
#######################################################
#                                                     #
#                        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:    34       1_A - 34_A        4.46     4.46
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_A - 34_A        1.62     5.09
  LCS_AVERAGE:     79.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       6_A - 34_A        0.79     5.36
  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    5   34      3    4    4    5    6    7    7    9    9   10   10   12   12   14   14   15   15   21   24   26 
LCS_GDT     G     2_B     G     2_A      4    5   34      3    4    4    4    6    7    7    9    9   10   10   12   16   20   21   25   32   33   33   33 
LCS_GDT     P     3_B     P     3_A      4    5   34      3    4    4    4    6    7    7    9   10   10   21   25   27   31   32   32   32   33   33   33 
LCS_GDT     N     4_B     N     4_A      4    6   34      0    4    4    5    6    8    8   14   20   25   27   31   31   31   32   32   32   33   33   33 
LCS_GDT     G     5_B     G     5_A      4   30   34      1    4    4    5    6    8    8   24   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     G     6_B     G     6_A     29   30   34      3   23   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     V     7_B     V     7_A     29   30   34      3    5   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     C     8_B     C     8_A     29   30   34      5   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     P     9_B     P     9_A     29   30   34     12   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     V    10_B     V    10_A     29   30   34     12   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     L    11_B     L    11_A     29   30   34      4   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     I    12_B     I    12_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     Y    13_B     Y    13_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     L    14_B     L    14_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     C    15_B     C    15_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     R    16_B     R    16_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     R    17_B     R    17_A     29   30   34      9   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     D    18_B     D    18_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     S    19_B     S    19_A     29   30   34     14   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     D    20_B     D    20_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     C    21_B     C    21_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     P    22_B     P    22_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     G    23_B     G    23_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     E    24_B     E    24_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     C    25_B     C    25_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     I    26_B     I    26_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     C    27_B     C    27_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     L    28_B     L    28_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     G    29_B     G    29_A     29   30   34     14   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     N    30_B     N    30_A     29   30   34      4   16   27   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     G    31_B     G    31_A     29   30   34      6   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     Y    32_B     Y    32_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     C    33_B     C    33_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_GDT     G    34_B     G    34_A     29   30   34     18   26   28   29   29   29   29   29   30   30   30   31   31   31   32   32   32   33   33   33 
LCS_AVERAGE  LCS_A:  84.72  (  74.48   79.67  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     18     26     28     29     29     29     29     29     30     30     30     31     31     31     32     32     32     33     33     33 
GDT PERCENT_AT  52.94  76.47  82.35  85.29  85.29  85.29  85.29  85.29  88.24  88.24  88.24  91.18  91.18  91.18  94.12  94.12  94.12  97.06  97.06  97.06
GDT RMS_LOCAL    0.34   0.56   0.73   0.79   0.79   0.79   0.79   0.79   1.62   1.62   1.62   2.54   2.54   2.54   3.30   3.30   3.30   3.90   3.90   3.90
GDT RMS_ALL_AT   5.46   5.44   5.40   5.36   5.36   5.36   5.36   5.36   5.09   5.09   5.09   4.78   4.78   4.78   4.57   4.57   4.57   4.49   4.49   4.49

# Checking swapping
#   possible swapping detected:  Y    13_B      Y    13_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A    16.015     0    0.452   0.556    18.820    0.000    0.000
LGA    G     2_B      G     2_A    15.352     0    0.028   0.028    15.352    0.000    0.000
LGA    P     3_B      P     3_A    15.343     0    0.465   0.556    16.131    0.000    0.000
LGA    N     4_B      N     4_A    12.766     0    0.166   1.220    15.016    0.000    0.000
LGA    G     5_B      G     5_A     8.328     0    0.601   0.601     9.776   17.143   17.143
LGA    G     6_B      G     6_A     1.475     0    0.577   0.577     3.969   78.810   78.810
LGA    V     7_B      V     7_A     1.912     0    0.085   0.122     3.797   68.929   59.864
LGA    C     8_B      C     8_A     0.790     0    0.074   0.116     1.131   88.214   90.556
LGA    P     9_B      P     9_A     0.673     0    0.019   0.300     1.025   90.476   89.184
LGA    V    10_B      V    10_A     0.764     0    0.376   0.991     2.717   84.048   79.524
LGA    L    11_B      L    11_A     0.916     3    0.093   0.124     1.225   88.214   55.417
LGA    I    12_B      I    12_A     0.256     0    0.162   0.163     1.395   92.976   91.786
LGA    Y    13_B      Y    13_A     0.127     0    0.061   0.533     2.631  100.000   85.198
LGA    L    14_B      L    14_A     0.265     0    0.039   0.075     0.952  100.000   96.429
LGA    C    15_B      C    15_A     0.215     0    0.046   0.063     0.571  100.000   98.413
LGA    R    16_B      R    16_A     0.302     0    0.121   1.621     9.176  100.000   60.390
LGA    R    17_B      R    17_A     0.948     0    0.090   1.344     7.986   90.476   57.662
LGA    D    18_B      D    18_A     0.810     0    0.020   0.058     0.979   90.476   90.476
LGA    S    19_B      S    19_A     0.969     0    0.014   0.015     1.179   90.476   87.460
LGA    D    20_B      D    20_A     0.244     0    0.043   0.171     0.534  100.000   98.810
LGA    C    21_B      C    21_A     0.587     0    0.017   0.045     0.950   97.619   95.238
LGA    P    22_B      P    22_A     0.460     0    0.072   0.142     1.151   97.619   93.265
LGA    G    23_B      G    23_A     0.498     0    0.013   0.013     0.498  100.000  100.000
LGA    E    24_B      E    24_A     0.474     0    0.033   0.299     1.731   97.619   89.788
LGA    C    25_B      C    25_A     0.360     0    0.009   0.038     0.611  100.000   98.413
LGA    I    26_B      I    26_A     0.365     0    0.081   1.448     4.697   95.238   79.286
LGA    C    27_B      C    27_A     0.590     0    0.044   0.066     0.659   92.857   92.063
LGA    L    28_B      L    28_A     0.553     0    0.024   0.043     1.624   95.238   87.321
LGA    G    29_B      G    29_A     0.590     0    0.029   0.029     1.571   86.190   86.190
LGA    N    30_B      N    30_A     1.751     0    0.047   0.110     2.709   77.143   71.012
LGA    G    31_B      G    31_A     0.856     0    0.108   0.108     0.928   95.238   95.238
LGA    Y    32_B      Y    32_A     0.299     0    0.038   0.046     1.562  100.000   89.167
LGA    C    33_B      C    33_A     0.576     0    0.021   0.038     0.984   92.857   92.063
LGA    G    34_B      G    34_A     0.791     0    0.265   0.265     1.336   85.952   85.952

# 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):     4.462          4.392                  4.364           79.230   73.298

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     29    0.79    85.294    84.521     3.241

LGA_LOCAL      RMSD:   0.795  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.364  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   4.462  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.651728 * X  +  -0.266155 * Y  +   0.710220 * Z  +  -2.503973
  Y_new =   0.694046 * X  +  -0.168343 * Y  +  -0.699972 * Z  +  10.480112
  Z_new =   0.305862 * X  +   0.949117 * Y  +   0.075010 * Z  + -18.014767 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.816833 -0.310843  1.491929   [DEG:   46.8011  -17.8100   85.4812 ]
ZXZ:  0.792665  1.495716  0.311751   [DEG:   45.4164   85.6982   17.8620 ]
 
# END of job
