
#######################################################
#                                                     #
#                        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   33 (  261),  selected   30 , name one
# Molecule2: number of CA atoms   43 (  346),  selected   30 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_B - 34_B        1.69     1.69
  LCS_AVERAGE:     69.77

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_B - 34_B        1.69     1.69
  LCS_AVERAGE:     69.77

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       5_B - 32_B        0.97     1.93
  LCS_AVERAGE:     61.55

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   30
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     S     5_B     S     5_B     28   30   30      9   19   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     L     6_B     L     6_B     28   30   30     17   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     E     7_B     E     7_B     28   30   30     17   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     T     8_B     T     8_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     K     9_B     K     9_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     K    10_B     K    10_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     A    11_B     A    11_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     Y    12_B     Y    12_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     A    13_B     A    13_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     A    14_B     A    14_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     R    15_B     R    15_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     T    16_B     T    16_B     28   30   30     17   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     R    17_B     R    17_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     R    18_B     R    18_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     S    19_B     S    19_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     N    20_B     N    20_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     Y    21_B     Y    21_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     A    22_B     A    22_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     A    23_B     A    23_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     S    24_B     S    24_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     L    25_B     L    25_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     R    26_B     R    26_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     L    27_B     L    27_B     28   30   30     18   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     E    28_B     E    28_B     28   30   30      6   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     G    29_B     G    29_B     28   30   30      8   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     F    30_B     F    30_B     28   30   30     19   23   26   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     K    31_B     K    31_B     28   30   30      3    7   14   27   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     V    32_B     V    32_B     28   30   30      3    7   21   25   28   28   28   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     T    33_B     T    33_B      5   30   30      3    4    7    9   13   23   27   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_GDT     F    34_B     F    34_B      5   30   30      3    5    7   10   18   23   27   29   30   30   30   30   30   30   30   30   30   30   30   30 
LCS_AVERAGE  LCS_A:  67.03  (  61.55   69.77   69.77 )

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     19     23     26     27     28     28     28     29     30     30     30     30     30     30     30     30     30     30     30     30 
GDT PERCENT_AT  44.19  53.49  60.47  62.79  65.12  65.12  65.12  67.44  69.77  69.77  69.77  69.77  69.77  69.77  69.77  69.77  69.77  69.77  69.77  69.77
GDT RMS_LOCAL    0.34   0.44   0.62   0.74   0.97   0.97   0.97   1.45   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69
GDT RMS_ALL_AT   2.09   2.14   2.14   2.08   1.93   1.93   1.93   1.73   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  F    34_B      F    34_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     1.907     0    0.025   0.200     3.330   72.976   67.778
LGA    L     6_B      L     6_B     1.662     0    0.027   1.225     4.485   77.143   68.631
LGA    E     7_B      E     7_B     1.167     0    0.076   0.961     5.127   85.952   65.873
LGA    T     8_B      T     8_B     0.255     0    0.052   1.225     2.519  100.000   87.483
LGA    K     9_B      K     9_B     0.450     0    0.024   0.126     1.668  100.000   88.783
LGA    K    10_B      K    10_B     0.627     0    0.019   0.848     3.475   92.857   82.063
LGA    A    11_B      A    11_B     0.816     0    0.042   0.044     0.949   90.476   90.476
LGA    Y    12_B      Y    12_B     0.817     0    0.024   0.055     2.188   90.476   81.667
LGA    A    13_B      A    13_B     0.270     0    0.042   0.041     0.422  100.000  100.000
LGA    A    14_B      A    14_B     0.842     0    0.064   0.066     1.236   85.952   85.048
LGA    R    15_B      R    15_B     1.432     0    0.038   1.218     4.651   79.286   63.506
LGA    T    16_B      T    16_B     1.287     0    0.043   0.062     1.805   85.952   82.789
LGA    R    17_B      R    17_B     0.341     0    0.043   0.983     3.329   97.619   87.792
LGA    R    18_B      R    18_B     0.936     0    0.027   0.673     2.519   85.952   74.069
LGA    S    19_B      S    19_B     1.348     0    0.053   0.695     1.759   81.429   78.571
LGA    N    20_B      N    20_B     0.898     0    0.054   0.428     1.567   88.214   87.143
LGA    Y    21_B      Y    21_B     0.385     0    0.051   0.155     0.894  100.000   93.651
LGA    A    22_B      A    22_B     0.712     0    0.023   0.026     0.977   90.476   90.476
LGA    A    23_B      A    23_B     0.771     0    0.025   0.026     0.775   90.476   90.476
LGA    S    24_B      S    24_B     0.524     0    0.093   0.128     0.670   90.476   93.651
LGA    L    25_B      L    25_B     0.615     0    0.024   0.042     0.716   90.476   90.476
LGA    R    26_B      R    26_B     0.737     0    0.035   0.950     4.697   90.476   70.087
LGA    L    27_B      L    27_B     0.886     0    0.011   0.208     2.159   90.476   81.726
LGA    E    28_B      E    28_B     1.131     0    0.076   1.064     3.719   85.952   79.259
LGA    G    29_B      G    29_B     0.983     0    0.068   0.068     0.983   90.476   90.476
LGA    F    30_B      F    30_B     0.607     0    0.080   0.095     3.000   88.214   76.580
LGA    K    31_B      K    31_B     1.890     0    0.160   0.859     9.356   83.929   48.942
LGA    V    32_B      V    32_B     2.303     0    0.131   1.287     3.730   57.738   58.844
LGA    T    33_B      T    33_B     5.326     0    0.113   0.141     8.174   32.976   22.857
LGA    F    34_B      F    34_B     5.408     0    0.618   0.484     6.114   23.810   21.905

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       30     120    120  100.00     242    242  100.00                43
SUMMARY(RMSD_GDC):     1.690          1.605                  2.389           58.610   53.513

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   43    4.0     29    1.45    63.372    66.320     1.871

LGA_LOCAL      RMSD:   1.450  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.734  Number of assigned atoms:   30 
Std_ASGN_ATOMS RMSD:   1.690  Standard rmsd on all 30 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.490065 * X  +  -0.718717 * Y  +  -0.493236 * Z  +  55.907566
  Y_new =  -0.820486 * X  +  -0.571402 * Y  +   0.017405 * Z  + -70.192146
  Z_new =  -0.294345 * X  +   0.396163 * Y  +  -0.869722 * Z  + -11.280425 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.032374  0.298770  2.714170   [DEG:  -59.1507   17.1183  155.5105 ]
ZXZ: -1.606069  2.625434 -0.638999   [DEG:  -92.0210  150.4263  -36.6119 ]
 
# END of job
