
#######################################################
#                                                     #
#                        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   39 (  329),  selected   39 , name one
# Molecule2: number of CA atoms   39 (  326),  selected   39 , 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:    39       1_A - 39_A        0.62     0.62
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.62     0.62
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.62     0.62
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   39
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     39   39   39      6   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     2_A     K     2_A     39   39   39     17   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     3_A     L     3_A     39   39   39     17   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     W     4_A     W     4_A     39   39   39     17   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     5_A     I     5_A     39   39   39     14   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     6_A     L     6_A     39   39   39     17   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q     7_A     Q     7_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     8_A     K     8_A     39   39   39     21   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     9_A     I     9_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    10_A     Y    10_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    11_A     E    11_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    12_A     I    12_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    13_A     M    13_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    14_A     V    14_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    15_A     R    15_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    16_A     L    16_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    17_A     D    17_A     39   39   39     17   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    18_A     E    18_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    19_A     E    19_A     39   39   39     20   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    20_A     G    20_A     39   39   39      8   29   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     H    21_A     H    21_A     39   39   39     20   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    22_A     G    22_A     39   39   39     15   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    23_A     E    23_A     39   39   39     15   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    24_A     A    24_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    25_A     S    25_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    26_A     L    26_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    27_A     M    27_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    28_A     V    28_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    29_A     S    29_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    30_A     D    30_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    31_A     L    31_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    32_A     I    32_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    33_A     Y    33_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    34_A     E    34_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F    35_A     F    35_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    36_A     M    36_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    37_A     K    37_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    38_A     R    38_A     39   39   39     11   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    39_A     D    39_A     39   39   39      6   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  100.00  100.00 )

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     23     38     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  58.97  97.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.59   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62
GDT RMS_ALL_AT   0.74   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    11_A      E    11_A
#   possible swapping detected:  Y    33_A      Y    33_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.943     0    0.446   1.167     6.740   84.048   57.798
LGA    K     2_A      K     2_A     0.734     0    0.053   0.216     1.535   90.476   88.519
LGA    L     3_A      L     3_A     0.605     0    0.068   1.417     3.489   90.476   78.333
LGA    W     4_A      W     4_A     0.573     0    0.023   0.058     0.774   90.476   90.476
LGA    I     5_A      I     5_A     0.890     0    0.088   1.342     4.685   92.857   77.738
LGA    L     6_A      L     6_A     0.545     0    0.031   1.390     2.980   95.238   82.321
LGA    Q     7_A      Q     7_A     0.174     0    0.019   1.421     5.320  100.000   73.757
LGA    K     8_A      K     8_A     0.328     0    0.034   0.193     0.900  100.000   97.884
LGA    I     9_A      I     9_A     0.193     0    0.031   0.646     2.132  100.000   95.595
LGA    Y    10_A      Y    10_A     0.356     0    0.031   0.072     1.270   97.619   92.897
LGA    E    11_A      E    11_A     0.475     0    0.044   0.799     3.050  100.000   79.101
LGA    I    12_A      I    12_A     0.279     0    0.055   0.795     1.964   97.619   88.631
LGA    M    13_A      M    13_A     0.455     0    0.008   0.117     0.948   95.238   92.857
LGA    V    14_A      V    14_A     0.647     0    0.021   0.027     0.902   90.476   90.476
LGA    R    15_A      R    15_A     0.476     0    0.010   1.205     5.458   97.619   72.554
LGA    L    16_A      L    16_A     0.347     0    0.008   0.058     0.576   97.619   98.810
LGA    D    17_A      D    17_A     0.735     0    0.018   0.900     2.948   90.476   77.798
LGA    E    18_A      E    18_A     0.539     0    0.034   0.160     2.534   97.619   83.228
LGA    E    19_A      E    19_A     0.611     0    0.097   0.158     2.023   90.595   81.746
LGA    G    20_A      G    20_A     1.216     0    0.053   0.053     1.758   81.548   81.548
LGA    H    21_A      H    21_A     0.478     0    0.025   0.203     0.722   95.238   94.286
LGA    G    22_A      G    22_A     0.945     0    0.083   0.083     0.945   90.476   90.476
LGA    E    23_A      E    23_A     0.888     0    0.037   0.648     1.590   90.476   86.508
LGA    A    24_A      A    24_A     0.362     0    0.042   0.040     0.432  100.000  100.000
LGA    S    25_A      S    25_A     0.182     0    0.021   0.071     0.650  100.000   98.413
LGA    L    26_A      L    26_A     0.533     0    0.028   0.040     0.917   92.857   91.667
LGA    M    27_A      M    27_A     0.602     0    0.022   0.775     1.920   90.476   86.012
LGA    V    28_A      V    28_A     0.380     0    0.043   0.102     0.458  100.000  100.000
LGA    S    29_A      S    29_A     0.436     0    0.015   0.035     0.608  100.000   98.413
LGA    D    30_A      D    30_A     0.428     0    0.027   0.101     0.673   97.619   97.619
LGA    L    31_A      L    31_A     0.452     0    0.009   0.072     0.579   95.238   96.429
LGA    I    32_A      I    32_A     0.561     0    0.031   0.083     0.681   90.476   94.048
LGA    Y    33_A      Y    33_A     0.671     0    0.051   1.405    10.100   92.857   51.667
LGA    E    34_A      E    34_A     0.685     0    0.026   0.228     2.061   90.476   82.698
LGA    F    35_A      F    35_A     0.760     0    0.012   0.954     4.322   90.476   73.636
LGA    M    36_A      M    36_A     0.680     0    0.102   0.163     2.253   92.857   85.119
LGA    K    37_A      K    37_A     0.462     0    0.053   1.044     4.357   95.238   81.005
LGA    R    38_A      R    38_A     0.714     0    0.135   1.257     4.589   88.214   78.831
LGA    D    39_A      D    39_A     0.960     3    0.609   0.571     2.078   84.048   53.333

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       39     156    156  100.00     326    326  100.00                39
SUMMARY(RMSD_GDC):     0.617          0.638                  1.691           93.770   85.185

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.62    99.359    99.798     5.441

LGA_LOCAL      RMSD:   0.617  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.617  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.617  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.658802 * X  +  -0.527003 * Y  +  -0.536887 * Z  + -17.828150
  Y_new =  -0.713354 * X  +   0.210910 * Y  +   0.668314 * Z  +   4.805819
  Z_new =  -0.238969 * X  +   0.823277 * Y  +  -0.514888 * Z  + -18.985540 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.316459  0.241304  2.129692   [DEG: -132.7233   13.8257  122.0224 ]
ZXZ: -2.464815  2.111673 -0.282502   [DEG: -141.2235  120.9899  -16.1862 ]
 
# END of job
