
#######################################################
#                                                     #
#                        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      32_A - 66_A        4.99    10.13
  LCS_AVERAGE:     51.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      56_A - 76_A        1.93    12.08
  LCS_AVERAGE:     29.78

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      57_A - 76_A        0.90    12.21
  LCS_AVERAGE:     24.54

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   10   35      0    3    3    7   11   16   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     T    33_A     T    33_A      8   16   35      6    8    8   11   12   19   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     M    34_A     M    34_A      8   19   35      6    8    8   15   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     A    35_A     A    35_A      8   19   35      6   13   14   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     D    36_A     D    36_A      8   19   35      6    8   11   14   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     L    37_A     L    37_A      8   19   35      6    8    8   15   21   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     K    38_A     K    38_A     14   19   35      6    8   11   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     M    39_A     M    39_A     14   19   35      4   12   14   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     Q    40_A     Q    40_A     14   19   35      4   13   14   18   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     A    41_A     A    41_A     14   19   35     11   13   14   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     V    42_A     V    42_A     14   19   35     11   13   14   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     K    43_A     K    43_A     14   19   35     11   14   17   18   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     E    44_A     E    44_A     14   19   35     11   13   14   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     I    45_A     I    45_A     14   19   35     11   13   14   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     C    46_A     C    46_A     14   19   35     11   13   17   18   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     Y    47_A     Y    47_A     14   19   35     11   13   14   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     E    48_A     E    48_A     14   19   35     11   13   14   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     V    49_A     V    49_A     14   19   35     11   13   14   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     A    50_A     A    50_A     14   19   35     11   13   14   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     L    51_A     L    51_A     14   19   35     11   13   14   17   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     A    52_A     A    52_A      4   19   35      3    4    4   12   18   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     D    53_A     D    53_A      4   16   35      3    4    4    4    9   16   22   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     F    54_A     F    54_A      4    4   35      3    4    4    4    6    8   12   15   18   25   29   31   36   41   44   45   48   50   54   56 
LCS_GDT     R    55_A     R    55_A      3    4   35      3    4    4    4    6    8   14   19   20   25   29   32   38   40   43   45   48   50   54   56 
LCS_GDT     H    56_A     H    56_A      3   21   35      0    4    4    4    6    9   12   20   23   25   27   29   35   39   42   44   48   50   54   56 
LCS_GDT     G    57_A     G    57_A     20   21   35      9   15   17   20   21   22   22   24   25   27   28   29   32   35   36   38   43   44   49   52 
LCS_GDT     R    58_A     R    58_A     20   21   35     10   16   18   20   21   22   22   24   25   27   28   29   32   35   35   38   40   44   49   52 
LCS_GDT     A    59_A     A    59_A     20   21   35     10   16   18   20   21   22   22   24   25   27   28   29   35   39   42   43   48   49   50   54 
LCS_GDT     E    60_A     E    60_A     20   21   35     10   16   18   20   21   22   22   24   25   27   29   34   38   40   42   44   48   50   54   56 
LCS_GDT     I    61_A     I    61_A     20   21   35     10   16   18   20   21   22   22   24   25   27   29   31   36   39   42   44   48   50   54   56 
LCS_GDT     E    62_A     E    62_A     20   21   35     10   16   18   20   21   22   22   24   25   27   28   29   36   39   42   44   48   50   54   56 
LCS_GDT     A    63_A     A    63_A     20   21   35     10   16   18   20   21   22   22   24   25   27   33   37   38   40   44   45   48   50   54   56 
LCS_GDT     L    64_A     L    64_A     20   21   35     10   16   18   20   21   22   26   27   30   32   35   37   39   42   44   45   48   50   54   56 
LCS_GDT     A    65_A     A    65_A     20   21   35     10   16   18   20   21   22   22   24   25   32   35   37   39   42   44   45   48   50   54   56 
LCS_GDT     A    66_A     A    66_A     20   21   35     10   16   18   20   21   22   22   24   25   27   29   36   39   42   44   45   48   50   54   56 
LCS_GDT     L    67_A     L    67_A     20   21   33     10   16   18   20   21   22   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     K    68_A     K    68_A     20   21   33      9   16   18   20   21   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     M    69_A     M    69_A     20   21   33     10   16   18   20   21   22   22   24   31   34   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     R    70_A     R    70_A     20   21   33     10   16   18   20   21   22   22   24   28   32   35   38   40   42   44   45   48   50   54   56 
LCS_GDT     E    71_A     E    71_A     20   21   33      9   16   18   20   21   22   22   27   31   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     L    72_A     L    72_A     20   21   33      9   16   18   20   21   22   22   27   31   33   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     C    73_A     C    73_A     20   21   33      9   16   18   20   21   22   22   24   25   27   32   38   39   42   43   45   47   50   54   56 
LCS_GDT     R    74_A     R    74_A     20   21   33      5   15   18   20   21   22   22   24   25   27   32   37   39   40   42   44   47   50   54   56 
LCS_GDT     T    75_A     T    75_A     20   21   33      5   12   18   20   21   22   22   24   25   27   32   33   37   40   42   44   47   50   54   56 
LCS_GDT     Y    76_A     Y    76_A     20   21   33      8   16   18   20   21   22   22   24   25   27   28   29   32   35   36   40   45   50   54   56 
LCS_GDT     G    83_A     G    83_A     16   16   23      3    5    8   15   18   19   21   25   25   27   29   29   30   32   37   41   44   46   47   48 
LCS_GDT     D    84_A     D    84_A     16   16   22      3   13   17   18   19   21   25   28   28   29   35   38   40   42   43   44   47   50   51   55 
LCS_GDT     A    85_A     A    85_A     16   16   22     10   14   17   18   19   21   25   28   28   29   35   38   40   42   43   45   47   50   54   56 
LCS_GDT     W    86_A     W    86_A     16   16   22     10   14   17   18   19   21   25   28   30   32   36   38   40   42   43   45   47   50   54   56 
LCS_GDT     R    87_A     R    87_A     16   16   22     10   14   17   18   19   21   25   28   31   35   37   38   40   42   43   45   47   50   54   56 
LCS_GDT     A    88_A     A    88_A     16   16   22     10   14   17   18   19   21   25   28   33   35   37   38   40   42   44   45   47   50   54   56 
LCS_GDT     V    89_A     V    89_A     16   16   22     10   14   17   18   19   21   25   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     A    90_A     A    90_A     16   16   22     10   14   17   18   19   23   25   29   33   35   37   38   40   42   44   45   47   50   54   56 
LCS_GDT     R    91_A     R    91_A     16   16   22     10   14   17   18   19   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     D    92_A     D    92_A     16   16   22     10   14   17   18   19   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     V    93_A     V    93_A     16   16   22     10   14   17   18   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     W    94_A     W    94_A     16   16   22     10   14   17   18   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     D    95_A     D    95_A     16   16   22      8   14   17   18   19   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     T    96_A     T    96_A     16   16   22      3   14   17   18   20   23   26   29   33   35   37   38   40   42   44   45   48   50   54   56 
LCS_GDT     V    97_A     V    97_A     16   16   22      4   14   17   18   20   23   26   28   30   34   35   38   40   42   44   45   48   50   54   56 
LCS_GDT     G    98_A     G    98_A     16   16   22      3    9   17   18   20   23   26   28   30   34   35   37   40   42   44   45   48   50   51   56 
LCS_AVERAGE  LCS_A:  35.20  (  24.54   29.78   51.28 )

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     11     16     18     20     21     23     26     29     33     35     37     38     40     42     44     45     48     50     54     56 
GDT PERCENT_AT  18.03  26.23  29.51  32.79  34.43  37.70  42.62  47.54  54.10  57.38  60.66  62.30  65.57  68.85  72.13  73.77  78.69  81.97  88.52  91.80
GDT RMS_LOCAL    0.28   0.52   0.72   0.90   1.16   1.94   2.32   2.57   2.95   3.18   3.36   3.47   3.73   3.99   4.46   4.55   5.42   5.43   6.21   6.39
GDT RMS_ALL_AT  10.87  12.13  12.24  12.21  12.54   9.04   8.57   8.46   8.23   8.28   8.26   8.26   8.35   8.42   7.84   7.84   7.85   7.77   7.35   7.33

# Checking swapping
#   possible swapping detected:  E    48_A      E    48_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  E    62_A      E    62_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     4.137     0    0.550   0.548     6.225   56.548   48.667
LGA    T    33_A      T    33_A     3.629     0    0.599   1.201     8.487   55.714   35.986
LGA    M    34_A      M    34_A     0.749     0    0.052   0.771     4.953   88.214   69.107
LGA    A    35_A      A    35_A     2.413     0    0.112   0.113     3.494   67.024   63.619
LGA    D    36_A      D    36_A     2.482     0    0.135   1.028     6.423   75.357   50.060
LGA    L    37_A      L    37_A     1.008     0    0.028   1.415     5.843   81.548   59.167
LGA    K    38_A      K    38_A     2.382     0    0.023   1.280     4.872   62.976   55.503
LGA    M    39_A      M    39_A     2.671     0    0.105   0.846     4.250   59.048   55.655
LGA    Q    40_A      Q    40_A     2.917     0    0.043   1.389     6.885   55.357   42.169
LGA    A    41_A      A    41_A     3.432     0    0.078   0.075     3.872   51.786   50.095
LGA    V    42_A      V    42_A     2.007     0    0.119   0.231     2.898   73.095   68.503
LGA    K    43_A      K    43_A     0.791     0    0.042   0.510     2.967   88.214   77.090
LGA    E    44_A      E    44_A     1.943     0    0.148   1.027     7.078   72.857   52.011
LGA    I    45_A      I    45_A     2.111     0    0.040   0.624     5.711   70.833   56.905
LGA    C    46_A      C    46_A     2.066     0    0.097   0.835     2.437   70.833   70.159
LGA    Y    47_A      Y    47_A     1.639     0    0.054   0.247     6.290   77.143   52.619
LGA    E    48_A      E    48_A     1.067     0    0.045   0.693     5.837   83.690   60.106
LGA    V    49_A      V    49_A     2.612     0    0.044   0.953     3.583   59.286   56.463
LGA    A    50_A      A    50_A     2.864     0    0.117   0.145     2.942   59.048   58.667
LGA    L    51_A      L    51_A     1.990     0    0.633   1.057     4.018   61.429   57.798
LGA    A    52_A      A    52_A     2.713     0    0.667   0.625     5.606   57.500   50.286
LGA    D    53_A      D    53_A     5.440     0    0.255   0.214     7.720   23.333   21.369
LGA    F    54_A      F    54_A    11.194     0    0.404   1.189    13.776    0.714    0.260
LGA    R    55_A      R    55_A    12.165     0    0.627   1.584    17.548    0.000    0.000
LGA    H    56_A      H    56_A    14.434     0    0.599   0.917    15.652    0.000    0.000
LGA    G    57_A      G    57_A    18.438     0    0.560   0.560    18.438    0.000    0.000
LGA    R    58_A      R    58_A    17.977     0    0.081   1.108    26.337    0.000    0.000
LGA    A    59_A      A    59_A    15.725     0    0.023   0.036    16.920    0.000    0.000
LGA    E    60_A      E    60_A    12.740     0    0.027   1.373    14.638    0.000    0.000
LGA    I    61_A      I    61_A    12.716     0    0.030   0.143    16.180    0.000    0.000
LGA    E    62_A      E    62_A    12.468     0    0.031   0.612    16.023    0.000    0.000
LGA    A    63_A      A    63_A     8.907     0    0.033   0.057    10.477    7.500    6.571
LGA    L    64_A      L    64_A     6.432     0    0.189   0.577     8.456   19.286   14.881
LGA    A    65_A      A    65_A     7.162     0    0.047   0.066     8.892   13.690   11.524
LGA    A    66_A      A    66_A     7.747     0    0.067   0.089     8.894   11.190    9.524
LGA    L    67_A      L    67_A     3.696     0    0.027   0.934     5.361   40.476   46.964
LGA    K    68_A      K    68_A     1.843     0    0.027   0.663     5.256   57.738   48.519
LGA    M    69_A      M    69_A     5.640     0    0.058   1.379    11.909   19.762   12.321
LGA    R    70_A      R    70_A     8.410     0    0.094   0.675    10.019    5.714   12.468
LGA    E    71_A      E    71_A     7.848     0    0.108   1.020    10.445    5.000    8.201
LGA    L    72_A      L    72_A     7.899     0    0.056   0.310    10.944    4.405   15.179
LGA    C    73_A      C    73_A    11.932     0    0.113   0.293    14.812    0.119    0.079
LGA    R    74_A      R    74_A    15.444     0    0.278   0.799    22.736    0.000    0.000
LGA    T    75_A      T    75_A    15.469     0    0.051   1.156    18.164    0.000    0.000
LGA    Y    76_A      Y    76_A    16.068     0    0.503   0.600    17.788    0.000    0.000
LGA    G    83_A      G    83_A    16.790     0    0.365   0.365    17.184    0.000    0.000
LGA    D    84_A      D    84_A    12.296     0    0.066   0.596    13.500    0.000    0.000
LGA    A    85_A      A    85_A    10.515     0    0.079   0.076    11.423    1.548    1.238
LGA    W    86_A      W    86_A     8.468     0    0.101   1.120     9.460    6.667    6.020
LGA    R    87_A      R    87_A     7.684     0    0.036   1.456    13.043   11.667    4.978
LGA    A    88_A      A    88_A     6.690     0    0.115   0.116     7.476   19.048   17.238
LGA    V    89_A      V    89_A     4.895     0    0.110   0.989     5.700   36.786   32.245
LGA    A    90_A      A    90_A     4.540     0    0.064   0.063     5.895   40.833   36.952
LGA    R    91_A      R    91_A     3.563     0    0.026   0.670     6.012   50.595   38.355
LGA    D    92_A      D    92_A     2.733     0    0.088   0.885     6.727   62.976   43.750
LGA    V    93_A      V    93_A     1.256     0    0.060   0.963     4.726   73.214   65.986
LGA    W    94_A      W    94_A     1.878     0    0.061   1.623     6.824   65.119   49.932
LGA    D    95_A      D    95_A     3.323     0    0.251   0.746     6.135   44.286   40.774
LGA    T    96_A      T    96_A     3.741     0    0.142   0.201     5.236   40.952   42.041
LGA    V    97_A      V    97_A     5.040     0    0.521   1.149     6.776   31.548   27.415
LGA    G    98_A      G    98_A     5.475     0    0.630   0.630     7.029   19.762   19.762

# 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):     7.248          7.143                  7.773           35.105   29.921

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     29    2.57    45.082    42.079     1.086

LGA_LOCAL      RMSD:   2.571  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.346  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   7.248  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.935956 * X  +   0.316606 * Y  +   0.154099 * Z  +   2.010474
  Y_new =  -0.300564 * X  +   0.946338 * Y  +  -0.118765 * Z  +  51.190495
  Z_new =  -0.183431 * X  +   0.064842 * Y  +   0.980892 * Z  + -29.805370 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.310728  0.184476  0.066009   [DEG:  -17.8034   10.5697    3.7821 ]
ZXZ:  0.914174  0.195804 -1.231010   [DEG:   52.3783   11.2187  -70.5317 ]
 
# END of job
