
#######################################################
#                                                     #
#                        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        1.35     1.35
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.35     1.35
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63      23_A - 85_A        0.89     1.38
  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    3    4    4    6   44   52   59   61   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     63   64   64      3    3    4   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     63   64   64      3    3    4   19   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     63   64   64      3   14   19   29   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     63   64   64     35   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     63   64   64     37   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     63   64   64     35   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     63   64   64     35   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     63   64   64     20   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     63   64   64     25   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     63   64   64     14   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     63   64   64     13   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     63   64   64     22   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     63   64   64      8   30   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     63   64   64     13   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     63   64   64     17   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     63   64   64     48   59   60   61   61   63   63   63   63   63   63   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     48     59     60     61     61     63     63     63     63     63     63     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  75.00  92.19  93.75  95.31  95.31  98.44  98.44  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
GDT RMS_LOCAL    0.29   0.44   0.46   0.66   0.61   0.89   0.89   0.89   0.89   0.89   0.89   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35
GDT RMS_ALL_AT   1.41   1.40   1.40   1.37   1.42   1.38   1.38   1.38   1.38   1.38   1.38   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35

# 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     8.426     0    0.613   0.559     9.784   11.548    9.333
LGA    D    23_A      D    23_A     3.520     0    0.216   0.191     4.853   40.476   40.417
LGA    G    24_A      G    24_A     3.671     0    0.251   0.251     3.671   55.714   55.714
LGA    D    25_A      D    25_A     3.060     0    0.451   1.017     5.057   47.619   42.440
LGA    G    26_A      G    26_A     0.332     0    0.055   0.055     0.645   97.619   97.619
LGA    Q    27_A      Q    27_A     0.312     0    0.028   0.150     0.829  100.000   98.942
LGA    G    28_A      G    28_A     0.162     0    0.041   0.041     0.280  100.000  100.000
LGA    L    29_A      L    29_A     0.272     0    0.029   0.086     0.494  100.000  100.000
LGA    Y    30_A      Y    30_A     0.353     0    0.018   0.087     0.522  100.000   98.413
LGA    A    31_A      A    31_A     0.406     0    0.026   0.032     0.501   97.619   98.095
LGA    A    32_A      A    32_A     0.283     0    0.015   0.028     0.374  100.000  100.000
LGA    N    33_A      N    33_A     0.424     0    0.019   0.083     0.554   97.619   98.810
LGA    C    34_A      C    34_A     0.459     0    0.038   0.095     0.538   97.619   96.825
LGA    A    35_A      A    35_A     0.628     0    0.016   0.023     0.834   92.857   92.381
LGA    A    36_A      A    36_A     0.605     0    0.016   0.022     0.814   90.476   90.476
LGA    C    37_A      C    37_A     0.571     0    0.014   0.053     0.679   90.476   90.476
LGA    H    38_A      H    38_A     0.629     0    0.012   0.118     0.812   90.476   92.381
LGA    G    39_A      G    39_A     0.890     0    0.082   0.082     0.890   90.476   90.476
LGA    A    40_A      A    40_A     0.441     0    0.034   0.036     0.642  100.000   98.095
LGA    L    41_A      L    41_A     0.361     0    0.016   0.031     0.511   97.619   98.810
LGA    A    42_A      A    42_A     0.629     0    0.044   0.052     0.715   90.476   90.476
LGA    T    43_A      T    43_A     0.547     0    0.135   0.112     0.818   90.476   91.837
LGA    S    44_A      S    44_A     0.602     0    0.069   0.091     0.602   92.857   92.063
LGA    E    45_A      E    45_A     1.076     0    0.045   0.706     4.434   88.214   65.450
LGA    K    46_A      K    46_A     0.308     0    0.079   0.533     3.053   95.238   87.196
LGA    K    47_A      K    47_A     0.368     0    0.010   0.110     0.489  100.000  100.000
LGA    G    48_A      G    48_A     0.431     0    0.068   0.068     0.551   97.619   97.619
LGA    T    49_A      T    49_A     0.383     0    0.090   0.129     0.497  100.000  100.000
LGA    T    50_A      T    50_A     0.242     0    0.015   0.107     0.862  100.000   95.918
LGA    L    51_A      L    51_A     0.313     0    0.037   0.097     0.891  100.000   98.810
LGA    A    52_A      A    52_A     0.495     0    0.015   0.025     0.643  100.000   98.095
LGA    R    53_A      R    53_A     0.423     0    0.022   1.244     5.339  100.000   70.260
LGA    L    54_A      L    54_A     0.134     0    0.045   0.080     0.365  100.000  100.000
LGA    Q    55_A      Q    55_A     0.124     0    0.029   0.184     0.532  100.000   98.942
LGA    S    56_A      S    56_A     0.251     0    0.023   0.022     0.307  100.000  100.000
LGA    A    57_A      A    57_A     0.179     0    0.010   0.013     0.241  100.000  100.000
LGA    V    58_A      V    58_A     0.313     0    0.026   0.037     0.513  100.000   98.639
LGA    S    59_A      S    59_A     0.313     0    0.014   0.554     1.903  100.000   95.476
LGA    A    60_A      A    60_A     0.136     0    0.018   0.035     0.239  100.000  100.000
LGA    N    61_A      N    61_A     0.309     0    0.038   0.138     1.160  100.000   94.107
LGA    A    62_A      A    62_A     0.420     0    0.043   0.051     0.678   97.619   96.190
LGA    G    63_A      G    63_A     0.369     0    0.056   0.056     0.581   97.619   97.619
LGA    G    64_A      G    64_A     0.737     0    0.053   0.053     1.065   90.595   90.595
LGA    M    65_A      M    65_A     0.906     0    0.074   1.029     3.223   90.476   82.083
LGA    G    66_A      G    66_A     0.662     0    0.011   0.011     0.831   90.476   90.476
LGA    F    67_A      F    67_A     1.347     0    0.065   0.206     2.250   81.429   73.030
LGA    L    68_A      L    68_A     1.108     0    0.054   0.095     1.905   85.952   80.476
LGA    S    69_A      S    69_A     0.602     0    0.037   0.070     0.956   90.476   90.476
LGA    S    70_A      S    70_A     0.840     0    0.010   0.014     0.957   90.476   90.476
LGA    L    71_A      L    71_A     0.599     0    0.037   0.070     0.787   90.476   90.476
LGA    T    72_A      T    72_A     0.394     0    0.039   0.067     0.505  100.000   98.639
LGA    S    73_A      S    73_A     0.330     0    0.015   0.598     2.557  100.000   92.857
LGA    A    74_A      A    74_A     0.293     0    0.045   0.059     0.380  100.000  100.000
LGA    Q    75_A      Q    75_A     0.320     0    0.017   0.073     0.763  100.000   95.767
LGA    L    76_A      L    76_A     0.221     0    0.006   0.048     0.417  100.000  100.000
LGA    Q    77_A      Q    77_A     0.241     0    0.071   0.161     0.517  100.000   98.942
LGA    A    78_A      A    78_A     0.303     0    0.024   0.031     0.379  100.000  100.000
LGA    I    79_A      I    79_A     0.236     0    0.018   0.043     0.303  100.000  100.000
LGA    V    80_A      V    80_A     0.252     0    0.023   0.058     0.270  100.000  100.000
LGA    D    81_A      D    81_A     0.347     0    0.047   0.065     0.697  100.000   96.429
LGA    V    82_A      V    82_A     0.370     0    0.038   1.255     2.495  100.000   89.932
LGA    L    83_A      L    83_A     0.207     0    0.091   0.093     0.381  100.000  100.000
LGA    A    84_A      A    84_A     0.139     0    0.144   0.159     0.580   97.619   98.095
LGA    V    85_A      V    85_A     0.281     0    0.337   1.333     3.158   97.619   86.463

# 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):     1.351          1.264                  1.469           93.030   90.681

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     63    0.89    96.484    97.807     6.333

LGA_LOCAL      RMSD:   0.895  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.377  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.351  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.454422 * X  +  -0.014726 * Y  +  -0.890665 * Z  +  23.145502
  Y_new =  -0.086996 * X  +   0.994350 * Y  +  -0.060826 * Z  + -12.844304
  Z_new =   0.886528 * X  +   0.105125 * Y  +   0.450573 * Z  +  -6.961163 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.189154 -1.089787  0.229213   [DEG:  -10.8377  -62.4402   13.1329 ]
ZXZ: -1.502609  1.103389  1.452767   [DEG:  -86.0931   63.2195   83.2374 ]
 
# END of job
