
#######################################################
#                                                     #
#                        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        0.69     0.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.69     0.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.69     0.69
  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      7   37   38   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     18   37   38   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     18   37   38   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     18   37   38   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     17   37   38   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     18   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     21   37   38   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     18   37   38   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     22   37   38   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     19   37   38   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   38   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   37   38   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   37   38   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   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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     22   37   38   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      6   37   38   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     18   37   38   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     22   37   38   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     22   37   38   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     11   23   38   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     22     37     38     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  56.41  94.87  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
GDT RMS_LOCAL    0.35   0.56   0.59   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69
GDT RMS_ALL_AT   0.76   0.69   0.70   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    11_A      E    11_A
#   possible swapping detected:  F    35_A      F    35_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     1.011     0    0.447   1.168     6.771   83.810   57.679
LGA    K     2_A      K     2_A     0.650     0    0.056   0.242     1.497   92.857   92.646
LGA    L     3_A      L     3_A     0.481     0    0.066   1.415     3.443   92.857   79.524
LGA    W     4_A      W     4_A     0.504     0    0.021   0.072     0.741   92.857   91.156
LGA    I     5_A      I     5_A     0.808     0    0.084   1.336     4.621   92.857   77.738
LGA    L     6_A      L     6_A     0.431     0    0.030   1.392     2.999   97.619   83.512
LGA    Q     7_A      Q     7_A     0.117     0    0.014   1.411     5.298  100.000   74.603
LGA    K     8_A      K     8_A     0.250     0    0.033   0.554     2.097  100.000   90.053
LGA    I     9_A      I     9_A     0.188     0    0.020   0.085     0.960  100.000   97.619
LGA    Y    10_A      Y    10_A     0.385     0    0.028   0.068     1.231   97.619   92.897
LGA    E    11_A      E    11_A     0.482     0    0.048   0.844     3.412  100.000   79.101
LGA    I    12_A      I    12_A     0.280     0    0.053   0.789     1.804   97.619   88.631
LGA    M    13_A      M    13_A     0.469     0    0.009   0.118     0.891   95.238   94.048
LGA    V    14_A      V    14_A     0.603     0    0.020   0.026     0.811   90.476   90.476
LGA    R    15_A      R    15_A     0.435     0    0.012   1.213     5.502   97.619   72.987
LGA    L    16_A      L    16_A     0.459     0    0.010   0.056     0.699   95.238   96.429
LGA    D    17_A      D    17_A     0.792     0    0.018   0.902     2.997   90.476   77.798
LGA    E    18_A      E    18_A     0.456     0    0.033   0.161     2.333  100.000   86.931
LGA    E    19_A      E    19_A     0.690     0    0.098   0.158     1.883   90.595   82.646
LGA    G    20_A      G    20_A     1.336     0    0.054   0.054     1.840   81.548   81.548
LGA    H    21_A      H    21_A     0.527     0    0.026   0.203     0.729   92.857   91.429
LGA    G    22_A      G    22_A     0.955     0    0.084   0.084     0.955   90.476   90.476
LGA    E    23_A      E    23_A     0.911     0    0.036   0.648     1.645   90.476   87.566
LGA    A    24_A      A    24_A     0.402     0    0.041   0.041     0.440  100.000  100.000
LGA    S    25_A      S    25_A     0.166     0    0.020   0.074     0.641  100.000   98.413
LGA    L    26_A      L    26_A     0.578     0    0.031   0.040     0.991   92.857   91.667
LGA    M    27_A      M    27_A     0.691     0    0.024   0.774     1.995   90.476   86.012
LGA    V    28_A      V    28_A     0.489     0    0.039   0.105     0.564   95.238   94.558
LGA    S    29_A      S    29_A     0.541     0    0.019   0.037     0.698   92.857   92.063
LGA    D    30_A      D    30_A     0.599     0    0.012   0.111     0.695   90.476   90.476
LGA    L    31_A      L    31_A     0.678     0    0.018   1.405     3.796   90.476   79.167
LGA    I    32_A      I    32_A     0.544     0    0.033   0.116     0.636   90.476   94.048
LGA    Y    33_A      Y    33_A     0.509     0    0.013   0.186     0.997   92.857   93.651
LGA    E    34_A      E    34_A     0.740     0    0.025   0.579     3.123   92.857   82.116
LGA    F    35_A      F    35_A     0.710     0    0.009   1.056     4.032   90.476   75.152
LGA    M    36_A      M    36_A     0.474     0    0.059   0.730     1.990  100.000   90.833
LGA    K    37_A      K    37_A     0.274     0    0.092   0.536     1.830   92.976   91.799
LGA    R    38_A      R    38_A     0.431     0    0.675   1.251     5.962   86.905   68.398
LGA    D    39_A      D    39_A     2.108     3    0.343   0.473     3.440   63.095   39.643

# 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):     0.686          0.752                  1.508           92.952   85.269

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.69    98.718    99.404     4.965

LGA_LOCAL      RMSD:   0.686  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.686  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.686  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.627381 * X  +  -0.530754 * Y  +  -0.569818 * Z  + -17.969067
  Y_new =  -0.735052 * X  +   0.162058 * Y  +   0.658358 * Z  +   4.917492
  Z_new =  -0.257083 * X  +   0.831888 * Y  +  -0.491804 * Z  + -18.978884 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.277330  0.260002  2.104713   [DEG: -130.4814   14.8970  120.5912 ]
ZXZ: -2.428160  2.084957 -0.299725   [DEG: -139.1233  119.4592  -17.1730 ]
 
# END of job
