
#######################################################
#                                                     #
#                        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   60 (  468),  selected   42 , name one
# Molecule2: number of CA atoms  336 ( 2631),  selected   42 , 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:    22      56_A - 77_A        4.91    21.85
  LONGEST_CONTINUOUS_SEGMENT:    22      57_A - 78_A        4.94    21.33
  LCS_AVERAGE:      5.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      51_A - 62_A        1.91    27.06
  LCS_AVERAGE:      2.20

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      51_A - 61_A        0.80    27.52
  LCS_AVERAGE:      1.70

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   42
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     T    38_A     T    38_A      3    5   12      3    3    3    5    5    5    5    5    6    9   10   11   12   13   14   15   15   15   16   17 
LCS_GDT     A    39_A     A    39_A      4    5   12      3    3    4    5    5    5    5    5    6    9   10   11   12   13   14   15   15   15   16   17 
LCS_GDT     T    40_A     T    40_A      4    5   12      3    3    4    5    5    5    5    5    6    9   10   11   12   13   14   15   15   15   16   17 
LCS_GDT     V    41_A     V    41_A      4    5   12      3    3    4    5    5    5    5    5    6    9   10   11   12   13   14   15   15   15   16   17 
LCS_GDT     N    42_A     N    42_A      4    5   12      3    3    4    5    5    5    5    6    7    9   10   11   12   13   14   15   15   15   16   17 
LCS_GDT     E    43_A     E    43_A      3    4   12      3    3    3    3    4    4    5    6    7    9   10   11   12   13   14   17   18   20   20   20 
LCS_GDT     L    44_A     L    44_A      3    5   12      3    3    3    4    4    4    5    6    7    9   10   11   12   13   14   17   18   20   20   20 
LCS_GDT     S    45_A     S    45_A      3    5   12      3    3    3    4    4    4    5    6    7    9   10   11   12   15   17   18   18   20   20   20 
LCS_GDT     G    46_A     G    46_A      3    5   18      3    3    3    4    4    4    5    6    7    9   10   12   16   18   19   19   19   20   21   22 
LCS_GDT     I    47_A     I    47_A      3    5   18      3    3    3    4    4    4    5    6    7    9   12   14   17   18   19   21   22   26   27   29 
LCS_GDT     P    48_A     P    48_A      3    5   18      3    3    3    3    4    4    5    7    8   10   10   15   17   18   20   21   22   26   27   29 
LCS_GDT     A    49_A     A    49_A      3    4   18      3    3    3    3    4    4    8    8   10   12   13   15   17   18   19   19   20   22   23   24 
LCS_GDT     V    50_A     V    50_A      3    4   18      3    3    3    3    5    7   10   12   12   13   13   15   17   18   20   22   24   26   27   29 
LCS_GDT     D    51_A     D    51_A     11   12   18      4    9   11   11   11   11   11   12   12   13   13   15   17   18   20   22   24   26   27   29 
LCS_GDT     R    52_A     R    52_A     11   12   18      4    9   11   11   11   11   11   12   12   13   13   16   17   19   20   22   24   26   27   29 
LCS_GDT     A    53_A     A    53_A     11   12   18      7    9   11   11   11   11   11   12   12   13   13   14   17   18   20   21   22   26   27   29 
LCS_GDT     H    54_A     H    54_A     11   12   18      7    9   11   11   11   11   11   12   12   13   13   15   17   18   20   22   24   26   27   29 
LCS_GDT     V    55_A     V    55_A     11   12   21      7    9   11   11   11   11   11   12   12   13   16   18   19   19   20   22   24   26   27   29 
LCS_GDT     L    56_A     L    56_A     11   12   22      7    9   11   11   11   11   11   12   12   14   16   18   19   22   22   22   24   26   27   29 
LCS_GDT     Q    57_A     Q    57_A     11   12   22      7    9   11   11   11   11   11   12   12   13   15   19   19   22   22   22   24   26   27   29 
LCS_GDT     T    58_A     T    58_A     11   12   22      7    9   11   11   11   11   11   12   12   16   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     A    59_A     A    59_A     11   12   22      7    9   11   11   11   11   11   12   13   15   16   19   20   22   22   22   24   26   27   29 
LCS_GDT     L    60_A     L    60_A     11   12   22      7    9   11   11   11   11   11   13   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     S    61_A     S    61_A     11   12   22      5    9   11   11   11   11   11   14   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     I    62_A     I    62_A      3   12   22      4    4    5    7    9    9   10   14   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     Y    63_A     Y    63_A      6    9   22      4    5    6    6    7    7    9   12   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     P    64_A     P    64_A      6    9   22      4    5    6    7    9    9   10   14   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     E    65_A     E    65_A      6    9   22      4    5    6    6    9    9   10   14   16   17   18   19   20   22   22   22   24   25   27   29 
LCS_GDT     V    66_A     V    66_A      6    9   22      4    5    6    7    9    9   10   14   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     E    67_A     E    67_A      6    9   22      4    5    6    7    9    9   10   14   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     N    68_A     N    68_A      6    9   22      4    4    6    6    9    9   10   14   16   17   18   19   20   22   22   22   24   25   27   29 
LCS_GDT     W    69_A     W    69_A      3    4   22      3    3    3    4    5    6   10   14   16   17   18   19   20   22   22   22   23   24   26   28 
LCS_GDT     V    70_A     V    70_A      3    4   22      3    3    3    4    6    8   10   14   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     A    71_A     A    71_A      3    5   22      3    3    3    4    5    7    9   13   16   17   18   19   20   22   22   22   23   24   25   28 
LCS_GDT     Q    72_A     Q    72_A      4    5   22      3    3    4    4    5    6   10   14   16   17   18   19   20   22   22   22   23   24   25   27 
LCS_GDT     F    73_A     F    73_A      4    5   22      3    3    4    4    4    6    8   12   13   17   18   18   20   22   22   22   24   26   27   29 
LCS_GDT     P    74_A     P    74_A      4    5   22      3    3    4    4    4    6    8   14   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     V    75_A     V    75_A      4    5   22      3    3    5    7    9    9   10   14   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     I    76_A     I    76_A      3    5   22      3    4    5    6    7    7   10   14   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     L    77_A     L    77_A      3    5   22      3    3    3    4    4    6   10   14   16   17   18   19   20   22   22   22   24   26   27   29 
LCS_GDT     P    78_A     P    78_A      3    5   22      3    3    3    4    4    6    6    6   11   13   15   18   18   19   20   22   24   26   27   29 
LCS_GDT     Q    79_A     Q    79_A      3    3   20      3    3    3    3    4    6    6    6    8    8    9   14   16   19   20   22   24   26   27   29 
LCS_AVERAGE  LCS_A:   3.20  (   1.70    2.20    5.70 )

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      7      9     11     11     11     11     11     14     16     17     18     19     20     22     22     22     24     26     27     29 
GDT PERCENT_AT   2.08   2.68   3.27   3.27   3.27   3.27   3.27   4.17   4.76   5.06   5.36   5.65   5.95   6.55   6.55   6.55   7.14   7.74   8.04   8.63
GDT RMS_LOCAL    0.29   0.49   0.80   0.80   0.80   0.80   0.80   3.29   3.39   3.48   3.68   4.14   4.31   4.91   4.91   4.91   6.16   6.53   6.66   7.01
GDT RMS_ALL_AT  27.40  27.51  27.52  27.52  27.52  27.52  27.52  23.15  22.90  22.87  22.71  22.16  22.00  21.85  21.85  21.85  17.29  15.46  15.67  15.73

# Checking swapping
#   possible swapping detected:  D    51_A      D    51_A
#   possible swapping detected:  Y    63_A      Y    63_A
#   possible swapping detected:  E    65_A      E    65_A
#   possible swapping detected:  F    73_A      F    73_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T    38_A      T    38_A    29.911     0    0.323   1.204    32.288    0.000    0.000
LGA    A    39_A      A    39_A    29.760     0    0.472   0.526    33.989    0.000    0.000
LGA    T    40_A      T    40_A    33.860     0    0.047   0.091    34.594    0.000    0.000
LGA    V    41_A      V    41_A    38.051     0    0.561   1.431    41.830    0.000    0.000
LGA    N    42_A      N    42_A    37.000     0    0.655   1.328    40.328    0.000    0.000
LGA    E    43_A      E    43_A    37.209     0    0.611   1.290    38.091    0.000    0.000
LGA    L    44_A      L    44_A    41.317     0    0.658   1.247    44.879    0.000    0.000
LGA    S    45_A      S    45_A    45.180     0    0.697   0.838    47.342    0.000    0.000
LGA    G    46_A      G    46_A    44.908     0    0.675   0.675    44.981    0.000    0.000
LGA    I    47_A      I    47_A    42.625     0    0.577   0.870    45.219    0.000    0.000
LGA    P    48_A      P    48_A    38.877     0    0.620   0.573    40.452    0.000    0.000
LGA    A    49_A      A    49_A    35.000     0    0.582   0.573    36.582    0.000    0.000
LGA    V    50_A      V    50_A    30.285     0    0.318   1.051    32.521    0.000    0.000
LGA    D    51_A      D    51_A    29.785     0    0.476   1.413    32.066    0.000    0.000
LGA    R    52_A      R    52_A    28.066     0    0.051   0.984    36.909    0.000    0.000
LGA    A    53_A      A    53_A    23.919     0    0.057   0.090    25.860    0.000    0.000
LGA    H    54_A      H    54_A    19.904     0    0.067   1.545    22.070    0.000    0.000
LGA    V    55_A      V    55_A    19.487     0    0.085   0.243    23.608    0.000    0.000
LGA    L    56_A      L    56_A    16.589     0    0.048   1.059    18.249    0.000    0.000
LGA    Q    57_A      Q    57_A    11.514     0    0.036   1.050    16.537    2.619    1.164
LGA    T    58_A      T    58_A     9.580     0    0.042   0.973    12.658    1.667    0.952
LGA    A    59_A      A    59_A    11.789     0    0.056   0.056    13.798    0.714    0.571
LGA    L    60_A      L    60_A     5.117     0    0.074   0.893     8.196   31.667   25.893
LGA    S    61_A      S    61_A     2.667     0    0.275   0.706     4.700   48.690   46.032
LGA    I    62_A      I    62_A     2.832     0    0.719   1.471     6.208   50.714   43.810
LGA    Y    63_A      Y    63_A     4.924     0    0.565   1.370    16.396   43.810   15.556
LGA    P    64_A      P    64_A     3.952     0    0.066   0.255     5.157   45.119   37.007
LGA    E    65_A      E    65_A     3.703     0    0.065   1.043     9.509   46.786   26.931
LGA    V    66_A      V    66_A     2.879     0    0.628   0.630     4.598   52.619   49.660
LGA    E    67_A      E    67_A     1.883     0    0.573   0.857     4.072   59.881   56.984
LGA    N    68_A      N    68_A     2.604     0    0.663   0.753     8.535   61.190   38.155
LGA    W    69_A      W    69_A     3.997     0    0.612   1.155    15.597   55.833   18.197
LGA    V    70_A      V    70_A     4.303     0    0.626   1.340     8.384   33.214   25.782
LGA    A    71_A      A    71_A     4.749     0    0.137   0.142     6.286   38.810   34.476
LGA    Q    72_A      Q    72_A     3.583     0    0.680   1.099     8.609   45.000   30.106
LGA    F    73_A      F    73_A     6.075     0    0.472   1.501    14.728   22.738    8.528
LGA    P    74_A      P    74_A     4.571     0    0.686   0.616     6.164   43.929   35.918
LGA    V    75_A      V    75_A     1.184     0    0.667   0.714     4.818   71.429   58.639
LGA    I    76_A      I    76_A     2.825     0    0.087   0.623     8.366   69.048   45.000
LGA    L    77_A      L    77_A     3.279     0    0.579   1.572     8.771   40.595   25.119
LGA    P    78_A      P    78_A     8.779     0    0.643   0.653    11.602    5.000    5.170
LGA    Q    79_A      Q    79_A    11.746     0    0.344   0.510    13.946    0.000    0.053

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       42     168    168  100.00     324    324  100.00               336
SUMMARY(RMSD_GDC):    12.866         12.742                 13.278            2.592    1.874

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   60  336    4.0     14    3.29     4.167     3.731     0.413

LGA_LOCAL      RMSD:   3.289  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  23.146  Number of assigned atoms:   42 
Std_ASGN_ATOMS RMSD:  12.866  Standard rmsd on all 42 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.588904 * X  +   0.565179 * Y  +   0.577723 * Z  +  40.856522
  Y_new =  -0.799666 * X  +  -0.303848 * Y  +  -0.517891 * Z  + -24.604053
  Z_new =  -0.117161 * X  +  -0.766974 * Y  +   0.630892 * Z  +  -1.180658 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.205561  0.117431 -0.882442   [DEG: -126.3693    6.7283  -50.5602 ]
ZXZ:  0.839954  0.888094 -2.990007   [DEG:   48.1258   50.8840 -171.3148 ]
 
# END of job
