
#######################################################
#                                                     #
#                        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:    41      32_A - 72_A        4.87    12.16
  LCS_AVERAGE:     65.06

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      33_A - 55_A        1.83    11.75
  LCS_AVERAGE:     32.65

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      33_A - 50_A        0.97    11.86
  LCS_AVERAGE:     24.51

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      3   21   41      0    3    3    4    6    6    9   13   17   19   27   29   32   34   35   36   38   38   39   41 
LCS_GDT     T    33_A     T    33_A     18   23   41      9   15   17   20   21   25   27   29   31   32   33   34   35   37   37   39   40   41   42   44 
LCS_GDT     M    34_A     M    34_A     18   23   41      5   13   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     A    35_A     A    35_A     18   23   41      9   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     D    36_A     D    36_A     18   23   41      9   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     L    37_A     L    37_A     18   23   41      9   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     K    38_A     K    38_A     18   23   41      9   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     M    39_A     M    39_A     18   23   41      9   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     Q    40_A     Q    40_A     18   23   41      9   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     A    41_A     A    41_A     18   23   41      9   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     V    42_A     V    42_A     18   23   41      9   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     K    43_A     K    43_A     18   23   41      8   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     E    44_A     E    44_A     18   23   41      4   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     I    45_A     I    45_A     18   23   41      6   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     C    46_A     C    46_A     18   23   41      4   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     Y    47_A     Y    47_A     18   23   41      6   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     E    48_A     E    48_A     18   23   41      6   15   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     V    49_A     V    49_A     18   23   41      6   12   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     A    50_A     A    50_A     18   23   41      6   11   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     L    51_A     L    51_A     17   23   41      6   11   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     A    52_A     A    52_A     15   23   41      6   11   17   20   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     D    53_A     D    53_A     15   23   41      6   10   14   18   21   22   27   29   31   32   33   34   35   37   38   39   41   41   42   44 
LCS_GDT     F    54_A     F    54_A      3   23   41      3    4    4    5    8   22   23   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     R    55_A     R    55_A      3   23   41      4    5   10   16   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     H    56_A     H    56_A      4    9   41      3    4    6   15   20   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     G    57_A     G    57_A      4   20   41      3    4   10   16   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     R    58_A     R    58_A     13   20   41      6    9   13   18   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     A    59_A     A    59_A     13   20   41      6    9   13   18   19   19   20   23   27   30   33   34   35   37   38   40   41   41   42   43 
LCS_GDT     E    60_A     E    60_A     13   20   41      6    9   14   18   19   19   20   23   27   30   33   34   35   37   37   40   41   41   42   43 
LCS_GDT     I    61_A     I    61_A     16   20   41      6   12   15   18   20   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     E    62_A     E    62_A     16   20   41      6    9   15   18   19   19   20   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     A    63_A     A    63_A     16   20   41      6   12   15   18   19   19   20   23   27   30   33   34   35   37   38   40   41   41   42   43 
LCS_GDT     L    64_A     L    64_A     16   20   41      6   12   15   18   21   25   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     A    65_A     A    65_A     16   20   41      6   12   15   18   19   19   24   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     A    66_A     A    66_A     16   20   41      8   12   15   18   19   19   20   22   27   30   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     L    67_A     L    67_A     16   20   41      8   12   15   18   19   23   27   29   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     K    68_A     K    68_A     16   20   41      4   12   15   18   19   19   22   28   31   32   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     M    69_A     M    69_A     16   20   41      8   12   15   18   19   19   20   23   27   30   33   34   35   35   38   40   41   41   42   44 
LCS_GDT     R    70_A     R    70_A     16   20   41      8   12   15   18   19   19   20   23   27   30   33   34   35   35   38   40   41   41   42   44 
LCS_GDT     E    71_A     E    71_A     16   20   41      8   12   15   18   19   19   20   27   30   31   33   34   35   37   38   40   41   41   42   44 
LCS_GDT     L    72_A     L    72_A     16   20   41      8   12   15   18   19   19   20   23   27   30   33   34   35   35   36   40   41   41   42   44 
LCS_GDT     C    73_A     C    73_A     16   20   37      8   12   15   18   19   19   20   23   27   30   33   34   35   35   36   36   37   40   42   44 
LCS_GDT     R    74_A     R    74_A     16   20   37      8   12   15   18   19   19   20   23   27   30   33   34   35   35   38   40   41   41   42   44 
LCS_GDT     T    75_A     T    75_A     16   20   37      8   12   15   18   19   19   20   21   27   29   33   34   35   35   36   40   41   41   42   43 
LCS_GDT     Y    76_A     Y    76_A     16   20   37      4   11   14   17   19   19   19   21   23   29   33   34   35   35   36   36   36   37   38   41 
LCS_GDT     G    83_A     G    83_A      4   16   37      3    3    4    8   12   17   17   19   20   25   28   34   35   35   36   36   36   37   38   41 
LCS_GDT     D    84_A     D    84_A     15   16   37      4   11   15   15   16   18   19   23   27   30   33   34   35   35   36   36   36   37   38   41 
LCS_GDT     A    85_A     A    85_A     15   16   37     10   13   15   15   16   18   20   23   27   30   33   34   35   35   36   36   36   37   38   41 
LCS_GDT     W    86_A     W    86_A     15   16   37     10   13   15   15   16   18   20   23   27   30   33   34   35   35   36   36   36   37   39   43 
LCS_GDT     R    87_A     R    87_A     15   16   37     10   13   15   15   16   18   19   23   27   30   33   34   35   35   36   36   36   37   38   43 
LCS_GDT     A    88_A     A    88_A     15   16   37     10   13   15   15   16   18   19   23   27   30   33   34   35   35   36   36   36   37   38   41 
LCS_GDT     V    89_A     V    89_A     15   16   37     10   13   15   15   16   18   19   23   27   30   33   34   35   35   36   36   36   39   42   44 
LCS_GDT     A    90_A     A    90_A     15   16   37     10   13   15   15   16   18   20   23   27   30   33   34   35   35   37   38   38   40   42   44 
LCS_GDT     R    91_A     R    91_A     15   16   37     10   13   15   15   16   18   19   23   27   30   33   34   35   35   36   36   37   40   42   44 
LCS_GDT     D    92_A     D    92_A     15   16   37     10   13   15   15   16   18   19   22   26   30   33   34   35   35   36   36   36   37   38   41 
LCS_GDT     V    93_A     V    93_A     15   16   37     10   13   15   15   16   18   19   23   27   30   33   34   35   35   36   36   37   40   42   44 
LCS_GDT     W    94_A     W    94_A     15   16   37     10   13   15   15   16   18   19   23   27   30   33   34   35   35   36   36   37   40   42   44 
LCS_GDT     D    95_A     D    95_A     15   16   37      6   13   15   15   16   18   19   22   26   30   33   34   35   35   36   36   36   37   38   41 
LCS_GDT     T    96_A     T    96_A     15   16   37      3   13   15   15   16   18   19   20   26   26   33   34   35   35   36   36   36   37   38   41 
LCS_GDT     V    97_A     V    97_A     15   16   37      5   13   15   15   16   18   19   22   26   30   33   34   35   35   36   36   36   37   38   41 
LCS_GDT     G    98_A     G    98_A     15   16   37      3    4   15   15   16   18   19   22   26   30   33   34   35   35   36   36   36   37   37   40 
LCS_AVERAGE  LCS_A:  40.74  (  24.51   32.65   65.06 )

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     10     15     17     20     21     25     27     29     31     32     33     34     35     37     38     40     41     41     42     44 
GDT PERCENT_AT  16.39  24.59  27.87  32.79  34.43  40.98  44.26  47.54  50.82  52.46  54.10  55.74  57.38  60.66  62.30  65.57  67.21  67.21  68.85  72.13
GDT RMS_LOCAL    0.24   0.65   0.80   1.20   1.36   2.02   2.16   2.34   2.59   2.70   2.92   3.11   3.28   3.70   4.42   5.02   5.08   4.85   5.12   6.25
GDT RMS_ALL_AT  13.55  11.87  11.85  11.80  11.86  12.72  12.60  12.62  12.47  12.37  12.19  12.13  12.26  12.63  11.86  11.81  11.83  11.92  11.85  10.42

# Checking swapping
#   possible swapping detected:  D    36_A      D    36_A
#   possible swapping detected:  Y    47_A      Y    47_A
#   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:  Y    76_A      Y    76_A
#   possible swapping detected:  D    92_A      D    92_A
#   possible swapping detected:  D    95_A      D    95_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     8.981     0    0.377   0.382    10.437    9.286    7.429
LGA    T    33_A      T    33_A     1.891     0    0.594   1.212     4.507   64.643   57.483
LGA    M    34_A      M    34_A     1.554     0    0.055   1.104     4.055   72.857   62.738
LGA    A    35_A      A    35_A     2.854     0    0.084   0.095     3.701   60.952   57.429
LGA    D    36_A      D    36_A     1.512     0    0.136   0.241     3.098   79.405   68.333
LGA    L    37_A      L    37_A     0.478     0    0.077   0.136     1.858   90.595   85.000
LGA    K    38_A      K    38_A     2.073     0    0.088   0.877     7.596   72.976   50.000
LGA    M    39_A      M    39_A     1.537     0    0.045   0.733     5.901   81.667   59.524
LGA    Q    40_A      Q    40_A     1.438     0    0.052   1.428     7.203   77.381   54.497
LGA    A    41_A      A    41_A     2.778     0    0.048   0.052     3.417   57.262   55.810
LGA    V    42_A      V    42_A     2.172     0    0.141   0.174     3.489   75.119   65.374
LGA    K    43_A      K    43_A     0.538     0    0.063   0.126     2.665   85.952   77.937
LGA    E    44_A      E    44_A     2.393     0    0.177   0.295     3.800   64.881   55.185
LGA    I    45_A      I    45_A     2.727     0    0.298   0.412     5.986   66.905   47.976
LGA    C    46_A      C    46_A     1.290     0    0.114   0.141     2.656   83.810   78.968
LGA    Y    47_A      Y    47_A     1.717     0    0.024   0.149     7.679   77.262   43.413
LGA    E    48_A      E    48_A     3.340     0    0.037   0.241     6.816   55.357   36.878
LGA    V    49_A      V    49_A     2.874     0    0.112   0.109     4.985   62.976   51.156
LGA    A    50_A      A    50_A     1.627     0    0.066   0.066     1.929   77.143   76.286
LGA    L    51_A      L    51_A     1.196     0    0.214   0.334     2.377   83.810   77.381
LGA    A    52_A      A    52_A     1.292     0    0.290   0.289     2.218   77.381   76.476
LGA    D    53_A      D    53_A     3.459     0    0.388   1.186     8.701   63.095   37.679
LGA    F    54_A      F    54_A     4.122     0    0.443   0.331     9.224   41.905   19.524
LGA    R    55_A      R    55_A     1.670     0    0.705   1.247    11.449   68.810   31.861
LGA    H    56_A      H    56_A     2.852     0    0.070   0.969     8.952   62.857   32.810
LGA    G    57_A      G    57_A     2.008     0    0.176   0.176     4.498   55.952   55.952
LGA    R    58_A      R    58_A     2.876     0    0.525   1.551     7.942   51.190   44.675
LGA    A    59_A      A    59_A     8.742     0    0.054   0.054    11.529    6.786    5.429
LGA    E    60_A      E    60_A     8.052     0    0.054   1.029    15.627   14.881    6.667
LGA    I    61_A      I    61_A     2.513     0    0.075   0.252     5.791   63.690   47.321
LGA    E    62_A      E    62_A     5.081     0    0.043   1.022    12.061   31.667   15.979
LGA    A    63_A      A    63_A     6.754     0    0.030   0.035     8.713   24.405   20.095
LGA    L    64_A      L    64_A     2.457     0    0.197   0.466     9.176   65.238   39.286
LGA    A    65_A      A    65_A     5.211     0    0.076   0.078     7.172   27.619   24.095
LGA    A    66_A      A    66_A     7.718     0    0.285   0.300     9.384   12.857   10.571
LGA    L    67_A      L    67_A     3.699     0    0.077   0.849     6.211   40.476   35.476
LGA    K    68_A      K    68_A     5.432     0    0.086   0.596     9.372   18.929   12.593
LGA    M    69_A      M    69_A    11.568     0    0.071   0.792    17.634    0.714    0.357
LGA    R    70_A      R    70_A    11.252     0    0.120   1.545    17.285    0.000    0.000
LGA    E    71_A      E    71_A     7.965     0    0.050   1.348    11.106    2.976   13.386
LGA    L    72_A      L    72_A    14.259     0    0.056   1.363    17.372    0.000    0.000
LGA    C    73_A      C    73_A    17.776     0    0.057   0.111    20.193    0.000    0.000
LGA    R    74_A      R    74_A    14.578     0    0.295   1.158    15.090    0.000    0.000
LGA    T    75_A      T    75_A    16.296     0    0.137   0.235    19.969    0.000    0.000
LGA    Y    76_A      Y    76_A    23.325     0    0.172   1.255    27.587    0.000    0.000
LGA    G    83_A      G    83_A    27.813     0    0.194   0.194    28.241    0.000    0.000
LGA    D    84_A      D    84_A    27.543     0    0.315   1.176    31.389    0.000    0.000
LGA    A    85_A      A    85_A    24.209     0    0.074   0.072    25.675    0.000    0.000
LGA    W    86_A      W    86_A    18.220     0    0.090   1.120    20.680    0.000    0.000
LGA    R    87_A      R    87_A    20.309     0    0.067   1.464    24.568    0.000    0.000
LGA    A    88_A      A    88_A    22.739     0    0.146   0.154    24.862    0.000    0.000
LGA    V    89_A      V    89_A    16.715     0    0.113   0.141    18.894    0.000    0.000
LGA    A    90_A      A    90_A    12.657     0    0.060   0.062    14.233    0.000    0.000
LGA    R    91_A      R    91_A    18.414     0    0.044   1.432    23.978    0.000    0.000
LGA    D    92_A      D    92_A    20.341     0    0.096   1.175    21.132    0.000    0.000
LGA    V    93_A      V    93_A    14.796     0    0.043   0.052    17.005    0.000    0.000
LGA    W    94_A      W    94_A    16.418     0    0.054   1.521    20.315    0.000    0.000
LGA    D    95_A      D    95_A    23.644     0    0.256   1.184    26.427    0.000    0.000
LGA    T    96_A      T    96_A    24.031     0    0.122   1.107    25.552    0.000    0.000
LGA    V    97_A      V    97_A    21.601     0    0.531   0.476    22.455    0.000    0.000
LGA    G    98_A      G    98_A    24.703     0    0.244   0.244    25.818    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):     9.760          9.569                 10.233           34.945   27.853

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     29    2.34    42.623    40.785     1.187

LGA_LOCAL      RMSD:   2.344  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  12.615  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   9.760  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.909058 * X  +   0.003710 * Y  +   0.416653 * Z  +   6.144312
  Y_new =  -0.215236 * X  +   0.852034 * Y  +  -0.477191 * Z  +  22.865158
  Z_new =  -0.356773 * X  +  -0.523473 * Y  +  -0.773750 * Z  + -17.829161 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.909106  0.364811 -2.546785   [DEG: -166.6795   20.9021 -145.9200 ]
ZXZ:  0.717773  2.455536 -2.543358   [DEG:   41.1254  140.6918 -145.7237 ]
 
# END of job
