
#######################################################
#                                                     #
#                        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        0.72     0.72
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.72     0.72
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.72     0.72
  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      5   25   37   38   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     24   36   37   38   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     26   36   37   38   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     23   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     26   36   37   38   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     16   36   37   38   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      9   36   37   38   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      9   36   37   38   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   36   37   38   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     26   36   37   38   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      9   36   37   38   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      9   36   37   38   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     25   36   37   38   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      9   36   37   38   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      4   14   31   38   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      0    3    3    3   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     26     36     37     38     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  66.67  92.31  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
GDT RMS_LOCAL    0.32   0.48   0.54   0.61   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72
GDT RMS_ALL_AT   0.74   0.73   0.73   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  Y    10_A      Y    10_A
#   possible swapping detected:  D    17_A      D    17_A
#   possible swapping detected:  Y    33_A      Y    33_A
#   possible swapping detected:  E    34_A      E    34_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     1.640     0    0.467   1.306     5.222   77.143   56.905
LGA    K     2_A      K     2_A     0.982     0    0.062   0.881     6.075   88.214   62.169
LGA    L     3_A      L     3_A     0.183     0    0.039   0.091     0.493  100.000  100.000
LGA    W     4_A      W     4_A     0.597     0    0.035   0.046     1.124   95.238   90.544
LGA    I     5_A      I     5_A     0.336     0    0.073   1.338     4.530  100.000   82.560
LGA    L     6_A      L     6_A     0.211     0    0.024   1.413     3.672  100.000   81.310
LGA    Q     7_A      Q     7_A     0.250     0    0.075   0.099     0.675  100.000   96.825
LGA    K     8_A      K     8_A     0.208     0    0.116   1.053     6.973  100.000   71.958
LGA    I     9_A      I     9_A     0.369     0    0.029   0.111     0.772  100.000   96.429
LGA    Y    10_A      Y    10_A     0.364     0    0.019   0.060     1.462  100.000   89.881
LGA    E    11_A      E    11_A     0.216     0    0.014   0.056     1.177  100.000   93.757
LGA    I    12_A      I    12_A     0.401     0    0.081   0.745     2.391   97.619   87.679
LGA    M    13_A      M    13_A     0.411     0    0.029   0.574     1.988  100.000   94.226
LGA    V    14_A      V    14_A     0.190     0    0.044   0.046     0.409  100.000  100.000
LGA    R    15_A      R    15_A     0.127     0    0.021   0.977     2.512  100.000   91.169
LGA    L    16_A      L    16_A     0.069     0    0.014   0.096     0.250  100.000  100.000
LGA    D    17_A      D    17_A     0.343     0    0.072   0.227     1.054  100.000   94.107
LGA    E    18_A      E    18_A     0.173     0    0.030   0.193     1.050  100.000   94.762
LGA    E    19_A      E    19_A     0.308     0    0.069   0.220     0.853   97.619   96.825
LGA    G    20_A      G    20_A     0.669     0    0.089   0.089     1.113   90.595   90.595
LGA    H    21_A      H    21_A     0.145     0    0.076   0.371     1.213  100.000   96.286
LGA    G    22_A      G    22_A     0.277     0    0.041   0.041     0.279  100.000  100.000
LGA    E    23_A      E    23_A     0.578     0    0.048   0.334     3.728   95.238   77.989
LGA    A    24_A      A    24_A     0.593     0    0.015   0.024     0.617   90.476   90.476
LGA    S    25_A      S    25_A     0.165     0    0.086   0.089     0.361  100.000  100.000
LGA    L    26_A      L    26_A     0.406     0    0.056   0.058     0.612   97.619   96.429
LGA    M    27_A      M    27_A     0.326     0    0.038   0.892     2.938  100.000   84.881
LGA    V    28_A      V    28_A     0.303     0    0.060   0.160     0.592   97.619   97.279
LGA    S    29_A      S    29_A     0.725     0    0.026   0.124     1.683   90.476   86.032
LGA    D    30_A      D    30_A     0.776     0    0.033   0.083     1.851   92.857   83.929
LGA    L    31_A      L    31_A     0.744     0    0.021   1.417     4.910   92.857   72.202
LGA    I    32_A      I    32_A     0.982     0    0.031   0.164     1.538   90.476   86.012
LGA    Y    33_A      Y    33_A     0.627     0    0.016   0.122     3.103   95.238   77.937
LGA    E    34_A      E    34_A     0.647     0    0.036   1.050     5.177   92.857   75.397
LGA    F    35_A      F    35_A     0.821     0    0.018   0.621     2.673   90.476   74.286
LGA    M    36_A      M    36_A     0.329     0    0.072   0.122     0.795  100.000   97.619
LGA    K    37_A      K    37_A     0.689     0    0.091   1.005     4.856   90.476   74.550
LGA    R    38_A      R    38_A     1.704     0    0.634   0.965     5.913   69.286   51.255
LGA    D    39_A      D    39_A     2.367     3    0.185   0.260     5.189   51.429   29.643

# 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):     0.718          0.825                  1.687           94.457   85.228

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.72    97.436    98.830     4.769

LGA_LOCAL      RMSD:   0.718  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.718  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.718  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.293606 * X  +   0.116901 * Y  +   0.948752 * Z  + -17.412724
  Y_new =  -0.642833 * X  +   0.710423 * Y  +  -0.286470 * Z  +   3.093931
  Z_new =  -0.707503 * X  +  -0.693998 * Y  +  -0.133436 * Z  +  32.213306 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.999239  0.785959 -1.760750   [DEG: -114.5479   45.0321 -100.8835 ]
ZXZ:  1.277557  1.704632 -2.346559   [DEG:   73.1986   97.6682 -134.4479 ]
 
# END of job
