
#######################################################
#                                                     #
#                        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   99 (  793),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   61 , 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:    35      35_A - 69_A        4.93     8.87
  LCS_AVERAGE:     51.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19      58_A - 76_A        1.55    11.44
  LCS_AVERAGE:     24.51

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      60_A - 74_A        0.99    11.91
  LONGEST_CONTINUOUS_SEGMENT:    15      62_A - 76_A        0.87    12.30
  LONGEST_CONTINUOUS_SEGMENT:    15      83_A - 97_A        0.82    11.61
  LONGEST_CONTINUOUS_SEGMENT:    15      84_A - 98_A        0.86    12.03
  LCS_AVERAGE:     19.99

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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    32_A     A    32_A      8   11   25      4    7    8   15   18   21   22   24   25   28   28   32   36   39   44   48   52   53   56   58 
LCS_GDT     T    33_A     T    33_A      8   11   34      4    7    8   11   13   19   22   24   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     M    34_A     M    34_A      8   11   34      4    7    8   11   12   14   16   21   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     A    35_A     A    35_A      8   11   35      4    7    8   11   12   13   16   21   25   29   33   37   41   43   46   47   51   53   56   58 
LCS_GDT     D    36_A     D    36_A      8   11   35      4    7    8   11   12   13   16   19   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     L    37_A     L    37_A      8   11   35      4    7    8   11   17   21   22   24   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     K    38_A     K    38_A      8   11   35      4    7    8   11   12   13   16   21   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     M    39_A     M    39_A      8   11   35      4    7   11   12   13   13   19   24   25   27   32   37   40   43   46   48   52   53   56   58 
LCS_GDT     Q    40_A     Q    40_A      8   11   35      4    7   13   15   18   21   22   24   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     A    41_A     A    41_A      6   12   35      4    7    8   16   17   21   22   24   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     V    42_A     V    42_A     11   13   35      5    8   11   12   17   21   22   24   25   28   32   37   41   43   46   48   52   53   56   58 
LCS_GDT     K    43_A     K    43_A     11   13   35      5    8   11   12   17   18   20   21   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     E    44_A     E    44_A     11   13   35      5    9   14   16   19   19   19   20   24   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     I    45_A     I    45_A     11   13   35      5    9   11   12   13   14   20   22   25   28   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     C    46_A     C    46_A     11   13   35      6    9   11   12   13   13   16   21   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     Y    47_A     Y    47_A     11   13   35      5    9   11   12   19   19   19   20   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     E    48_A     E    48_A     11   13   35      6    9   11   12   13   14   18   20   24   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     V    49_A     V    49_A     11   13   35      6    9   11   12   13   13   19   21   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     A    50_A     A    50_A     11   13   35      6    9   11   13   19   19   19   20   21   27   31   35   41   43   46   48   52   53   56   58 
LCS_GDT     L    51_A     L    51_A     11   13   35      6    9   11   12   13   13   16   19   20   24   29   35   38   43   45   47   50   53   55   58 
LCS_GDT     A    52_A     A    52_A     11   13   35      6    9   11   12   13   14   18   21   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     D    53_A     D    53_A     10   13   35      3    4    9   12   13   14   18   21   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     F    54_A     F    54_A      3   13   35      3    4    7    9   12   14   18   20   24   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     R    55_A     R    55_A      4    5   35      3    4    4    9   12   14   16   21   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     H    56_A     H    56_A      4    5   35      3    3    4    5    5   10   11   15   22   26   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     G    57_A     G    57_A      4    5   35      3    3    4    6    9   13   15   18   22   27   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     R    58_A     R    58_A     12   19   35      5    8   11   14   17   19   20   22   24   28   28   31   36   38   44   46   52   53   56   58 
LCS_GDT     A    59_A     A    59_A     13   19   35      5   10   14   16   18   19   20   23   25   28   29   36   39   42   46   48   52   53   56   58 
LCS_GDT     E    60_A     E    60_A     15   19   35      5   12   15   17   18   21   22   24   25   28   30   36   39   42   46   48   52   53   56   58 
LCS_GDT     I    61_A     I    61_A     15   19   35      5   10   14   17   18   21   22   24   25   28   29   35   39   42   46   48   52   53   56   58 
LCS_GDT     E    62_A     E    62_A     15   19   35      5   12   15   17   18   21   22   24   25   28   29   36   39   42   46   48   52   53   56   58 
LCS_GDT     A    63_A     A    63_A     15   19   35      4   12   15   17   18   21   22   24   25   28   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     L    64_A     L    64_A     15   19   35      6   13   15   17   18   21   22   24   25   28   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     A    65_A     A    65_A     15   19   35      7   13   15   17   18   21   22   24   25   28   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     A    66_A     A    66_A     15   19   35      7   13   15   17   18   21   22   24   25   28   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     L    67_A     L    67_A     15   19   35      7   13   15   17   18   21   22   24   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     K    68_A     K    68_A     15   19   35      7   13   15   17   18   21   22   24   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     M    69_A     M    69_A     15   19   35      7   13   15   17   18   21   22   24   25   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     R    70_A     R    70_A     15   19   32      7   13   15   17   18   21   22   24   25   28   32   37   41   43   46   48   52   53   56   58 
LCS_GDT     E    71_A     E    71_A     15   19   32      7   13   15   17   18   21   22   24   25   29   32   37   41   43   46   48   52   53   56   58 
LCS_GDT     L    72_A     L    72_A     15   19   32      7   13   15   17   18   21   22   24   25   29   32   37   41   43   46   48   52   53   56   58 
LCS_GDT     C    73_A     C    73_A     15   19   32      7   13   15   17   18   21   22   24   25   28   32   37   40   42   44   48   52   53   56   58 
LCS_GDT     R    74_A     R    74_A     15   19   32      7   13   15   17   18   21   22   24   25   28   32   37   40   42   44   48   52   53   56   58 
LCS_GDT     T    75_A     T    75_A     15   19   32      7   13   15   17   18   21   22   24   25   28   32   37   40   42   44   48   52   53   56   58 
LCS_GDT     Y    76_A     Y    76_A     15   19   32      4   13   15   17   18   21   22   24   25   28   30   34   36   42   43   48   52   53   56   58 
LCS_GDT     G    83_A     G    83_A     15   16   23      3    5   14   16   19   19   19   20   21   23   27   28   35   39   41   44   45   51   52   53 
LCS_GDT     D    84_A     D    84_A     15   16   23      8   13   14   16   19   19   19   20   24   27   31   34   37   40   42   44   45   51   52   53 
LCS_GDT     A    85_A     A    85_A     15   16   23      8   13   14   16   19   19   19   21   25   27   32   35   40   42   44   46   49   52   56   58 
LCS_GDT     W    86_A     W    86_A     15   16   23      8   13   14   16   19   19   19   21   25   27   32   37   40   42   44   46   49   53   56   58 
LCS_GDT     R    87_A     R    87_A     15   16   23      8   13   14   16   19   19   19   21   25   27   32   37   40   42   44   46   49   53   56   58 
LCS_GDT     A    88_A     A    88_A     15   16   23      8   13   14   16   19   19   19   21   25   29   32   37   40   42   44   48   52   53   56   58 
LCS_GDT     V    89_A     V    89_A     15   16   23      8   13   14   16   19   19   19   21   25   29   32   37   41   43   46   48   52   53   56   58 
LCS_GDT     A    90_A     A    90_A     15   16   23      6   13   14   16   19   19   19   20   24   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     R    91_A     R    91_A     15   16   23      8   13   14   16   19   19   19   20   24   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     D    92_A     D    92_A     15   16   23      6   13   14   16   19   19   19   20   24   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     V    93_A     V    93_A     15   16   23      3   11   14   16   19   19   19   20   24   29   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     W    94_A     W    94_A     15   16   23      8   13   14   16   19   19   19   20   23   28   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     D    95_A     D    95_A     15   16   23      3   13   14   16   19   19   19   20   22   27   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     T    96_A     T    96_A     15   16   23      6   13   14   16   19   19   19   20   22   27   33   37   41   43   46   48   52   53   56   58 
LCS_GDT     V    97_A     V    97_A     15   16   23      6   13   14   16   19   19   19   20   22   25   30   36   39   42   45   47   50   53   55   58 
LCS_GDT     G    98_A     G    98_A     15   16   22      0    3   13   16   19   19   19   20   22   24   29   35   37   42   44   45   46   49   51   52 
LCS_AVERAGE  LCS_A:  31.94  (  19.99   24.51   51.30 )

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      8     13     15     17     19     21     22     24     25     29     33     37     41     43     46     48     52     53     56     58 
GDT PERCENT_AT  13.11  21.31  24.59  27.87  31.15  34.43  36.07  39.34  40.98  47.54  54.10  60.66  67.21  70.49  75.41  78.69  85.25  86.89  91.80  95.08
GDT RMS_LOCAL    0.33   0.59   0.87   1.08   1.42   1.72   1.82   2.24   2.39   3.73   4.12   4.36   4.67   4.80   5.16   5.45   5.85   5.89   6.25   6.41
GDT RMS_ALL_AT  11.93  12.68  12.30  12.00  11.96  11.93  11.76  11.89  11.75   7.36   7.51   7.45   7.19   7.26   7.38   7.18   7.22   7.14   7.03   7.00

# Checking swapping
#   possible swapping detected:  F    54_A      F    54_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  E    62_A      E    62_A
#   possible swapping detected:  D    92_A      D    92_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     2.984     0    0.503   0.506     4.888   52.857   49.714
LGA    T    33_A      T    33_A     4.169     0    0.089   0.845     7.110   47.262   32.789
LGA    M    34_A      M    34_A     7.723     0    0.059   1.088    14.297    9.405    4.702
LGA    A    35_A      A    35_A     9.272     0    0.130   0.138    11.034    5.119    4.095
LGA    D    36_A      D    36_A     5.341     0    0.128   1.000     9.242   39.524   24.107
LGA    L    37_A      L    37_A     2.636     0    0.059   0.993     6.624   53.571   39.167
LGA    K    38_A      K    38_A     5.507     0    0.039   0.962    10.436   33.333   16.720
LGA    M    39_A      M    39_A     4.134     0    0.141   0.963     9.963   51.071   31.726
LGA    Q    40_A      Q    40_A     1.351     0    0.059   0.976     6.274   75.119   56.984
LGA    A    41_A      A    41_A     3.442     0    0.172   0.167     4.737   52.024   47.905
LGA    V    42_A      V    42_A     2.783     0    0.518   1.409     4.223   48.690   51.565
LGA    K    43_A      K    43_A     8.029     0    0.061   1.029    10.389    6.905    4.815
LGA    E    44_A      E    44_A    11.159     0    0.154   0.994    17.903    0.357    0.159
LGA    I    45_A      I    45_A     6.708     0    0.066   0.631     7.748   10.238   17.381
LGA    C    46_A      C    46_A     7.670     0    0.085   0.786    11.308    6.071    5.635
LGA    Y    47_A      Y    47_A    14.481     0    0.091   1.452    25.073    0.000    0.000
LGA    E    48_A      E    48_A    15.209     0    0.075   0.769    18.271    0.000    0.000
LGA    V    49_A      V    49_A    11.215     0    0.119   0.153    14.496    0.000    3.265
LGA    A    50_A      A    50_A    17.130     0    0.054   0.077    20.737    0.000    0.000
LGA    L    51_A      L    51_A    22.361     0    0.223   0.881    24.144    0.000    0.000
LGA    A    52_A      A    52_A    19.791     0    0.584   0.547    19.937    0.000    0.000
LGA    D    53_A      D    53_A    21.352     0    0.057   0.306    23.377    0.000    0.000
LGA    F    54_A      F    54_A    19.698     0    0.381   1.390    24.393    0.000    0.000
LGA    R    55_A      R    55_A    21.579     0    0.116   1.561    26.495    0.000    0.000
LGA    H    56_A      H    56_A    15.967     0    0.597   0.527    19.819    0.000    0.000
LGA    G    57_A      G    57_A    12.403     0    0.614   0.614    13.104    0.000    0.000
LGA    R    58_A      R    58_A     7.267     0    0.587   1.044    14.318   15.595    8.658
LGA    A    59_A      A    59_A     5.181     0    0.027   0.035     5.903   35.238   32.476
LGA    E    60_A      E    60_A     2.664     0    0.031   0.492     3.539   57.619   56.561
LGA    I    61_A      I    61_A     3.485     0    0.064   0.664     5.716   55.476   42.202
LGA    E    62_A      E    62_A     2.669     0    0.029   0.208     5.047   62.976   48.889
LGA    A    63_A      A    63_A     1.842     0    0.038   0.053     2.033   75.119   73.048
LGA    L    64_A      L    64_A     1.058     0    0.275   1.040     5.219   81.429   67.560
LGA    A    65_A      A    65_A     1.151     0    0.031   0.061     1.151   81.429   81.429
LGA    A    66_A      A    66_A     1.057     0    0.055   0.077     1.150   83.690   83.238
LGA    L    67_A      L    67_A     1.076     0    0.038   0.889     2.348   81.429   80.476
LGA    K    68_A      K    68_A     1.196     0    0.124   0.808     4.470   83.690   68.624
LGA    M    69_A      M    69_A     1.238     0    0.028   0.832     3.965   81.429   73.512
LGA    R    70_A      R    70_A     1.275     0    0.090   1.338     3.965   81.429   70.779
LGA    E    71_A      E    71_A     0.986     0    0.053   1.020     2.943   85.952   75.238
LGA    L    72_A      L    72_A     1.039     0    0.053   0.799     4.146   83.690   70.952
LGA    C    73_A      C    73_A     1.206     0    0.075   0.256     2.126   81.429   78.651
LGA    R    74_A      R    74_A     1.239     0    0.280   1.381     8.370   77.262   48.961
LGA    T    75_A      T    75_A     0.855     0    0.111   0.213     1.434   85.952   87.891
LGA    Y    76_A      Y    76_A     1.860     0    0.589   1.377    11.502   71.071   37.421
LGA    G    83_A      G    83_A    16.857     0    0.518   0.518    16.857    0.000    0.000
LGA    D    84_A      D    84_A    16.858     0    0.287   0.315    21.594    0.000    0.000
LGA    A    85_A      A    85_A    12.005     0    0.039   0.042    13.901    0.000    0.000
LGA    W    86_A      W    86_A    12.573     0    0.058   1.338    15.242    0.000    0.000
LGA    R    87_A      R    87_A    14.886     0    0.100   1.394    22.843    0.000    0.000
LGA    A    88_A      A    88_A    11.123     0    0.141   0.147    12.289    0.000    0.095
LGA    V    89_A      V    89_A     9.153     0    0.044   1.085    10.476    0.476    2.041
LGA    A    90_A      A    90_A    12.686     0    0.050   0.048    14.303    0.000    0.000
LGA    R    91_A      R    91_A    15.190     0    0.033   1.526    16.290    0.000    0.000
LGA    D    92_A      D    92_A    13.406     0    0.097   0.888    15.691    0.000    0.000
LGA    V    93_A      V    93_A    13.898     0    0.099   0.716    17.323    0.000    0.000
LGA    W    94_A      W    94_A    18.892     0    0.062   0.274    27.763    0.000    0.000
LGA    D    95_A      D    95_A    20.827     0    0.207   0.479    22.670    0.000    0.000
LGA    T    96_A      T    96_A    20.598     0    0.161   1.188    23.153    0.000    0.000
LGA    V    97_A      V    97_A    21.761     0    0.482   1.077    23.313    0.000    0.000
LGA    G    98_A      G    98_A    26.522     0    0.141   0.141    27.523    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     480    480  100.00                61
SUMMARY(RMSD_GDC):     6.941          6.733                  8.157           30.392   25.892

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     24    2.24    41.803    37.455     1.027

LGA_LOCAL      RMSD:   2.236  Number of atoms:   24  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.890  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   6.941  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.804585 * X  +  -0.294349 * Y  +  -0.515753 * Z  +  62.603340
  Y_new =   0.567460 * X  +  -0.125122 * Y  +  -0.813839 * Z  + -30.991241
  Z_new =   0.175020 * X  +  -0.947472 * Y  +   0.267702 * Z  +  39.528751 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.527330 -0.175927 -1.295431   [DEG:  144.8054  -10.0798  -74.2227 ]
ZXZ: -0.564852  1.299789  2.958928   [DEG:  -32.3636   74.4724  169.5341 ]
 
# END of job
