
#######################################################
#                                                     #
#                        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   48 (  393),  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      52_A - 99_A        0.55     0.55
  LCS_AVERAGE:     49.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48      52_A - 99_A        0.55     0.55
  LCS_AVERAGE:     49.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48      52_A - 99_A        0.55     0.55
  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     G    52_A     G    52_A     48   48   48      5   27   47   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48   48 
LCS_GDT     E    53_A     E    53_A     48   48   48      4   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     36   44   47   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     23   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     38   44   47   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     27   44   47   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     38   44   47   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     27   44   47   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     33   44   47   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      4   44   47   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     11   37   47   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      3   35   47   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     38     44     47     48     48     48     48     48     48     48     48     48     48     48     48     48     48     48     48     48 
GDT PERCENT_AT  39.18  45.36  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
GDT RMS_LOCAL    0.28   0.39   0.49   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55
GDT RMS_ALL_AT   0.61   0.58   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55

# Checking swapping
#   possible swapping detected:  E    55_A      E    55_A
#   possible swapping detected:  F    69_A      F    69_A
#   possible swapping detected:  E    73_A      E    73_A
#   possible swapping detected:  E    74_A      E    74_A
#   possible swapping detected:  F    85_A      F    85_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G    52_A      G    52_A     1.705     0    0.039   0.039     2.062   75.119   75.119
LGA    E    53_A      E    53_A     1.134     0    0.074   0.845     4.311   85.952   70.265
LGA    W    54_A      W    54_A     0.529     0    0.055   0.107     1.136   88.214   92.551
LGA    E    55_A      E    55_A     0.366     0    0.053   0.990     4.443   97.619   76.772
LGA    I    56_A      I    56_A     0.293     0    0.047   0.617     2.584  100.000   94.643
LGA    I    57_A      I    57_A     0.316     0    0.032   0.083     0.471  100.000  100.000
LGA    D    58_A      D    58_A     0.304     0    0.070   0.548     2.110  100.000   94.405
LGA    I    59_A      I    59_A     0.455     0    0.058   0.106     0.481  100.000  100.000
LGA    G    60_A      G    60_A     0.258     0    0.047   0.047     0.320  100.000  100.000
LGA    P    61_A      P    61_A     0.445     0    0.013   0.047     0.562  100.000   98.639
LGA    F    62_A      F    62_A     0.544     0    0.029   0.161     0.905   97.619   93.074
LGA    T    63_A      T    63_A     0.449     0    0.008   1.056     2.132  100.000   89.728
LGA    Q    64_A      Q    64_A     0.195     0    0.014   0.102     0.314  100.000  100.000
LGA    N    65_A      N    65_A     0.417     0    0.068   0.234     1.014  100.000   94.107
LGA    L    66_A      L    66_A     0.368     0    0.021   0.253     0.536  100.000   98.810
LGA    G    67_A      G    67_A     0.082     0    0.021   0.021     0.199  100.000  100.000
LGA    K    68_A      K    68_A     0.143     0    0.040   1.408     6.972  100.000   72.857
LGA    F    69_A      F    69_A     0.320     0    0.006   0.107     0.698  100.000   97.403
LGA    A    70_A      A    70_A     0.227     0    0.026   0.034     0.342  100.000  100.000
LGA    V    71_A      V    71_A     0.138     0    0.040   0.048     0.296  100.000  100.000
LGA    D    72_A      D    72_A     0.287     0    0.015   0.090     0.564  100.000   98.810
LGA    E    73_A      E    73_A     0.350     0    0.032   0.133     0.581  100.000   98.942
LGA    E    74_A      E    74_A     0.371     0    0.046   0.221     0.519  100.000   98.942
LGA    N    75_A      N    75_A     0.181     0    0.049   0.119     0.511  100.000   98.810
LGA    K    76_A      K    76_A     0.141     0    0.036   0.115     0.421  100.000  100.000
LGA    I    77_A      I    77_A     0.183     0    0.013   0.121     0.521  100.000   98.810
LGA    G    78_A      G    78_A     0.571     0    0.036   0.036     0.680   92.857   92.857
LGA    Q    79_A      Q    79_A     0.710     0    0.016   0.971     4.646   90.476   76.349
LGA    Y    80_A      Y    80_A     0.452     0    0.015   0.063     0.850   97.619   93.651
LGA    G    81_A      G    81_A     0.495     0    0.039   0.039     0.495  100.000  100.000
LGA    R    82_A      R    82_A     0.340     0    0.088   1.136     5.467   97.619   79.654
LGA    L    83_A      L    83_A     0.159     0    0.019   0.132     0.556  100.000   98.810
LGA    T    84_A      T    84_A     0.272     0    0.098   0.127     0.514   97.619   98.639
LGA    F    85_A      F    85_A     0.272     0    0.008   0.065     0.406  100.000  100.000
LGA    N    86_A      N    86_A     0.314     0    0.049   0.939     2.099  100.000   91.190
LGA    K    87_A      K    87_A     0.323     0    0.016   0.110     0.412  100.000  100.000
LGA    V    88_A      V    88_A     0.339     0    0.021   0.048     0.434  100.000  100.000
LGA    I    89_A      I    89_A     0.276     0    0.006   0.043     0.402  100.000  100.000
LGA    R    90_A      R    90_A     0.361     0    0.026   0.946     4.554   97.619   81.039
LGA    P    91_A      P    91_A     0.337     0    0.040   0.069     0.647  100.000   98.639
LGA    C    92_A      C    92_A     0.195     0    0.105   0.156     0.515   97.619   98.413
LGA    M    93_A      M    93_A     0.630     0    0.028   0.997     4.561   95.238   84.345
LGA    K    94_A      K    94_A     0.253     0    0.125   0.638     3.598   97.619   80.212
LGA    K    95_A      K    95_A     0.856     0    0.035   0.584     1.315   90.476   87.460
LGA    T    96_A      T    96_A     0.553     0    0.031   0.069     1.459   92.857   90.544
LGA    I    97_A      I    97_A     0.950     0    0.042   0.367     1.639   90.476   83.810
LGA    Y    98_A      Y    98_A     1.099     0    0.073   0.121     1.795   79.286   82.222
LGA    E    99_A      E    99_A     1.310     0    0.145   0.818     2.963   77.143   68.730

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       48     192    192  100.00     393    393  100.00                97
SUMMARY(RMSD_GDC):     0.548          0.563                  1.162           47.825   45.662

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   48   97    4.0     48    0.55    48.454    49.082     7.410

LGA_LOCAL      RMSD:   0.548  Number of atoms:   48  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.548  Number of assigned atoms:   48 
Std_ASGN_ATOMS RMSD:   0.548  Standard rmsd on all 48 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.130297 * X  +   0.976239 * Y  +  -0.173150 * Z  +  -4.264991
  Y_new =  -0.950309 * X  +   0.172768 * Y  +   0.258967 * Z  +  11.385162
  Z_new =   0.282729 * X  +   0.130803 * Y  +   0.950239 * Z  +  45.095139 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.434536 -0.286638  0.136793   [DEG:  -82.1928  -16.4231    7.8377 ]
ZXZ: -2.552242  0.316793  1.137477   [DEG: -146.2327   18.1509   65.1726 ]
 
# END of job
