
#######################################################
#                                                     #
#                        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   49 (  406),  selected   48 , name one
# Molecule2: number of CA atoms   97 (  780),  selected   48 , 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:    48      53_A - 100_A       0.44     0.44
  LCS_AVERAGE:     49.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48      53_A - 100_A       0.44     0.44
  LCS_AVERAGE:     49.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48      53_A - 100_A       0.44     0.44
  LCS_AVERAGE:     49.48

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   48
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     E    53_A     E    53_A     48   48   48     10   42   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     W    54_A     W    54_A     48   48   48     36   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     E    55_A     E    55_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    56_A     I    56_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    57_A     I    57_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     D    58_A     D    58_A     48   48   48     42   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    59_A     I    59_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     G    60_A     G    60_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     P    61_A     P    61_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     F    62_A     F    62_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     T    63_A     T    63_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     Q    64_A     Q    64_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     N    65_A     N    65_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     L    66_A     L    66_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     G    67_A     G    67_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     K    68_A     K    68_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     F    69_A     F    69_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     A    70_A     A    70_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     V    71_A     V    71_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     D    72_A     D    72_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     E    73_A     E    73_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     E    74_A     E    74_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     N    75_A     N    75_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     K    76_A     K    76_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    77_A     I    77_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     G    78_A     G    78_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     Q    79_A     Q    79_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     Y    80_A     Y    80_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     G    81_A     G    81_A     48   48   48     33   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     R    82_A     R    82_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     L    83_A     L    83_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     T    84_A     T    84_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     F    85_A     F    85_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     N    86_A     N    86_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     K    87_A     K    87_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     V    88_A     V    88_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    89_A     I    89_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     R    90_A     R    90_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     P    91_A     P    91_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     C    92_A     C    92_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     M    93_A     M    93_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     K    94_A     K    94_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     K    95_A     K    95_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     T    96_A     T    96_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     I    97_A     I    97_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     Y    98_A     Y    98_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     E    99_A     E    99_A     48   48   48     43   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     N   100_A     N   100_A     48   48   48      3   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_AVERAGE  LCS_A:  49.48  (  49.48   49.48   49.48 )

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     43     47     48     48     48     48     48     48     48     48     48     48     48     48     48     48     48     48     48     48 
GDT PERCENT_AT  44.33  48.45  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48  49.48
GDT RMS_LOCAL    0.31   0.37   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44
GDT RMS_ALL_AT   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44

# Checking swapping
#   possible swapping detected:  E    55_A      E    55_A
#   possible swapping detected:  F    62_A      F    62_A
#   possible swapping detected:  E    74_A      E    74_A
#   possible swapping detected:  E    99_A      E    99_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E    53_A      E    53_A     1.597     0    0.712   1.354     6.031   73.690   54.550
LGA    W    54_A      W    54_A     0.770     0    0.039   0.083     1.437   88.214   84.014
LGA    E    55_A      E    55_A     0.441     0    0.014   1.058     5.824   97.619   68.571
LGA    I    56_A      I    56_A     0.168     0    0.034   0.615     2.064   97.619   93.214
LGA    I    57_A      I    57_A     0.393     0    0.016   0.091     0.421  100.000  100.000
LGA    D    58_A      D    58_A     0.542     0    0.033   0.169     1.398   95.238   89.464
LGA    I    59_A      I    59_A     0.483     0    0.116   0.138     0.724  100.000   96.429
LGA    G    60_A      G    60_A     0.184     0    0.051   0.051     0.403  100.000  100.000
LGA    P    61_A      P    61_A     0.330     0    0.041   0.096     0.375  100.000  100.000
LGA    F    62_A      F    62_A     0.398     0    0.021   0.102     0.522  100.000   99.134
LGA    T    63_A      T    63_A     0.270     0    0.030   0.039     0.345  100.000  100.000
LGA    Q    64_A      Q    64_A     0.209     0    0.036   0.093     0.240  100.000  100.000
LGA    N    65_A      N    65_A     0.466     0    0.044   0.207     0.727  100.000   98.810
LGA    L    66_A      L    66_A     0.499     0    0.024   0.058     0.758  100.000   95.238
LGA    G    67_A      G    67_A     0.206     0    0.037   0.037     0.303  100.000  100.000
LGA    K    68_A      K    68_A     0.284     0    0.038   1.503     7.010  100.000   72.910
LGA    F    69_A      F    69_A     0.402     0    0.006   0.062     0.462  100.000  100.000
LGA    A    70_A      A    70_A     0.277     0    0.081   0.091     0.319  100.000  100.000
LGA    V    71_A      V    71_A     0.127     0    0.034   0.063     0.445  100.000  100.000
LGA    D    72_A      D    72_A     0.183     0    0.023   0.073     0.331  100.000  100.000
LGA    E    73_A      E    73_A     0.369     0    0.029   0.171     0.625   97.619   97.884
LGA    E    74_A      E    74_A     0.471     0    0.052   1.319     5.370   97.619   72.222
LGA    N    75_A      N    75_A     0.297     0    0.075   0.082     0.498  100.000  100.000
LGA    K    76_A      K    76_A     0.280     0    0.051   0.132     0.740  100.000   98.942
LGA    I    77_A      I    77_A     0.205     0    0.016   0.087     0.391  100.000  100.000
LGA    G    78_A      G    78_A     0.277     0    0.051   0.051     0.363  100.000  100.000
LGA    Q    79_A      Q    79_A     0.303     0    0.025   0.706     3.327  100.000   85.767
LGA    Y    80_A      Y    80_A     0.369     0    0.016   0.083     0.631   97.619   99.206
LGA    G    81_A      G    81_A     0.659     0    0.057   0.057     0.659   90.476   90.476
LGA    R    82_A      R    82_A     0.450     0    0.079   1.451     6.732   95.238   68.918
LGA    L    83_A      L    83_A     0.200     0    0.030   0.087     0.301  100.000  100.000
LGA    T    84_A      T    84_A     0.297     0    0.078   0.959     2.471  100.000   89.728
LGA    F    85_A      F    85_A     0.263     0    0.011   0.100     0.369  100.000  100.000
LGA    N    86_A      N    86_A     0.210     0    0.052   0.072     0.412  100.000  100.000
LGA    K    87_A      K    87_A     0.066     0    0.019   0.187     1.072  100.000   94.815
LGA    V    88_A      V    88_A     0.124     0    0.015   0.021     0.170  100.000  100.000
LGA    I    89_A      I    89_A     0.134     0    0.020   0.087     0.369  100.000  100.000
LGA    R    90_A      R    90_A     0.176     0    0.023   0.936     3.822  100.000   87.576
LGA    P    91_A      P    91_A     0.294     0    0.021   0.060     0.446  100.000  100.000
LGA    C    92_A      C    92_A     0.354     0    0.049   0.104     0.412  100.000  100.000
LGA    M    93_A      M    93_A     0.323     0    0.057   1.136     4.639  100.000   85.833
LGA    K    94_A      K    94_A     0.186     0    0.042   0.312     2.601  100.000   90.106
LGA    K    95_A      K    95_A     0.136     0    0.032   0.848     3.034  100.000   90.370
LGA    T    96_A      T    96_A     0.295     0    0.028   0.040     0.715  100.000   95.918
LGA    I    97_A      I    97_A     0.469     0    0.067   0.483     1.166   97.619   92.917
LGA    Y    98_A      Y    98_A     0.483     0    0.031   0.079     0.868   92.857   91.270
LGA    E    99_A      E    99_A     0.297     0    0.073   1.109     3.098   95.357   78.730
LGA    N   100_A      N   100_A     0.992     0    0.545   1.217     5.849   82.143   59.464

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       48     192    192  100.00     397    397  100.00                97
SUMMARY(RMSD_GDC):     0.436          0.493                  1.388           48.443   45.593

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   49   97    4.0     48    0.44    49.227    49.403     8.949

LGA_LOCAL      RMSD:   0.436  Number of atoms:   48  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.436  Number of assigned atoms:   48 
Std_ASGN_ATOMS RMSD:   0.436  Standard rmsd on all 48 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.522901 * X  +  -0.851133 * Y  +  -0.046336 * Z  +  10.450930
  Y_new =  -0.814159 * X  +   0.514805 * Y  +  -0.268553 * Z  +   1.962018
  Z_new =   0.252429 * X  +  -0.102702 * Y  +  -0.962150 * Z  +  26.200811 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.141710 -0.255189 -3.035253   [DEG: -122.7110  -14.6213 -173.9072 ]
ZXZ: -0.170856  2.865580  1.957199   [DEG:   -9.7893  164.1856  112.1393 ]
 
# END of job
