
#######################################################
#                                                     #
#                        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   37 (  320),  selected   37 , name one
# Molecule2: number of CA atoms   79 (  632),  selected   37 , 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:    23      32_A - 54_A        4.62    20.37
  LCS_AVERAGE:     27.78

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      35_A - 50_A        1.78    22.72
  LCS_AVERAGE:     16.87

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      36_A - 49_A        0.61    22.70
  LCS_AVERAGE:     12.76

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   37
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     V    32_A     V    32_A      4    6   23      3    4    5    5    6    6    7    8    9   13   16   19   19   21   22   23   23   23   23   24 
LCS_GDT     W    33_A     W    33_A      4    6   23      3    4    5    5    6    6   11   14   16   18   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     L    34_A     L    34_A      4    6   23      3    4    4    4    6    6   12   15   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     D    35_A     D    35_A      4   16   23      3    4    5    6   11   14   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     K    36_A     K    36_A     14   16   23      9   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     G    37_A     G    37_A     14   16   23      9   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     E    38_A     E    38_A     14   16   23      9   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     L    39_A     L    39_A     14   16   23      9   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     E    40_A     E    40_A     14   16   23      9   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     K    41_A     K    41_A     14   16   23      9   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     L    42_A     L    42_A     14   16   23      9   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     L    43_A     L    43_A     14   16   23      9   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     A    44_A     A    44_A     14   16   23      9   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     E    45_A     E    45_A     14   16   23      9   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     A    46_A     A    46_A     14   16   23      9   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     E    47_A     E    47_A     14   16   23      8   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     E    48_A     E    48_A     14   16   23      6   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     V    49_A     V    49_A     14   16   23      8   14   14   14   14   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     E    50_A     E    50_A      4   16   23      3    4    4    4   11   15   15   16   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     R    51_A     R    51_A      4    5   23      3    4    4    4    7   10   13   14   17   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     R    52_A     R    52_A      4   14   23      3    4    4    6    7   10   13   14   16   19   20   21   21   21   22   23   23   23   23   24 
LCS_GDT     Y    53_A     Y    53_A     11   14   23      6   11   11   11   12   12   13   14   16   17   19   21   21   21   22   23   23   23   23   24 
LCS_GDT     E    54_A     E    54_A     11   14   23      6   11   11   11   12   12   13   14   15   17   18   19   19   21   22   23   23   23   23   24 
LCS_GDT     E    55_A     E    55_A     11   14   21      6   11   11   11   12   12   13   14   15   17   17   17   19   20   21   22   22   23   23   24 
LCS_GDT     E    56_A     E    56_A     11   14   21      6   11   11   11   12   12   13   14   15   17   17   17   19   20   21   22   22   22   23   24 
LCS_GDT     L    57_A     L    57_A     11   14   21      7   11   11   11   12   12   13   14   15   17   17   17   19   20   21   22   22   22   22   23 
LCS_GDT     E    58_A     E    58_A     11   14   21      7   11   11   11   12   12   13   14   15   17   17   17   19   20   21   22   22   22   22   23 
LCS_GDT     G    59_A     G    59_A     11   14   21      7   11   11   11   12   12   13   14   15   17   17   17   19   20   21   22   22   22   22   23 
LCS_GDT     F    60_A     F    60_A     11   14   21      7   11   11   11   12   12   13   14   15   17   17   17   19   20   21   22   22   22   22   23 
LCS_GDT     Y    61_A     Y    61_A     11   14   21      7   11   11   11   12   12   13   14   15   17   17   17   19   20   21   22   22   22   22   23 
LCS_GDT     R    62_A     R    62_A     11   14   21      7   11   11   11   12   12   13   14   15   17   17   17   19   20   21   22   22   22   22   23 
LCS_GDT     K    63_A     K    63_A     11   14   21      7   11   11   11   12   12   13   14   15   17   17   17   19   20   21   22   22   22   22   23 
LCS_GDT     E    64_A     E    64_A      8   14   21      3    5    5    9   12   12   13   14   15   17   17   17   19   20   21   22   22   22   22   23 
LCS_GDT     G    65_A     G    65_A      5   14   21      3    5    5    6    6    9   12   14   14   17   17   17   19   20   21   22   22   22   22   23 
LCS_GDT     K    66_A     K    66_A      5    6   21      3    5    5    6    6    6    6    9   13   15   17   17   19   20   21   22   22   22   22   23 
LCS_GDT     P    67_A     P    67_A      5    6   21      3    5    5    6    6    6    6    6    6    6   12   15   17   18   21   22   22   22   22   23 
LCS_GDT     Y    68_A     Y    68_A      5    6   10      0    3    5    6    6    6    6    6    6    6    7    7    9   10   10   10   10   18   21   22 
LCS_AVERAGE  LCS_A:  19.14  (  12.76   16.87   27.78 )

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      9     14     14     14     14     15     15     16     17     19     20     21     21     21     22     23     23     23     23     24 
GDT PERCENT_AT  11.39  17.72  17.72  17.72  17.72  18.99  18.99  20.25  21.52  24.05  25.32  26.58  26.58  26.58  27.85  29.11  29.11  29.11  29.11  30.38
GDT RMS_LOCAL    0.25   0.61   0.61   0.61   0.61   1.11   1.11   1.78   2.51   3.25   3.56   3.77   3.77   3.77   4.16   4.62   4.62   4.62   4.62   5.19
GDT RMS_ALL_AT  23.01  22.70  22.70  22.70  22.70  22.79  22.79  22.72  22.60  21.84  21.81  21.38  21.38  21.38  21.05  20.37  20.37  20.37  20.37  19.84

# Checking swapping
#   possible swapping detected:  D    35_A      D    35_A
#   possible swapping detected:  E    38_A      E    38_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    48_A      E    48_A
#   possible swapping detected:  E    58_A      E    58_A
#   possible swapping detected:  F    60_A      F    60_A
#   possible swapping detected:  Y    61_A      Y    61_A
#   possible swapping detected:  E    64_A      E    64_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    V    32_A      V    32_A    17.708     0    0.171   0.198    19.492    0.000    0.000
LGA    W    33_A      W    33_A    13.569     0    0.091   1.125    15.148    0.000    0.000
LGA    L    34_A      L    34_A     8.807     0    0.079   0.972    10.432    7.500    5.238
LGA    D    35_A      D    35_A     4.939     0    0.150   1.104     8.875   37.262   24.583
LGA    K    36_A      K    36_A     1.901     0    0.618   1.126    11.086   79.405   43.069
LGA    G    37_A      G    37_A     1.752     0    0.059   0.059     1.878   77.143   77.143
LGA    E    38_A      E    38_A     1.360     0    0.051   1.101     5.742   81.548   58.889
LGA    L    39_A      L    39_A     1.149     0    0.039   1.080     2.573   83.690   77.381
LGA    E    40_A      E    40_A     1.078     0    0.036   0.792     3.119   85.952   71.852
LGA    K    41_A      K    41_A     0.291     0    0.046   0.838     5.026   95.238   74.233
LGA    L    42_A      L    42_A     0.157     0    0.026   0.959     3.939  100.000   87.202
LGA    L    43_A      L    43_A     0.608     0    0.048   0.160     0.918   92.857   91.667
LGA    A    44_A      A    44_A     1.159     0    0.050   0.050     1.400   83.690   83.238
LGA    E    45_A      E    45_A     1.209     0    0.040   1.063     3.542   81.429   67.513
LGA    A    46_A      A    46_A     0.796     0    0.021   0.031     0.981   92.857   92.381
LGA    E    47_A      E    47_A     0.464     0    0.020   0.631     2.957   92.857   77.566
LGA    E    48_A      E    48_A     0.896     0    0.022   0.774     2.569   88.214   77.196
LGA    V    49_A      V    49_A     0.797     0    0.586   1.437     3.646   84.048   77.551
LGA    E    50_A      E    50_A     3.145     0    0.045   1.372     9.062   50.119   27.407
LGA    R    51_A      R    51_A     7.849     0    0.635   1.542    13.541   10.119    3.680
LGA    R    52_A      R    52_A     9.836     0    0.632   0.714    17.075    0.952    0.346
LGA    Y    53_A      Y    53_A     9.508     0    0.467   1.485    13.677    0.833    1.667
LGA    E    54_A      E    54_A    14.416     0    0.058   1.215    18.862    0.000    0.000
LGA    E    55_A      E    55_A    19.423     0    0.041   1.007    23.864    0.000    0.000
LGA    E    56_A      E    56_A    19.210     0    0.046   1.044    22.869    0.000    0.000
LGA    L    57_A      L    57_A    20.758     0    0.048   1.303    25.098    0.000    0.000
LGA    E    58_A      E    58_A    25.893     0    0.037   0.696    30.193    0.000    0.000
LGA    G    59_A      G    59_A    29.344     0    0.043   0.043    32.882    0.000    0.000
LGA    F    60_A      F    60_A    30.362     0    0.049   1.546    34.411    0.000    0.000
LGA    Y    61_A      Y    61_A    32.833     0    0.041   0.341    37.371    0.000    0.000
LGA    R    62_A      R    62_A    37.200     0    0.036   1.402    41.641    0.000    0.000
LGA    K    63_A      K    63_A    40.694     2    0.617   0.895    43.089    0.000    0.000
LGA    E    64_A      E    64_A    44.201     0    0.225   0.659    46.219    0.000    0.000
LGA    G    65_A      G    65_A    45.285     0    0.080   0.080    46.660    0.000    0.000
LGA    K    66_A      K    66_A    46.288     3    0.082   0.144    47.313    0.000    0.000
LGA    P    67_A      P    67_A    45.637     0    0.629   0.566    46.350    0.000    0.000
LGA    Y    68_A      Y    68_A    45.059     0    0.383   1.032    45.558    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       37     148    148  100.00     315    315  100.00                79
SUMMARY(RMSD_GDC):    13.730         13.610                 14.189           16.781   14.175

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   37   79    4.0     16    1.78    21.203    20.089     0.850

LGA_LOCAL      RMSD:   1.783  Number of atoms:   16  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  22.715  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:  13.730  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.497328 * X  +   0.600995 * Y  +  -0.625675 * Z  + -54.575077
  Y_new =  -0.820109 * X  +   0.560923 * Y  +  -0.113079 * Z  +   6.336320
  Z_new =   0.282996 * X  +   0.569359 * Y  +   0.771844 * Z  + -24.751024 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.025672 -0.286916  0.635557   [DEG:  -58.7667  -16.4391   36.4148 ]
ZXZ: -1.391995  0.689060  0.461278   [DEG:  -79.7554   39.4802   26.4293 ]
 
# END of job
