
#######################################################
#                                                     #
#                        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     11   35   46   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     35   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     22   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     23   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     23   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     34   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      4   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   34   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     1.697     0    0.042   0.042     2.063   75.119   75.119
LGA    E    53_A      E    53_A     1.119     0    0.081   0.847     4.305   85.952   70.265
LGA    W    54_A      W    54_A     0.533     0    0.062   0.131     1.196   88.214   92.551
LGA    E    55_A      E    55_A     0.375     0    0.053   0.995     4.378   97.619   76.032
LGA    I    56_A      I    56_A     0.299     0    0.045   0.618     2.577  100.000   94.643
LGA    I    57_A      I    57_A     0.326     0    0.034   0.087     0.479  100.000  100.000
LGA    D    58_A      D    58_A     0.322     0    0.067   0.558     2.155  100.000   93.214
LGA    I    59_A      I    59_A     0.452     0    0.053   0.109     0.469  100.000  100.000
LGA    G    60_A      G    60_A     0.258     0    0.048   0.048     0.322  100.000  100.000
LGA    P    61_A      P    61_A     0.436     0    0.017   0.037     0.538  100.000   97.279
LGA    F    62_A      F    62_A     0.543     0    0.025   0.166     0.885   97.619   93.074
LGA    T    63_A      T    63_A     0.459     0    0.010   1.070     2.182  100.000   89.728
LGA    Q    64_A      Q    64_A     0.205     0    0.014   0.102     0.325  100.000  100.000
LGA    N    65_A      N    65_A     0.419     0    0.069   0.229     1.004  100.000   94.107
LGA    L    66_A      L    66_A     0.374     0    0.019   0.250     0.539  100.000   98.810
LGA    G    67_A      G    67_A     0.121     0    0.026   0.026     0.227  100.000  100.000
LGA    K    68_A      K    68_A     0.155     0    0.039   1.402     6.939  100.000   73.439
LGA    F    69_A      F    69_A     0.323     0    0.012   0.086     0.713  100.000   96.537
LGA    A    70_A      A    70_A     0.236     0    0.028   0.037     0.340  100.000  100.000
LGA    V    71_A      V    71_A     0.150     0    0.036   0.062     0.332  100.000  100.000
LGA    D    72_A      D    72_A     0.283     0    0.019   0.085     0.586  100.000   98.810
LGA    E    73_A      E    73_A     0.362     0    0.030   0.145     0.650  100.000   98.942
LGA    E    74_A      E    74_A     0.372     0    0.049   0.224     0.523  100.000   98.942
LGA    N    75_A      N    75_A     0.182     0    0.049   0.093     0.461  100.000  100.000
LGA    K    76_A      K    76_A     0.139     0    0.037   0.117     0.432  100.000  100.000
LGA    I    77_A      I    77_A     0.180     0    0.015   0.124     0.535  100.000   98.810
LGA    G    78_A      G    78_A     0.572     0    0.042   0.042     0.667   92.857   92.857
LGA    Q    79_A      Q    79_A     0.704     0    0.012   0.963     4.599   90.476   76.349
LGA    Y    80_A      Y    80_A     0.445     0    0.021   0.052     1.006   95.238   92.103
LGA    G    81_A      G    81_A     0.490     0    0.039   0.039     0.490  100.000  100.000
LGA    R    82_A      R    82_A     0.347     0    0.084   1.136     5.470   97.619   79.654
LGA    L    83_A      L    83_A     0.162     0    0.018   0.122     0.519  100.000   98.810
LGA    T    84_A      T    84_A     0.291     0    0.102   0.133     0.527   97.619   98.639
LGA    F    85_A      F    85_A     0.297     0    0.007   0.063     0.414  100.000  100.000
LGA    N    86_A      N    86_A     0.306     0    0.050   0.934     2.140  100.000   92.202
LGA    K    87_A      K    87_A     0.313     0    0.016   0.113     0.405  100.000  100.000
LGA    V    88_A      V    88_A     0.344     0    0.019   0.055     0.467  100.000  100.000
LGA    I    89_A      I    89_A     0.275     0    0.009   0.049     0.414  100.000  100.000
LGA    R    90_A      R    90_A     0.362     0    0.021   0.946     4.563   97.619   81.039
LGA    P    91_A      P    91_A     0.351     0    0.042   0.070     0.658   97.619   97.279
LGA    C    92_A      C    92_A     0.201     0    0.114   0.170     0.545   97.619   98.413
LGA    M    93_A      M    93_A     0.641     0    0.030   0.998     4.576   95.238   84.345
LGA    K    94_A      K    94_A     0.250     0    0.124   0.635     3.598   97.619   80.212
LGA    K    95_A      K    95_A     0.837     0    0.031   0.584     1.328   90.476   87.460
LGA    T    96_A      T    96_A     0.541     0    0.036   0.076     1.426   92.857   90.544
LGA    I    97_A      I    97_A     0.955     0    0.055   0.368     1.692   90.476   83.810
LGA    Y    98_A      Y    98_A     1.096     0    0.081   0.123     1.797   79.286   82.222
LGA    E    99_A      E    99_A     1.306     0    0.147   0.828     3.028   77.143   67.937

# 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):     0.547          0.565                  1.164           47.776   45.610

#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     7.415

LGA_LOCAL      RMSD:   0.547  Number of atoms:   48  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.547  Number of assigned atoms:   48 
Std_ASGN_ATOMS RMSD:   0.547  Standard rmsd on all 48 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.130360 * X  +   0.976331 * Y  +  -0.172580 * Z  +  -4.264886
  Y_new =  -0.950299 * X  +   0.172677 * Y  +   0.259063 * Z  +  11.386551
  Z_new =   0.282732 * X  +   0.130231 * Y  +   0.950317 * Z  +  45.098385 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.434469 -0.286641  0.136192   [DEG:  -82.1890  -16.4233    7.8032 ]
ZXZ: -2.553934  0.316544  1.139148   [DEG: -146.3296   18.1366   65.2684 ]
 
# END of job
