
#######################################################
#                                                     #
#                        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   82 (  642),  selected   45 , name one
# Molecule2: number of CA atoms  126 (  936),  selected   45 , 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:    33      69_A - 101_A       4.98    11.78
  LONGEST_CONTINUOUS_SEGMENT:    33      70_A - 102_A       4.75    12.13
  LONGEST_CONTINUOUS_SEGMENT:    33      71_A - 103_A       4.88    12.45
  LCS_AVERAGE:     22.19

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      81_A - 100_A       1.64    12.25
  LCS_AVERAGE:      9.01

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      83_A - 100_A       0.95    12.73
  LCS_AVERAGE:      7.37

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   45
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     R    59_A     R    59_A      3    3   10      0    3    3    3    3    4    5    7    7   12   13   15   15   17   19   21   22   24   26   30 
LCS_GDT     R    60_A     R    60_A      3    3   10      0    3    3    3    4    5    7    9   10   12   13   15   16   18   20   22   26   29   31   31 
LCS_GDT     V    61_A     V    61_A      3    3   10      3    3    3    3    4    5    7    9   10   12   13   15   16   18   19   22   24   29   30   31 
LCS_GDT     K    62_A     K    62_A      3    3   10      3    4    4    4    4    5    7    9   10   12   13   15   15   17   19   22   23   27   30   30 
LCS_GDT     L    63_A     L    63_A      3    4   10      3    4    4    4    4    5    5    7    8   12   13   15   15   17   18   22   22   24   29   30 
LCS_GDT     R    64_A     R    64_A      4    5   10      3    4    4    5    6    6    7    7    8    9    9   15   15   17   18   22   22   23   24   26 
LCS_GDT     K    65_A     K    65_A      4    5   10      3    4    4    5    6    6    7    7    8   12   13   15   15   17   18   18   21   23   23   25 
LCS_GDT     H    66_A     H    66_A      4    5   11      3    4    4    5    6    6    7    7    8   12   13   15   15   17   18   19   21   21   23   25 
LCS_GDT     L    67_A     L    67_A      4    5   11      3    4    4    5    6    6    7    9   10   12   13   15   16   18   19   22   24   29   30   31 
LCS_GDT     V    68_A     V    68_A      3    5   11      1    3    4    5    6    6    7    9   10   12   13   16   20   22   24   27   28   30   31   31 
LCS_GDT     E    69_A     E    69_A      3    5   33      1    3    3    4    5    6    6    7    8    8   13   15   15   22   25   27   28   30   31   31 
LCS_GDT     I    70_A     I    70_A      4    5   33      3    4    4    4    5    6    6    7    8   10   13   15   22   25   25   29   29   30   32   32 
LCS_GDT     N    71_A     N    71_A      4    5   33      3    4    4    4    5   12   18   23   23   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     A    72_A     A    72_A      4    5   33      3    4    4    5    5    6   10   13   20   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     D    73_A     D    73_A      4    5   33      3    4    4    5    5   10   11   13   14   24   26   30   30   30   31   31   31   31   32   32 
LCS_GDT     E    74_A     E    74_A      4    5   33      3    4    4    5    5    6    6    7    8    9   12   25   26   30   31   31   31   31   31   32 
LCS_GDT     I    75_A     I    75_A      4    5   33      3    4    4    5    5    5    6    7   18   24   26   30   30   30   31   31   31   31   32   32 
LCS_GDT     T    76_A     T    76_A      3    5   33      0    3    6    9    9   13   20   22   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     I    77_A     I    77_A      3    3   33      1    3   12   17   20   20   21   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     T    78_A     T    78_A      3    3   33      0   14   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     L    79_A     L    79_A      3    4   33      0    3   16   18   19   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     S    80_A     S    80_A      3    5   33      3    3    4    5    7    9   15   19   23   25   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     R    81_A     R    81_A      3   20   33      3    3    4    7   11   17   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     Y    82_A     Y    82_A      3   20   33      3    3    4    6   11   19   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     T    83_A     T    83_A     18   20   33      3    5   10   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     S    84_A     S    84_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     P    85_A     P    85_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     E    86_A     E    86_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     A    87_A     A    87_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     L    88_A     L    88_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     E    89_A     E    89_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     R    90_A     R    90_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     S    91_A     S    91_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     I    92_A     I    92_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     T    93_A     T    93_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     A    94_A     A    94_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     L    95_A     L    95_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     A    96_A     A    96_A     18   20   33     13   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     A    97_A     A    97_A     18   20   33      7   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     M    98_A     M    98_A     18   20   33      3   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     T    99_A     T    99_A     18   20   33     10   16   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     G   100_A     G   100_A     18   20   33      3   12   17   18   20   20   22   23   24   26   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     H   101_A     H   101_A      4    5   33      3    4    4    5    6    7    9   18   22   24   28   30   30   30   31   31   31   31   32   32 
LCS_GDT     A   102_A     A   102_A      4    5   33      3    4    4    5    6    6    6   10   10   11   13   15   15   18   22   26   28   30   32   32 
LCS_GDT     P   103_A     P   103_A      4    5   33      3    4    4    5    6    6    6    7    8   11   13   15   15   17   18   19   20   22   23   25 
LCS_AVERAGE  LCS_A:  12.86  (   7.37    9.01   22.19 )

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     13     16     17     18     20     20     22     23     24     26     28     30     30     30     31     31     31     31     32     32 
GDT PERCENT_AT  10.32  12.70  13.49  14.29  15.87  15.87  17.46  18.25  19.05  20.63  22.22  23.81  23.81  23.81  24.60  24.60  24.60  24.60  25.40  25.40
GDT RMS_LOCAL    0.26   0.47   0.61   0.80   1.10   1.10   1.71   1.84   2.01   2.76   3.20   3.53   3.53   3.53   3.83   3.83   3.83   3.83   4.48   4.28
GDT RMS_ALL_AT  12.70  12.32  12.67  12.62  13.08  13.08  12.22  12.50  12.54  11.98  11.80  12.20  12.20  12.20  12.54  12.54  12.54  12.54  11.80  12.48

# Checking swapping
#   possible swapping detected:  E    69_A      E    69_A
#   possible swapping detected:  D    73_A      D    73_A
#   possible swapping detected:  E    74_A      E    74_A
#   possible swapping detected:  Y    82_A      Y    82_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    R    59_A      R    59_A    23.498     6    0.168   0.197    24.776    0.000    0.000
LGA    R    60_A      R    60_A    20.736     6    0.594   0.535    21.584    0.000    0.000
LGA    V    61_A      V    61_A    21.507     0    0.598   1.341    25.207    0.000    0.000
LGA    K    62_A      K    62_A    24.634     0    0.620   0.968    31.131    0.000    0.000
LGA    L    63_A      L    63_A    26.016     0    0.604   0.541    30.595    0.000    0.000
LGA    R    64_A      R    64_A    25.048     6    0.573   0.573    25.506    0.000    0.000
LGA    K    65_A      K    65_A    28.473     0    0.050   0.805    39.496    0.000    0.000
LGA    H    66_A      H    66_A    26.948     0    0.200   1.316    31.231    0.000    0.000
LGA    L    67_A      L    67_A    19.828     0    0.600   1.537    22.642    0.000    0.000
LGA    V    68_A      V    68_A    16.249     0    0.642   0.603    18.249    0.000    0.000
LGA    E    69_A      E    69_A    14.703     0    0.677   1.169    17.511    0.000    0.000
LGA    I    70_A      I    70_A    14.211     0    0.607   1.032    17.341    0.000    0.000
LGA    N    71_A      N    71_A     8.384     0    0.428   1.104    10.364    1.905    6.429
LGA    A    72_A      A    72_A     8.745     0    0.514   0.482     8.913    6.071    5.429
LGA    D    73_A      D    73_A     7.130     0    0.311   0.740     7.862    9.405   10.179
LGA    E    74_A      E    74_A     9.664     0    0.163   1.433    15.927    1.310    0.582
LGA    I    75_A      I    75_A     7.666     0    0.565   0.791     9.392    7.500    5.595
LGA    T    76_A      T    76_A     4.488     0    0.633   0.557     6.783   34.524   27.279
LGA    I    77_A      I    77_A     3.332     0    0.611   0.710     8.276   53.571   36.131
LGA    T    78_A      T    78_A     1.641     0    0.623   0.942     2.346   70.952   73.061
LGA    L    79_A      L    79_A     2.915     0    0.698   0.766     8.282   47.857   33.274
LGA    S    80_A      S    80_A     5.830     0    0.638   0.885     9.570   33.333   23.492
LGA    R    81_A      R    81_A     4.638     0    0.000   1.039    13.641   34.524   16.667
LGA    Y    82_A      Y    82_A     3.857     0    0.655   1.044    10.477   43.690   21.746
LGA    T    83_A      T    83_A     2.908     0    0.645   0.927     6.931   67.024   46.395
LGA    S    84_A      S    84_A     0.627     0    0.128   0.533     1.098   88.214   87.460
LGA    P    85_A      P    85_A     0.616     0    0.105   0.280     1.921   90.476   86.667
LGA    E    86_A      E    86_A     0.438     0    0.161   1.188     5.296   92.857   72.222
LGA    A    87_A      A    87_A     0.184     0    0.052   0.053     0.262  100.000  100.000
LGA    L    88_A      L    88_A     0.412     0    0.103   0.136     0.632  100.000   96.429
LGA    E    89_A      E    89_A     0.377     0    0.000   1.014     4.522  100.000   79.471
LGA    R    90_A      R    90_A     0.167     0    0.092   0.989     5.642   97.619   78.701
LGA    S    91_A      S    91_A     0.440     0    0.000   0.060     0.613   95.238   93.651
LGA    I    92_A      I    92_A     0.733     0    0.000   0.132     1.589   90.476   83.810
LGA    T    93_A      T    93_A     0.744     0    0.064   0.082     0.744   90.476   90.476
LGA    A    94_A      A    94_A     0.446     0    0.051   0.068     0.637   95.238   96.190
LGA    L    95_A      L    95_A     0.606     0    0.106   0.134     0.723   92.857   91.667
LGA    A    96_A      A    96_A     0.932     0    0.000   0.000     1.205   85.952   85.048
LGA    A    97_A      A    97_A     1.342     0    0.078   0.047     1.981   85.952   83.333
LGA    M    98_A      M    98_A     1.067     0    0.087   1.051     5.260   85.952   73.750
LGA    T    99_A      T    99_A     0.461     0    0.115   0.152     0.632   92.857   94.558
LGA    G   100_A      G   100_A     1.821     0    0.086   0.086     5.466   52.976   52.976
LGA    H   101_A      H   101_A     8.931     5    0.000   0.047    10.442    5.357    2.143
LGA    A   102_A      A   102_A    14.296     0    0.660   0.619    16.399    0.000    0.000
LGA    P   103_A      P   103_A    17.298     0    0.538   0.570    18.497    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       45     180    180  100.00     329    329  100.00               126
SUMMARY(RMSD_GDC):     9.510          9.319                 10.526           15.509   13.927

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   82  126    4.0     23    1.84    17.460    15.756     1.187

LGA_LOCAL      RMSD:   1.837  Number of atoms:   23  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  12.501  Number of assigned atoms:   45 
Std_ASGN_ATOMS RMSD:   9.510  Standard rmsd on all 45 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.124587 * X  +  -0.267406 * Y  +  -0.955496 * Z  + 435.865479
  Y_new =   0.030706 * X  +  -0.963577 * Y  +   0.265663 * Z  + 226.782333
  Z_new =  -0.991733 * X  +   0.003759 * Y  +   0.128261 * Z  + 617.482788 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.899948  1.442126  0.029299   [DEG:  166.1548   82.6277    1.6787 ]
ZXZ: -1.841984  1.442181 -1.567006   [DEG: -105.5379   82.6309  -89.7828 ]
 
# END of job
