
#######################################################
#                                                     #
#                        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   34 (  238),  selected   34 , name one
# Molecule2: number of CA atoms   34 (  235),  selected   34 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       2_A - 34_A        4.43     5.07
  LCS_AVERAGE:     95.07

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_A - 34_A        1.49     5.78
  LCS_AVERAGE:     80.28

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       6_A - 34_A        0.66     6.10
  LCS_AVERAGE:     74.48

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   34
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     1_B     S     1_A      4    7   10      4    5    5    6    6    6    7    7    7    8    8   10   11   11   12   13   16   19   20   22 
LCS_GDT     G     2_B     G     2_A      4    7   33      4    5    5    6    6    6    7    7    8    8    9   10   14   16   17   18   23   24   30   31 
LCS_GDT     P     3_B     P     3_A      4    7   33      4    5    5    6    6    6    8    9    9    9   12   14   16   17   19   22   30   30   32   32 
LCS_GDT     N     4_B     N     4_A      4    7   33      4    5    5    6    6    9   14   18   23   25   27   30   31   31   31   31   31   31   32   32 
LCS_GDT     G     5_B     G     5_A      4   30   33      3    3    4    8   18   23   28   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     G     6_B     G     6_A     29   30   33     11   22   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     V     7_B     V     7_A     29   30   33      5   25   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     C     8_B     C     8_A     29   30   33      7   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     P     9_B     P     9_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     V    10_B     V    10_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     L    11_B     L    11_A     29   30   33     14   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     I    12_B     I    12_A     29   30   33      7   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     Y    13_B     Y    13_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     L    14_B     L    14_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     C    15_B     C    15_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     R    16_B     R    16_A     29   30   33     18   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     R    17_B     R    17_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     D    18_B     D    18_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     S    19_B     S    19_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     D    20_B     D    20_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     C    21_B     C    21_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     P    22_B     P    22_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     G    23_B     G    23_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     E    24_B     E    24_A     29   30   33     18   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     C    25_B     C    25_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     I    26_B     I    26_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     C    27_B     C    27_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     L    28_B     L    28_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     G    29_B     G    29_A     29   30   33     15   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     N    30_B     N    30_A     29   30   33      5   15   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     G    31_B     G    31_A     29   30   33     12   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     Y    32_B     Y    32_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     C    33_B     C    33_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_GDT     G    34_B     G    34_A     29   30   33     19   26   28   29   29   29   29   30   30   30   30   30   31   31   31   31   31   31   32   32 
LCS_AVERAGE  LCS_A:  83.28  (  74.48   80.28   95.07 )

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     26     28     29     29     29     29     30     30     30     30     30     31     31     31     31     31     31     32     32 
GDT PERCENT_AT  55.88  76.47  82.35  85.29  85.29  85.29  85.29  88.24  88.24  88.24  88.24  88.24  91.18  91.18  91.18  91.18  91.18  91.18  94.12  94.12
GDT RMS_LOCAL    0.31   0.49   0.59   0.66   0.66   0.66   0.66   1.49   1.49   1.49   1.49   1.49   2.44   2.44   2.44   2.44   2.44   2.44   3.69   3.69
GDT RMS_ALL_AT   6.13   6.16   6.12   6.10   6.10   6.10   6.10   5.78   5.78   5.78   5.78   5.78   5.45   5.45   5.45   5.45   5.45   5.45   5.17   5.17

# Checking swapping
#   possible swapping detected:  E    24_B      E    24_A
#   possible swapping detected:  Y    32_B      Y    32_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A    17.253     0    0.222   0.637    20.440    0.000    0.000
LGA    G     2_B      G     2_A    17.460     0    0.060   0.060    17.460    0.000    0.000
LGA    P     3_B      P     3_A    18.196     0    0.310   0.356    20.850    0.000    0.000
LGA    N     4_B      N     4_A    11.636     0    0.427   1.207    13.730    1.071    0.536
LGA    G     5_B      G     5_A     6.735     0    0.538   0.538     8.818   18.452   18.452
LGA    G     6_B      G     6_A     0.454     0    0.699   0.699     2.578   82.262   82.262
LGA    V     7_B      V     7_A     2.023     0    0.049   0.582     4.943   72.976   61.497
LGA    C     8_B      C     8_A     1.518     0    0.018   0.067     1.855   77.143   77.143
LGA    P     9_B      P     9_A     0.998     0    0.042   0.077     1.250   90.595   86.667
LGA    V    10_B      V    10_A     0.577     0    0.316   0.268     1.484   88.214   90.544
LGA    L    11_B      L    11_A     1.007     3    0.160   0.198     1.720   81.548   50.952
LGA    I    12_B      I    12_A     0.774     0    0.097   0.628     1.243   92.857   89.405
LGA    Y    13_B      Y    13_A     0.454     0    0.046   0.905     5.636   97.619   69.841
LGA    L    14_B      L    14_A     0.207     0    0.045   0.134     0.503  100.000   98.810
LGA    C    15_B      C    15_A     0.170     0    0.029   0.060     0.592  100.000   98.413
LGA    R    16_B      R    16_A     0.267     0    0.029   1.172     7.081  100.000   71.385
LGA    R    17_B      R    17_A     0.674     0    0.059   0.241     1.437   90.476   88.831
LGA    D    18_B      D    18_A     0.528     0    0.019   0.135     1.353   95.238   90.595
LGA    S    19_B      S    19_A     0.436     0    0.030   0.037     0.530  100.000   98.413
LGA    D    20_B      D    20_A     0.222     0    0.060   0.159     0.515   97.619   98.810
LGA    C    21_B      C    21_A     0.596     0    0.027   0.075     0.713   92.857   92.063
LGA    P    22_B      P    22_A     0.963     0    0.106   0.179     1.147   88.214   86.599
LGA    G    23_B      G    23_A     1.173     0    0.044   0.044     1.242   81.429   81.429
LGA    E    24_B      E    24_A     1.245     0    0.053   0.379     3.300   81.429   70.635
LGA    C    25_B      C    25_A     0.723     0    0.035   0.068     0.884   92.857   92.063
LGA    I    26_B      I    26_A     0.796     0    0.023   0.097     1.482   90.476   85.952
LGA    C    27_B      C    27_A     0.804     0    0.051   0.049     0.829   90.476   90.476
LGA    L    28_B      L    28_A     0.466     0    0.031   0.056     0.937   92.857   92.857
LGA    G    29_B      G    29_A     1.124     0    0.030   0.030     1.847   81.548   81.548
LGA    N    30_B      N    30_A     1.518     0    0.064   0.076     2.209   79.286   76.131
LGA    G    31_B      G    31_A     0.723     0    0.028   0.028     0.888   95.238   95.238
LGA    Y    32_B      Y    32_A     0.364     0    0.027   0.109     1.762  100.000   88.413
LGA    C    33_B      C    33_A     0.340     0    0.058   0.070     0.651   97.619   95.238
LGA    G    34_B      G    34_A     0.317     0    0.686   0.686     1.957   88.571   88.571

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       34     136    136  100.00     235    235  100.00                34
SUMMARY(RMSD_GDC):     5.040          4.982                  4.905           77.616   73.228

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     30    1.49    85.294    84.504     1.883

LGA_LOCAL      RMSD:   1.493  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.780  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   5.040  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.020193 * X  +   0.975039 * Y  +  -0.221114 * Z  +  -9.620110
  Y_new =   0.973428 * X  +  -0.069630 * Y  +  -0.218150 * Z  +  -7.572960
  Z_new =  -0.228100 * X  +  -0.210833 * Y  +  -0.950536 * Z  + -16.517344 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.550055  0.230126 -2.923321   [DEG:   88.8116   13.1853 -167.4940 ]
ZXZ: -0.792147  2.825754 -2.316876   [DEG:  -45.3867  161.9038 -132.7472 ]
 
# END of job
