
#######################################################
#                                                     #
#                        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   38 (  321),  selected   38 , name one
# Molecule2: number of CA atoms   39 (  326),  selected   38 , 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:    38       1_A - 38_A        0.54     0.54
  LCS_AVERAGE:     97.44

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    38       1_A - 38_A        0.54     0.54
  LCS_AVERAGE:     97.44

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    38       1_A - 38_A        0.54     0.54
  LCS_AVERAGE:     97.44

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   38
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     D     1_A     D     1_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     K     2_A     K     2_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     L     3_A     L     3_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     W     4_A     W     4_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     I     5_A     I     5_A     38   38   38     19   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     L     6_A     L     6_A     38   38   38     28   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     Q     7_A     Q     7_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     K     8_A     K     8_A     38   38   38     27   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     I     9_A     I     9_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     Y    10_A     Y    10_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     E    11_A     E    11_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     I    12_A     I    12_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     M    13_A     M    13_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     V    14_A     V    14_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     R    15_A     R    15_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     L    16_A     L    16_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     D    17_A     D    17_A     38   38   38     28   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     E    18_A     E    18_A     38   38   38     19   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     E    19_A     E    19_A     38   38   38     28   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     G    20_A     G    20_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     H    21_A     H    21_A     38   38   38     18   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     G    22_A     G    22_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     E    23_A     E    23_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     A    24_A     A    24_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     S    25_A     S    25_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     L    26_A     L    26_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     M    27_A     M    27_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     V    28_A     V    28_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     S    29_A     S    29_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     D    30_A     D    30_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     L    31_A     L    31_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     I    32_A     I    32_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     Y    33_A     Y    33_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     E    34_A     E    34_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     F    35_A     F    35_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     M    36_A     M    36_A     38   38   38     29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     K    37_A     K    37_A     38   38   38     18   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     R    38_A     R    38_A     38   38   38      3    3   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_AVERAGE  LCS_A:  97.44  (  97.44   97.44   97.44 )

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     29     36     38     38     38     38     38     38     38     38     38     38     38     38     38     38     38     38     38     38 
GDT PERCENT_AT  74.36  92.31  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44
GDT RMS_LOCAL    0.32   0.43   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54
GDT RMS_ALL_AT   0.55   0.56   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.503     0    0.545   1.310     6.494   86.429   62.738
LGA    K     2_A      K     2_A     0.331     0    0.017   0.854     4.910   97.619   74.180
LGA    L     3_A      L     3_A     0.501     0    0.000   0.084     1.011   95.238   92.917
LGA    W     4_A      W     4_A     0.474     0    0.087   1.192     8.395   95.238   51.361
LGA    I     5_A      I     5_A     1.104     0    0.018   1.341     5.074   88.214   72.738
LGA    L     6_A      L     6_A     0.656     0    0.051   0.066     0.791   95.238   92.857
LGA    Q     7_A      Q     7_A     0.229     0    0.000   0.043     0.372  100.000  100.000
LGA    K     8_A      K     8_A     0.639     0    0.046   0.903     6.527   92.857   71.481
LGA    I     9_A      I     9_A     0.463     0    0.039   0.049     1.079   97.619   92.917
LGA    Y    10_A      Y    10_A     0.059     0    0.049   0.096     0.958  100.000   96.825
LGA    E    11_A      E    11_A     0.285     0    0.020   0.116     0.803  100.000   97.884
LGA    I    12_A      I    12_A     0.466     0    0.049   0.783     2.495  100.000   87.679
LGA    M    13_A      M    13_A     0.393     0    0.062   1.008     2.168  100.000   89.762
LGA    V    14_A      V    14_A     0.409     0    0.000   0.000     0.836  100.000   95.918
LGA    R    15_A      R    15_A     0.352     0    0.020   1.111     5.018  100.000   76.364
LGA    L    16_A      L    16_A     0.329     0    0.062   0.111     0.648  100.000   98.810
LGA    D    17_A      D    17_A     0.521     0    0.048   0.952     2.653   97.619   84.464
LGA    E    18_A      E    18_A     0.808     0    0.042   0.262     2.349   92.857   80.899
LGA    E    19_A      E    19_A     0.680     0    0.129   0.182     2.922   92.857   78.307
LGA    G    20_A      G    20_A     0.393     0    0.045   0.045     0.742   95.238   95.238
LGA    H    21_A      H    21_A     0.802     0    0.072   0.270     2.116   92.857   81.762
LGA    G    22_A      G    22_A     0.352     0    0.000   0.000     0.495  100.000  100.000
LGA    E    23_A      E    23_A     0.204     0    0.029   0.643     2.105  100.000   89.947
LGA    A    24_A      A    24_A     0.141     0    0.013   0.014     0.249  100.000  100.000
LGA    S    25_A      S    25_A     0.124     0    0.025   0.056     0.188  100.000  100.000
LGA    L    26_A      L    26_A     0.183     0    0.030   0.044     0.273  100.000  100.000
LGA    M    27_A      M    27_A     0.240     0    0.038   0.131     0.576  100.000   98.810
LGA    V    28_A      V    28_A     0.262     0    0.019   0.073     0.326  100.000  100.000
LGA    S    29_A      S    29_A     0.393     0    0.000   0.000     0.863  100.000   96.825
LGA    D    30_A      D    30_A     0.333     0    0.032   0.080     0.615  100.000   97.619
LGA    L    31_A      L    31_A     0.246     0    0.039   1.416     3.928  100.000   83.155
LGA    I    32_A      I    32_A     0.162     0    0.000   0.061     0.308  100.000  100.000
LGA    Y    33_A      Y    33_A     0.333     0    0.000   0.156     1.726  100.000   90.714
LGA    E    34_A      E    34_A     0.309     0    0.000   0.751     3.617  100.000   84.709
LGA    F    35_A      F    35_A     0.423     0    0.040   0.491     1.416  100.000   91.515
LGA    M    36_A      M    36_A     0.253     0    0.040   0.100     1.129  100.000   94.167
LGA    K    37_A      K    37_A     0.908     0    0.080   0.751     3.333   85.952   80.000
LGA    R    38_A      R    38_A     1.687     0    0.000   1.411     8.049   61.905   46.883

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       38     152    152  100.00     321    321  100.00                39
SUMMARY(RMSD_GDC):     0.539          0.628                  1.830           94.045   85.370

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   39    4.0     38    0.54    96.154    97.031     5.949

LGA_LOCAL      RMSD:   0.539  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.539  Number of assigned atoms:   38 
Std_ASGN_ATOMS RMSD:   0.539  Standard rmsd on all 38 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.278496 * X  +  -0.771368 * Y  +  -0.572217 * Z  + 214.829941
  Y_new =  -0.934444 * X  +  -0.355289 * Y  +   0.024152 * Z  + 250.959793
  Z_new =  -0.221932 * X  +   0.527978 * Y  +  -0.819747 * Z  + 151.239120 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.281145  0.223796  2.569394   [DEG:  -73.4042   12.8226  147.2154 ]
ZXZ: -1.612979  2.531765 -0.397920   [DEG:  -92.4169  145.0595  -22.7991 ]
 
# END of job
