64   64     30   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     63   64   64     20   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     63   64   64     30   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     63   64   64     38   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     63   64   64     13   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     63   64   64     36   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     63   64   64     32   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     63   64   64     13   31   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     63   64   64     13   31   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     63   64   64     34   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     63   64   64      4   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     63   64   64     39   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     63   64   64     29   57   59   59   63   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     62   64   64      3    4    4   38   54   60   62   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  99.47  (  98.41  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     39     57     59     59     63     63     63     64     64     64     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  60.94  89.06  92.19  92.19  98.44  98.44  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.49   0.53   0.53   0.97   0.97   0.97   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11
GDT RMS_ALL_AT   1.13   1.14   1.16   1.16   1.12   1.12   1.12   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11   1.11

# Checking swapping
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  E    45_A      E    45_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     3.419     0    0.014   0.018     4.098   48.571   48.857
LGA    D    23_A      D    23_A     2.792     0    0.123   0.130     4.805   55.357   48.690
LGA    G    24_A      G    24_A     3.212     0    0.110   0.110     3.212   55.357   55.357
LGA    D    25_A      D    25_A     2.901     0    0.682   0.615     4.790   48.929   49.524
LGA    G    26_A      G    26_A     0.333     0    0.093   0.093     0.540   97.619   97.619
LGA    Q    27_A      Q    27_A     0.186     0    0.017   1.420     5.330  100.000   79.206
LGA    G    28_A      G    28_A     0.331     0    0.017   0.017     0.331  100.000  100.000
LGA    L    29_A      L    29_A     0.077     0    0.008   1.257     2.603  100.000   90.238
LGA    Y    30_A      Y    30_A     0.224     0    0.040   0.115     0.430  100.000  100.000
LGA    A    31_A      A    31_A     0.356     0    0.020   0.024     0.657   97.619   98.095
LGA    A    32_A      A    32_A     0.411     0    0.035   0.040     0.582   97.619   98.095
LGA    N    33_A      N    33_A     0.315     0    0.015   0.056     0.412  100.000  100.000
LGA    C    34_A      C    34_A     0.439     0    0.007   0.069     0.572   95.238   96.825
LGA    A    35_A      A    35_A     0.675     0    0.046   0.052     1.121   88.214   88.667
LGA    A    36_A      A    36_A     0.794     0    0.007   0.012     1.006   88.214   88.667
LGA    C    37_A      C    37_A     0.833     0    0.053   0.052     0.883   90.476   90.476
LGA    H    38_A      H    38_A     0.979     0    0.031   0.107     1.225   85.952   85.952
LGA    G    39_A      G    39_A     1.014     0    0.078   0.078     1.037   85.952   85.952
LGA    A    40_A      A    40_A     0.392     0    0.021   0.031     0.571  100.000   98.095
LGA    L    41_A      L    41_A     0.319     0    0.017   0.048     0.638  100.000   97.619
LGA    A    42_A      A    42_A     0.487     0    0.009   0.015     0.572  100.000   98.095
LGA    T    43_A      T    43_A     0.323     0    0.076   0.065     0.550   97.619   98.639
LGA    S    44_A      S    44_A     0.515     0    0.014   0.021     0.656   97.619   95.238
LGA    E    45_A      E    45_A     0.699     0    0.054   0.767     3.895   92.857   71.323
LGA    K    46_A      K    46_A     0.374     0    0.044   0.173     1.874   97.619   89.788
LGA    K    47_A      K    47_A     0.513     0    0.013   0.082     0.777   92.857   94.709
LGA    G    48_A      G    48_A     0.703     0    0.084   0.084     0.703   90.476   90.476
LGA    T    49_A      T    49_A     0.662     0    0.034   0.090     0.879   92.857   91.837
LGA    T    50_A      T    50_A     0.610     0    0.038   0.081     0.962   90.476   90.476
LGA    L    51_A      L    51_A     0.364     0    0.010   0.083     0.662  100.000   98.810
LGA    A    52_A      A    52_A     0.634     0    0.012   0.013     0.756   90.476   90.476
LGA    R    53_A      R    53_A     0.877     0    0.008   0.606     3.382   90.476   76.580
LGA    L    54_A      L    54_A     0.619     0    0.017   0.104     0.834   90.476   90.476
LGA    Q    55_A      Q    55_A     0.434     0    0.018   0.175     0.576   97.619   97.884
LGA    S    56_A      S    56_A     0.458     0    0.031   0.690     2.189  100.000   94.127
LGA    A    57_A      A    57_A     0.470     0    0.024   0.026     0.520   97.619   96.190
LGA    V    58_A      V    58_A     0.550     0    0.023   1.340     3.060   95.238   83.742
LGA    S    59_A      S    59_A     0.253     0    0.012   0.739     2.158  100.000   94.127
LGA    A    60_A      A    60_A     0.255     0    0.020   0.029     0.552   97.619   98.095
LGA    N    61_A      N    61_A     0.528     0    0.059   0.105     1.475   97.619   90.655
LGA    A    62_A      A    62_A     0.291     0    0.017   0.020     0.388  100.000  100.000
LGA    G    63_A      G    63_A     0.392     0    0.030   0.030     0.820   95.238   95.238
LGA    G    64_A      G    64_A     0.887     0    0.091   0.091     1.402   88.214   88.214
LGA    M    65_A      M    65_A     0.713     0    0.027   0.171     0.760   90.476   92.857
LGA    G    66_A      G    66_A     0.828     0    0.008   0.008     1.063   85.952   85.952
LGA    F    67_A      F    67_A     1.622     0    0.038   0.198     2.515   75.000   73.030
LGA    L    68_A      L    68_A     1.478     0    0.086   1.248     4.112   81.429   71.667
LGA    S    69_A      S    69_A     0.873     0    0.018   0.042     1.093   88.214   88.968
LGA    S    70_A      S    70_A     0.783     0    0.031   0.067     1.068   88.214   85.952
LGA    L    71_A      L    71_A     0.643     0    0.021   1.240     2.988   92.857   84.286
LGA    T    72_A      T    72_A     0.387     0    0.011   0.041     0.652  100.000   98.639
LGA    S    73_A      S    73_A     0.264     0    0.015   0.631     2.763  100.000   92.857
LGA    A    74_A      A    74_A     0.581     0    0.022   0.025     0.737   92.857   92.381
LGA    Q    75_A      Q    75_A     0.401     0    0.041   0.150     0.806  100.000   95.767
LGA    L    76_A      L    76_A     0.232     0    0.012   1.246     2.540  100.000   90.238
LGA    Q    77_A      Q    77_A     0.274     0    0.007   0.142     0.577  100.000   97.884
LGA    A    78_A      A    78_A     0.236     0    0.013   0.014     0.245  100.000  100.000
LGA    I    79_A      I    79_A     0.156     0    0.021   0.045     0.286  100.000  100.000
LGA    V    80_A      V    80_A     0.209     0    0.021   1.341     2.684  100.000   88.844
LGA    D    81_A      D    81_A     0.288     0    0.012   0.023     0.700  100.000   96.429
LGA    V    82_A      V    82_A     0.541     0    0.081   1.241     2.706   92.857   83.401
LGA    L    83_A      L    83_A     0.561     0    0.041   1.230     2.549   90.476   85.476
LGA    A    84_A      A    84_A     0.755     0    0.574   0.516     1.237   88.214   90.571
LGA    V    85_A      V    85_A     4.341     0    0.462   0.807     7.077   29.167   22.993

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     433    433  100.00                64
SUMMARY(RMSD_GDC):     1.110          1.185                  1.478           90.997   87.989

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     64    1.11    95.312    97.718     5.289

LGA_LOCAL      RMSD:   1.110  Number of atoms:   64  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.110  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.110  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.723748 * X  +   0.412103 * Y  +  -0.553498 * Z  +  22.293249
  Y_new =   0.426333 * X  +  -0.363674 * Y  +  -0.828240 * Z  + -10.197830
  Z_new =  -0.542613 * X  +  -0.835411 * Y  +   0.087515 * Z  + -13.926963 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.609253  0.573545 -1.466421   [DEG:  149.4992   32.8617  -84.0197 ]
ZXZ: -0.589121  1.483170 -2.565557   [DEG:  -33.7541   84.9794 -146.9956 ]
 
# END of job
