
#######################################################
#                                                     #
#                        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   43 (  321),  selected   43 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   43 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       3_F - 45_F        0.57     0.57
  LCS_AVERAGE:     87.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       3_F - 45_F        0.57     0.57
  LCS_AVERAGE:     87.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       3_F - 45_F        0.57     0.57
  LCS_AVERAGE:     87.76

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
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     K     3_F     K     3_F     43   43   43      7   39   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     I     4_F     I     4_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K     5_F     K     5_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R     6_F     R     6_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F     7_F     F     7_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F     8_F     F     8_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A     9_F     A     9_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    10_F     K    10_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    11_F     D    11_F     43   43   43     30   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    12_F     M    12_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    13_F     R    13_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    14_F     A    14_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    15_F     A    15_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    16_F     L    16_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    17_F     A    17_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Q    18_F     Q    18_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    19_F     V    19_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    20_F     K    20_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    21_F     D    21_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    22_F     T    22_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    23_F     L    23_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    24_F     G    24_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    25_F     S    25_F     43   43   43     31   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    26_F     D    26_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    27_F     A    27_F     43   43   43      8   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    28_F     V    28_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     I    29_F     I    29_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    30_F     M    30_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    31_F     S    31_F     43   43   43      8   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    32_F     N    32_F     43   43   43      4   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    33_F     K    33_F     43   43   43     11   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    34_F     K    34_F     43   43   43      4   14   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    35_F     V    35_F     43   43   43      4    7   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    36_F     N    36_F     43   43   43      4   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    37_F     G    37_F     43   43   43      3   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    38_F     G    38_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     I    39_F     I    39_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    40_F     E    40_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     I    41_F     I    41_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    42_F     V    42_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    43_F     A    43_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    44_F     A    44_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    45_F     V    45_F     43   43   43     32   40   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  87.76  (  87.76   87.76   87.76 )

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     32     40     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  65.31  81.63  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76  87.76
GDT RMS_LOCAL    0.34   0.48   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57
GDT RMS_ALL_AT   0.59   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57

# Checking swapping
#   possible swapping detected:  F     7_F      F     7_F
#   possible swapping detected:  E    40_F      E    40_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K     3_F      K     3_F     1.232     0    0.155   1.038     5.318   86.190   65.767
LGA    I     4_F      I     4_F     0.396     0    0.097   0.114     0.682   97.619   96.429
LGA    K     5_F      K     5_F     0.347     0    0.034   0.994     2.277  100.000   85.238
LGA    R     6_F      R     6_F     0.249     0    0.022   1.240     7.748  100.000   67.056
LGA    F     7_F      F     7_F     0.329     0    0.031   0.091     0.518   97.619   99.134
LGA    F     8_F      F     8_F     0.294     0    0.030   1.247     6.849  100.000   65.195
LGA    A     9_F      A     9_F     0.366     0    0.065   0.085     0.592   97.619   98.095
LGA    K    10_F      K    10_F     0.662     0    0.030   1.098     3.900   95.238   82.434
LGA    D    11_F      D    11_F     0.489     0    0.116   1.187     3.680  100.000   85.952
LGA    M    12_F      M    12_F     0.316     0    0.012   1.155     3.452  100.000   86.964
LGA    R    13_F      R    13_F     0.479     0    0.054   1.589     7.823  100.000   65.455
LGA    A    14_F      A    14_F     0.298     0    0.013   0.017     0.455  100.000  100.000
LGA    A    15_F      A    15_F     0.273     0    0.058   0.064     0.487  100.000  100.000
LGA    L    16_F      L    16_F     0.291     0    0.028   1.099     2.548  100.000   89.048
LGA    A    17_F      A    17_F     0.391     0    0.067   0.075     0.400  100.000  100.000
LGA    Q    18_F      Q    18_F     0.427     0    0.028   0.118     1.021  100.000   93.704
LGA    V    19_F      V    19_F     0.392     0    0.013   0.099     0.421  100.000  100.000
LGA    K    20_F      K    20_F     0.199     0    0.031   0.982     3.883  100.000   85.714
LGA    D    21_F      D    21_F     0.082     0    0.025   0.862     3.086  100.000   85.952
LGA    T    22_F      T    22_F     0.308     0    0.181   1.047     2.162   95.357   87.279
LGA    L    23_F      L    23_F     0.285     0    0.189   1.066     2.460   97.619   91.012
LGA    G    24_F      G    24_F     0.419     0    0.057   0.057     0.596   97.619   97.619
LGA    S    25_F      S    25_F     0.436     0    0.063   0.189     0.779  100.000   96.825
LGA    D    26_F      D    26_F     0.299     0    0.485   0.835     3.923   93.214   75.893
LGA    A    27_F      A    27_F     0.965     0    0.222   0.288     1.878   81.548   83.333
LGA    V    28_F      V    28_F     0.536     0    0.045   0.079     1.016   97.619   93.265
LGA    I    29_F      I    29_F     0.348     0    0.028   0.459     1.823  100.000   94.226
LGA    M    30_F      M    30_F     0.424     0    0.057   0.122     1.263   97.619   92.917
LGA    S    31_F      S    31_F     0.608     0    0.023   0.558     2.656   92.857   85.000
LGA    N    32_F      N    32_F     0.989     0    0.434   1.251     4.003   79.881   71.131
LGA    K    33_F      K    33_F     0.769     0    0.143   1.067     4.445   88.214   76.190
LGA    K    34_F      K    34_F     1.120     0    0.066   0.746     3.003   83.690   74.339
LGA    V    35_F      V    35_F     1.257     0    0.058   1.247     3.553   85.952   76.190
LGA    N    36_F      N    36_F     0.886     0    0.141   1.128     5.708   85.952   64.405
LGA    G    37_F      G    37_F     0.949     0    0.237   0.237     0.949   92.857   92.857
LGA    G    38_F      G    38_F     0.256     0    0.048   0.048     0.635   95.238   95.238
LGA    I    39_F      I    39_F     0.503     0    0.095   1.302     3.189   92.857   79.464
LGA    E    40_F      E    40_F     0.441     0    0.068   0.283     0.968   95.238   94.709
LGA    I    41_F      I    41_F     0.580     0    0.042   1.250     3.166   97.619   84.583
LGA    V    42_F      V    42_F     0.157     0    0.040   1.118     2.533  100.000   87.483
LGA    A    43_F      A    43_F     0.236     0    0.052   0.060     0.319  100.000  100.000
LGA    A    44_F      A    44_F     0.148     0    0.029   0.026     0.217  100.000  100.000
LGA    V    45_F      V    45_F     0.468     0    0.160   0.877     2.724   95.238   84.762

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     321    321  100.00                49
SUMMARY(RMSD_GDC):     0.566          0.634                  1.756           84.091   76.140

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   43   49    4.0     43    0.57    86.224    87.272     6.460

LGA_LOCAL      RMSD:   0.566  Number of atoms:   43  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.566  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   0.566  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.737029 * X  +  -0.413042 * Y  +   0.534963 * Z  +  29.169525
  Y_new =   0.488101 * X  +   0.872786 * Y  +   0.001406 * Z  + -109.408485
  Z_new =  -0.467489 * X  +   0.260080 * Y  +   0.844875 * Z  + -34.663807 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.584942  0.486448  0.298627   [DEG:   33.5147   27.8714   17.1100 ]
ZXZ:  1.573425  0.564466 -1.063104   [DEG:   90.1506   32.3415  -60.9114 ]
 
# END of job
