
#######################################################
#                                                     #
#                        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        1.19     1.19
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.19     1.19
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63      23_A - 85_A        0.83     1.21
  LCS_AVERAGE:     96.97

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      3   64   64      3    3    3    4    5    6   39   53   60   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     63   64   64      3    3    5   26   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     63   64   64      3    3    5   36   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     63   64   64      3   15   20   31   61   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     63   64   64     28   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     63   64   64     33   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     63   64   64     33   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     63   64   64     33   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     63   64   64     21   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     63   64   64     30   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     63   64   64     13   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     63   64   64      9   47   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     63   64   64     13   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     63   64   64     51   59   60   60   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  98.99  (  96.97  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     51     59     60     60     62     63     63     63     63     64     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  79.69  92.19  93.75  93.75  96.88  98.44  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
GDT RMS_LOCAL    0.31   0.42   0.44   0.44   0.74   0.83   0.83   0.83   0.83   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19
GDT RMS_ALL_AT   1.25   1.23   1.24   1.24   1.20   1.21   1.21   1.21   1.21   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19   1.19

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     7.121     0    0.456   0.418     8.130   17.738   15.143
LGA    D    23_A      D    23_A     3.107     0    0.570   0.445     4.909   40.476   45.298
LGA    G    24_A      G    24_A     3.274     0    0.108   0.108     3.684   53.810   53.810
LGA    D    25_A      D    25_A     2.991     0    0.394   1.006     5.017   51.310   43.512
LGA    G    26_A      G    26_A     0.323     0    0.051   0.051     0.592   97.619   97.619
LGA    Q    27_A      Q    27_A     0.311     0    0.037   1.174     3.654  100.000   84.709
LGA    G    28_A      G    28_A     0.233     0    0.034   0.034     0.312  100.000  100.000
LGA    L    29_A      L    29_A     0.262     0    0.031   0.074     0.422  100.000  100.000
LGA    Y    30_A      Y    30_A     0.372     0    0.021   0.084     0.555  100.000   99.206
LGA    A    31_A      A    31_A     0.440     0    0.032   0.039     0.515   97.619   98.095
LGA    A    32_A      A    32_A     0.375     0    0.012   0.024     0.439  100.000  100.000
LGA    N    33_A      N    33_A     0.424     0    0.019   0.103     0.576   97.619   97.619
LGA    C    34_A      C    34_A     0.404     0    0.030   0.102     0.499  100.000  100.000
LGA    A    35_A      A    35_A     0.605     0    0.015   0.023     0.812   92.857   92.381
LGA    A    36_A      A    36_A     0.630     0    0.017   0.023     0.820   90.476   90.476
LGA    C    37_A      C    37_A     0.581     0    0.022   0.045     0.660   90.476   90.476
LGA    H    38_A      H    38_A     0.626     0    0.026   0.162     0.848   90.476   92.381
LGA    G    39_A      G    39_A     0.834     0    0.114   0.114     0.865   90.476   90.476
LGA    A    40_A      A    40_A     0.573     0    0.034   0.037     0.838   97.619   96.190
LGA    L    41_A      L    41_A     0.407     0    0.013   0.028     0.546   95.238   97.619
LGA    A    42_A      A    42_A     0.726     0    0.021   0.023     0.761   90.476   90.476
LGA    T    43_A      T    43_A     0.625     0    0.177   0.156     1.042   88.214   89.184
LGA    S    44_A      S    44_A     0.648     0    0.090   0.122     0.650   90.476   92.063
LGA    E    45_A      E    45_A     1.032     0    0.020   0.656     4.023   88.214   67.566
LGA    K    46_A      K    46_A     0.289     0    0.083   0.233     1.718   97.619   91.746
LGA    K    47_A      K    47_A     0.317     0    0.010   0.122     0.456  100.000  100.000
LGA    G    48_A      G    48_A     0.360     0    0.060   0.060     0.451  100.000  100.000
LGA    T    49_A      T    49_A     0.351     0    0.093   0.127     0.467  100.000  100.000
LGA    T    50_A      T    50_A     0.256     0    0.015   0.076     0.737  100.000   97.279
LGA    L    51_A      L    51_A     0.306     0    0.035   0.109     0.940  100.000   95.238
LGA    A    52_A      A    52_A     0.471     0    0.013   0.019     0.645  100.000   98.095
LGA    R    53_A      R    53_A     0.397     0    0.015   1.116     4.422  100.000   81.602
LGA    L    54_A      L    54_A     0.170     0    0.054   0.086     0.418  100.000  100.000
LGA    Q    55_A      Q    55_A     0.155     0    0.025   0.206     0.503  100.000   98.942
LGA    S    56_A      S    56_A     0.320     0    0.034   0.033     0.407  100.000  100.000
LGA    A    57_A      A    57_A     0.288     0    0.017   0.023     0.384  100.000  100.000
LGA    V    58_A      V    58_A     0.268     0    0.036   0.046     0.443  100.000  100.000
LGA    S    59_A      S    59_A     0.268     0    0.014   0.735     2.272  100.000   94.127
LGA    A    60_A      A    60_A     0.119     0    0.017   0.035     0.212  100.000  100.000
LGA    N    61_A      N    61_A     0.297     0    0.044   0.155     1.174  100.000   94.107
LGA    A    62_A      A    62_A     0.436     0    0.041   0.049     0.641  100.000   98.095
LGA    G    63_A      G    63_A     0.510     0    0.055   0.055     0.530   95.238   95.238
LGA    G    64_A      G    64_A     0.523     0    0.062   0.062     0.795   92.857   92.857
LGA    M    65_A      M    65_A     0.725     0    0.058   0.203     0.939   90.476   90.476
LGA    G    66_A      G    66_A     0.530     0    0.014   0.014     0.734   90.476   90.476
LGA    F    67_A      F    67_A     1.203     0    0.055   0.119     1.970   83.690   76.797
LGA    L    68_A      L    68_A     0.969     0    0.052   0.073     1.623   88.214   82.679
LGA    S    69_A      S    69_A     0.453     0    0.036   0.068     0.881   92.857   92.063
LGA    S    70_A      S    70_A     0.726     0    0.017   0.041     0.919   90.476   90.476
LGA    L    71_A      L    71_A     0.547     0    0.025   0.070     0.744   90.476   90.476
LGA    T    72_A      T    72_A     0.451     0    0.039   0.049     0.555  100.000   98.639
LGA    S    73_A      S    73_A     0.340     0    0.023   0.620     2.677  100.000   92.857
LGA    A    74_A      A    74_A     0.194     0    0.073   0.087     0.417  100.000  100.000
LGA    Q    75_A      Q    75_A     0.350     0    0.017   0.047     0.649  100.000   95.767
LGA    L    76_A      L    76_A     0.209     0    0.013   0.046     0.379  100.000  100.000
LGA    Q    77_A      Q    77_A     0.248     0    0.073   0.180     0.569  100.000   98.942
LGA    A    78_A      A    78_A     0.296     0    0.023   0.033     0.300  100.000  100.000
LGA    I    79_A      I    79_A     0.206     0    0.024   0.057     0.284  100.000  100.000
LGA    V    80_A      V    80_A     0.263     0    0.017   0.063     0.301  100.000  100.000
LGA    D    81_A      D    81_A     0.345     0    0.058   0.071     0.603  100.000   96.429
LGA    V    82_A      V    82_A     0.329     0    0.047   1.267     2.520  100.000   88.844
LGA    L    83_A      L    83_A     0.182     0    0.101   0.100     0.378  100.000  100.000
LGA    A    84_A      A    84_A     0.134     0    0.153   0.169     0.737   97.619   98.095
LGA    V    85_A      V    85_A     0.239     0    0.361   1.337     2.978   97.619   87.483

# 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):     1.185          1.169                  1.336           93.263   91.127

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     63    0.83    96.094    97.930     6.797

LGA_LOCAL      RMSD:   0.827  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.210  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.185  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.012328 * X  +  -0.281980 * Y  +  -0.959341 * Z  +  23.438591
  Y_new =  -0.563534 * X  +  -0.794496 * Y  +   0.226285 * Z  +  -8.992020
  Z_new =  -0.826001 * X  +   0.537832 * Y  +  -0.168700 * Z  + -10.015228 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.548924  0.971975  1.874744   [DEG:  -88.7468   55.6901  107.4149 ]
ZXZ: -1.802438  1.740307 -0.993629   [DEG: -103.2721   99.7122  -56.9307 ]
 
# END of job
