
#######################################################
#                                                     #
#                        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   42 (  310),  selected   42 , name one
# Molecule2: number of CA atoms   63 (  471),  selected   42 , 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:    27      29_A - 55_A        4.86    14.35
  LONGEST_CONTINUOUS_SEGMENT:    27      30_A - 56_A        4.90    14.77
  LCS_AVERAGE:     36.66

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      31_A - 40_A        1.84    15.63
  LCS_AVERAGE:     10.81

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      32_A - 40_A        0.93    15.79
  LCS_AVERAGE:      8.43

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   42
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    17_A     S    17_A      3    4   14      3    4    4    4    5    6    8    9   11   11   12   14   18   20   22   25   27   30   30   32 
LCS_GDT     A    18_A     A    18_A      3    4   14      0    3    4    4    5    6    8    9   11   11   13   15   18   20   23   26   28   30   30   32 
LCS_GDT     H    19_A     H    19_A      6    6   14      4    5    6    6    6    8    8   10   11   11   13   15   18   20   23   26   28   30   30   32 
LCS_GDT     D    20_A     D    20_A      6    6   14      4    5    6    6    6    8    8   10   11   11   13   13   18   20   23   26   28   30   30   32 
LCS_GDT     R    21_A     R    21_A      6    6   15      4    5    6    6    6    7    8   10   11   11   13   13   18   20   23   26   27   30   30   32 
LCS_GDT     C    22_A     C    22_A      6    6   15      4    5    6    6    6    6    8   11   11   12   13   15   18   20   23   26   28   30   30   32 
LCS_GDT     L    23_A     L    23_A      6    6   15      3    5    6    6    6    6   10   11   11   12   15   17   19   22   23   26   28   30   30   32 
LCS_GDT     K    24_A     K    24_A      6    6   15      3    5    6    6    6    6   10   11   11   12   15   17   19   22   23   26   28   30   30   33 
LCS_GDT     Y    25_A     Y    25_A      4    5   15      3    3    4    4    5    8   10   11   11   12   13   16   18   22   23   26   28   30   30   33 
LCS_GDT     C    26_A     C    26_A      4    5   15      3    3    4    4    5    6    8    9   11   11   12   13   16   17   17   22   24   27   29   32 
LCS_GDT     G    27_A     G    27_A      4    5   15      4    4    4    4    5    8   10   11   11   12   13   17   19   22   24   27   28   30   30   33 
LCS_GDT     I    28_A     I    28_A      4    5   23      4    4    4    4    5    6    8    9   11   12   15   17   19   22   24   27   28   30   30   33 
LCS_GDT     C    29_A     C    29_A      4    5   27      4    4    5    5    5    6    6    7    8   10   14   17   19   22   25   27   28   30   30   33 
LCS_GDT     C    30_A     C    30_A      4    5   27      4    4    5    5    5    8   10   11   11   12   17   22   24   26   26   27   28   30   30   33 
LCS_GDT     E    31_A     E    31_A      3   10   27      3    3    5    6    9   11   15   17   18   20   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     K    32_A     K    32_A      9   10   27      3    4   10   12   13   15   15   17   18   20   22   24   25   26   26   27   28   29   30   33 
LCS_GDT     C    33_A     C    33_A      9   10   27      5    8   11   12   13   15   15   17   18   20   22   24   25   26   26   27   28   29   30   33 
LCS_GDT     N    34_A     N    34_A      9   10   27      4    8   11   12   13   15   15   17   18   20   22   24   25   26   26   27   27   29   29   29 
LCS_GDT     C    35_A     C    35_A      9   10   27      3    8   11   12   13   15   15   17   18   20   22   24   25   26   26   27   28   29   29   33 
LCS_GDT     V    36_A     V    36_A      9   10   27      5    8   11   12   13   15   15   17   18   20   22   24   25   26   26   27   28   29   29   33 
LCS_GDT     P    37_A     P    37_A      9   10   27      5    8   11   12   13   15   15   17   18   20   22   24   25   26   26   27   28   29   30   33 
LCS_GDT     P    38_A     P    38_A      9   10   27      5    8   11   12   13   15   15   17   18   20   22   24   25   26   26   27   28   29   29   33 
LCS_GDT     G    39_A     G    39_A      9   10   27      5    8   11   12   13   15   15   17   18   20   22   24   25   26   26   27   28   29   29   33 
LCS_GDT     T    40_A     T    40_A      9   10   27      4    8   11   12   13   15   15   17   18   20   22   24   25   26   26   27   28   29   29   33 
LCS_GDT     Y    41_A     Y    41_A      5    8   27      3    5    5    6    7    9   12   13   18   20   22   24   25   26   26   27   28   29   30   33 
LCS_GDT     G    42_A     G    42_A      5    8   27      3    5    5    6    7    9   12   13   18   18   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     N    43_A     N    43_A      5    8   27      3    5   11   12   13   15   15   17   18   20   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     E    44_A     E    44_A      5    8   27      3    5   10   10   11   15   15   17   18   20   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     D    45_A     D    45_A      4    8   27      3    5   10   10   11   15   15   16   17   18   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     S    46_A     S    46_A      4    7   27      3    4    5    7    9   15   15   17   18   20   22   24   25   26   26   27   28   29   30   33 
LCS_GDT     C    47_A     C    47_A      4    7   27      3    4   11   12   13   15   15   17   18   20   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     P    48_A     P    48_A      4    7   27      3    3   11   12   13   15   15   17   18   20   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     C    49_A     C    49_A      4    7   27      3    4    4    7    9   10   15   17   18   20   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     Y    50_A     Y    50_A      4    7   27      3    3    4    5    9   10   13   14   15   18   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     A    51_A     A    51_A      4    5   27      3    4    4    4    5    6    8   11   17   20   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     N    52_A     N    52_A      4    5   27      3    4    4    4    5    8    8   10   15   19   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     L    53_A     L    53_A      4    5   27      3    4    4    4    6   10   15   16   17   20   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     K    54_A     K    54_A      4    5   27      3    4    6   12   13   13   15   17   18   20   22   24   25   26   26   27   28   30   30   33 
LCS_GDT     N    55_A     N    55_A      4    5   27      3    4    4    4    6   11   12   15   18   19   22   23   25   26   26   27   28   30   30   33 
LCS_GDT     S    56_A     S    56_A      3    5   27      3    3    3    4    4    5    5    6    7    9   11   14   16   19   22   26   28   30   30   33 
LCS_GDT     K    57_A     K    57_A      3    4   15      3    3    3    3    5    6    8    8   10   10   14   17   19   22   23   26   28   30   30   33 
LCS_GDT     G    58_A     G    58_A      3    3   15      3    3    3    4    5    6    8    9   10   12   15   17   19   22   23   26   28   30   30   33 
LCS_AVERAGE  LCS_A:  18.63  (   8.43   10.81   36.66 )

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      5      8     11     12     13     15     15     17     18     20     22     24     25     26     26     27     28     30     30     33 
GDT PERCENT_AT   7.94  12.70  17.46  19.05  20.63  23.81  23.81  26.98  28.57  31.75  34.92  38.10  39.68  41.27  41.27  42.86  44.44  47.62  47.62  52.38
GDT RMS_LOCAL    0.24   0.65   1.03   1.15   1.33   1.84   1.84   2.62   2.68   3.16   3.47   3.78   3.95   4.33   4.33   4.86   5.70   6.54   6.54   7.18
GDT RMS_ALL_AT  15.89  16.06  16.05  15.78  15.91  15.81  15.81  15.68  15.73  15.62  15.71  15.65  15.45  14.91  14.91  14.35  12.60   9.64   9.64  10.44

# Checking swapping
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  D    45_A      D    45_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S    17_A      S    17_A    36.388     0    0.421   0.753    40.635    0.000    0.000
LGA    A    18_A      A    18_A    32.393     0    0.465   0.509    33.258    0.000    0.000
LGA    H    19_A      H    19_A    30.641     0    0.642   1.342    34.419    0.000    0.000
LGA    D    20_A      D    20_A    27.706     0    0.154   0.376    28.787    0.000    0.000
LGA    R    21_A      R    21_A    28.916     0    0.187   0.900    30.611    0.000    0.000
LGA    C    22_A      C    22_A    30.029     0    0.019   0.779    31.184    0.000    0.000
LGA    L    23_A      L    23_A    27.983     0    0.521   0.507    31.675    0.000    0.000
LGA    K    24_A      K    24_A    25.284     0    0.512   0.940    28.524    0.000    0.000
LGA    Y    25_A      Y    25_A    24.108     0    0.030   0.996    31.257    0.000    0.000
LGA    C    26_A      C    26_A    20.920     0    0.236   0.622    21.856    0.000    0.000
LGA    G    27_A      G    27_A    18.597     0    0.657   0.657    19.601    0.000    0.000
LGA    I    28_A      I    28_A    17.620     0    0.240   0.946    22.350    0.000    0.000
LGA    C    29_A      C    29_A    13.827     0    0.364   0.739    16.368    0.000    0.000
LGA    C    30_A      C    30_A    10.658     0    0.578   0.579    12.245    2.976    2.063
LGA    E    31_A      E    31_A     5.718     0    0.226   1.167     9.673   36.429   19.259
LGA    K    32_A      K    32_A     2.637     0    0.592   0.709    12.133   62.976   32.328
LGA    C    33_A      C    33_A     1.017     0    0.563   0.703     3.247   75.357   72.143
LGA    N    34_A      N    34_A     1.765     0    0.137   0.465     2.540   66.905   74.286
LGA    C    35_A      C    35_A     1.432     0    0.029   0.334     2.350   77.143   74.365
LGA    V    36_A      V    36_A     1.219     0    0.106   0.153     1.347   81.429   82.721
LGA    P    37_A      P    37_A     0.960     0    0.022   0.145     1.172   85.952   85.306
LGA    P    38_A      P    38_A     1.101     0    0.158   0.321     1.295   85.952   84.014
LGA    G    39_A      G    39_A     0.989     0    0.270   0.270     1.983   86.071   86.071
LGA    T    40_A      T    40_A     0.868     0    0.072   0.146     4.639   67.381   56.463
LGA    Y    41_A      Y    41_A     5.883     0    0.117   1.163    15.496   35.238   12.143
LGA    G    42_A      G    42_A     6.124     0    0.084   0.084     6.714   27.738   27.738
LGA    N    43_A      N    43_A     2.129     0    0.224   1.067     3.543   71.905   62.798
LGA    E    44_A      E    44_A     3.557     0    0.576   1.203    11.540   55.833   27.725
LGA    D    45_A      D    45_A     4.853     0    0.082   0.816     7.476   39.048   25.833
LGA    S    46_A      S    46_A     3.488     0    0.261   0.309     5.050   51.905   44.206
LGA    C    47_A      C    47_A     1.358     0    0.247   0.423     3.435   67.262   66.746
LGA    P    48_A      P    48_A     1.476     0    0.341   0.418     4.067   83.810   68.503
LGA    C    49_A      C    49_A     4.388     0    0.579   0.800     6.746   33.452   28.095
LGA    Y    50_A      Y    50_A     6.297     0    0.128   1.225    13.669   21.667    7.897
LGA    A    51_A      A    51_A     5.221     0    0.501   0.494     6.621   31.548   27.905
LGA    N    52_A      N    52_A     7.278     0    0.273   0.482    11.656   12.976    6.548
LGA    L    53_A      L    53_A     5.350     0    0.520   0.809    10.417   32.024   18.631
LGA    K    54_A      K    54_A     3.638     0    0.426   1.067     7.660   34.881   27.513
LGA    N    55_A      N    55_A     7.239     0    0.642   1.248    10.867    9.167    6.786
LGA    S    56_A      S    56_A    13.172     0    0.168   0.675    16.811    0.000    0.000
LGA    K    57_A      K    57_A    16.932     0    0.239   0.519    24.350    0.000    0.000
LGA    G    58_A      G    58_A    15.391     0    0.689   0.689    15.391    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       42     168    168  100.00     310    310  100.00                63
SUMMARY(RMSD_GDC):     8.822          8.691                  9.594           21.223   17.906

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   63    4.0     17    2.62    25.397    22.599     0.624

LGA_LOCAL      RMSD:   2.624  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.683  Number of assigned atoms:   42 
Std_ASGN_ATOMS RMSD:   8.822  Standard rmsd on all 42 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.412587 * X  +  -0.663272 * Y  +  -0.624374 * Z  +  20.308453
  Y_new =  -0.477054 * X  +   0.741251 * Y  +  -0.472192 * Z  +   7.055462
  Z_new =   0.776010 * X  +   0.103040 * Y  +  -0.622247 * Z  +   7.650436 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.283857 -0.888314  2.977489   [DEG: -130.8553  -50.8967  170.5975 ]
ZXZ: -0.923297  2.242407  1.438787   [DEG:  -52.9010  128.4804   82.4364 ]
 
# END of job
