
#######################################################
#                                                     #
#                        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        0.61     0.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.61     0.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.61     0.61
  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     11   37   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     18   37   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     20   37   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     24   37   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     16   37   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     24   37   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     24   37   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   37   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     24   37   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     17   37   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     16   37   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     21   37   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     17   37   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     16   36   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     17   37   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     24   37   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     16   37   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     17   37   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     19   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     24   37   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     10   34   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     24   37   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     24     37     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  61.54  94.87 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.26   0.57   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61
GDT RMS_ALL_AT   0.70   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    11_A      E    11_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    19_A      E    19_A
#   possible swapping detected:  E    23_A      E    23_A
#   possible swapping detected:  Y    33_A      Y    33_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     1.017     0    0.480   0.986     3.308   79.524   69.345
LGA    K     2_A      K     2_A     0.882     0    0.037   0.239     1.590   90.476   87.513
LGA    L     3_A      L     3_A     0.714     0    0.049   1.382     3.479   92.857   78.333
LGA    W     4_A      W     4_A     0.498     0    0.022   0.132     1.612   95.238   88.027
LGA    I     5_A      I     5_A     0.918     0    0.075   1.391     5.034   92.857   76.131
LGA    L     6_A      L     6_A     0.441     0    0.016   0.110     0.645   97.619   94.048
LGA    Q     7_A      Q     7_A     0.185     0    0.044   1.360     4.734  100.000   75.926
LGA    K     8_A      K     8_A     0.538     0    0.036   0.155     0.977   97.619   93.651
LGA    I     9_A      I     9_A     0.260     0    0.015   0.086     1.163  100.000   95.298
LGA    Y    10_A      Y    10_A     0.708     0    0.015   1.331     5.827   92.857   70.913
LGA    E    11_A      E    11_A     0.964     0    0.026   0.130     2.171   88.214   80.688
LGA    I    12_A      I    12_A     0.460     0    0.047   0.808     2.217   95.238   86.429
LGA    M    13_A      M    13_A     0.580     0    0.019   0.753     2.743   92.857   87.500
LGA    V    14_A      V    14_A     1.073     0    0.038   0.054     1.646   88.214   82.857
LGA    R    15_A      R    15_A     0.877     0    0.022   0.683     2.226   90.476   81.688
LGA    L    16_A      L    16_A     0.289     0    0.029   0.056     0.545  100.000   98.810
LGA    D    17_A      D    17_A     0.755     0    0.035   0.260     1.083   92.857   90.536
LGA    E    18_A      E    18_A     0.957     0    0.028   0.135     2.669   90.476   78.095
LGA    E    19_A      E    19_A     0.663     0    0.117   0.191     2.052   90.476   81.693
LGA    G    20_A      G    20_A     0.676     0    0.020   0.020     1.126   90.595   90.595
LGA    H    21_A      H    21_A     0.511     0    0.069   0.235     1.100   90.476   90.524
LGA    G    22_A      G    22_A     0.622     0    0.034   0.034     0.622   92.857   92.857
LGA    E    23_A      E    23_A     0.518     0    0.018   0.217     1.672   95.238   89.630
LGA    A    24_A      A    24_A     0.317     0    0.024   0.035     0.404  100.000  100.000
LGA    S    25_A      S    25_A     0.398     0    0.017   0.021     0.472  100.000  100.000
LGA    L    26_A      L    26_A     0.336     0    0.060   0.059     0.618  100.000   97.619
LGA    M    27_A      M    27_A     0.190     0    0.018   0.176     0.616  100.000   98.810
LGA    V    28_A      V    28_A     0.252     0    0.021   0.085     0.519  100.000   98.639
LGA    S    29_A      S    29_A     0.326     0    0.006   0.718     1.977  100.000   95.476
LGA    D    30_A      D    30_A     0.261     0    0.026   0.054     0.634  100.000   97.619
LGA    L    31_A      L    31_A     0.153     0    0.017   0.179     1.060  100.000   95.298
LGA    I    32_A      I    32_A     0.125     0    0.023   0.087     0.483  100.000  100.000
LGA    Y    33_A      Y    33_A     0.233     0    0.011   0.229     1.707  100.000   91.508
LGA    E    34_A      E    34_A     0.338     0    0.015   1.137     4.370   97.619   81.111
LGA    F    35_A      F    35_A     0.317     0    0.024   0.508     1.283  100.000   94.892
LGA    M    36_A      M    36_A     0.068     0    0.098   0.701     2.172   97.619   90.893
LGA    K    37_A      K    37_A     0.697     0    0.035   0.992     4.898   92.857   77.566
LGA    R    38_A      R    38_A     1.086     0    0.161   1.251     5.698   81.548   67.056
LGA    D    39_A      D    39_A     0.726     3    0.628   0.600     1.191   88.214   56.607

# 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):     0.608          0.627                  1.354           94.741   87.287

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.61    98.718    99.595     5.506

LGA_LOCAL      RMSD:   0.608  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.608  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.608  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.696744 * X  +  -0.348681 * Y  +   0.626873 * Z  + -36.500889
  Y_new =  -0.127822 * X  +  -0.799572 * Y  +  -0.586810 * Z  +   6.740739
  Z_new =   0.705840 * X  +  -0.488984 * Y  +   0.512528 * Z  + -12.180672 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.960154 -0.783608 -0.761895   [DEG: -169.6043  -44.8974  -43.6533 ]
ZXZ:  0.818395  1.032670  2.176653   [DEG:   46.8906   59.1676  124.7130 ]
 
# END of job
