
#######################################################
#                                                     #
#                        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   22 (  149),  selected   22 , name one
# Molecule2: number of CA atoms   33 (  231),  selected   22 , 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:    20      10_A - 29_A        4.96     6.37
  LCS_AVERAGE:     58.68

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8      14_A - 21_A        1.90     8.06
  LONGEST_CONTINUOUS_SEGMENT:     8      15_A - 22_A        1.96    12.10
  LONGEST_CONTINUOUS_SEGMENT:     8      17_A - 24_A        1.78    11.51
  LONGEST_CONTINUOUS_SEGMENT:     8      18_A - 25_A        1.75    11.41
  LCS_AVERAGE:     21.07

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      18_A - 23_A        0.94    11.48
  LCS_AVERAGE:     12.53

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   22
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     F    10_A     F    10_A      3    5   20      3    4    4    6    8   10   12   12   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     G    11_A     G    11_A      3    5   20      3    3    4    5    6    7    9   11   14   14   14   15   18   19   20   20   20   20   21   21 
LCS_GDT     G    12_A     G    12_A      3    5   20      3    4    4    6    8   10   12   12   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     L    13_A     L    13_A      4    7   20      3    4    5    6    8    9   12   12   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     G    14_A     G    14_A      4    8   20      3    4    5    6    8   10   12   13   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     G    15_A     G    15_A      4    8   20      3    4    5    6    8   10   12   13   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     G    16_A     G    16_A      4    8   20      3    4    5    6    8   10   12   13   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     S    17_A     S    17_A      4    8   20      3    4    6    6    8   10   12   13   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     V    18_A     V    18_A      6    8   20      3    5    6    7    8   10   12   13   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     R    19_A     R    19_A      6    8   20      3    5    6    7    8    9   12   13   14   14   15   15   17   19   20   20   20   20   21   21 
LCS_GDT     F    20_A     F    20_A      6    8   20      3    5    6    7    8   10   12   13   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     G    21_A     G    21_A      6    8   20      3    5    6    7    8   10   12   13   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     P    22_A     P    22_A      6    8   20      3    5    6    7    8   10   12   13   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     G    23_A     G    23_A      6    8   20      3    5    6    7    8    9   11   13   14   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     V    24_A     V    24_A      5    8   20      3    3    6    7    7    9   11   13   13   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     A    25_A     A    25_A      3    8   20      3    3    4    5    8    9   11   13   13   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     F    26_A     F    26_A      3    6   20      3    3    4    6    6    8   10   13   13   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     R    27_A     R    27_A      3    6   20      3    3    5    6    6    8    9   10   11   14   16   16   18   19   20   20   20   20   21   21 
LCS_GDT     A    28_A     A    28_A      3    6   20      3    3    4    5    6    7    8   10   10   11   15   16   18   19   20   20   20   20   21   21 
LCS_GDT     P    29_A     P    29_A      3    6   20      3    3    4    5    6    8    9   10   10   10   15   16   16   18   20   20   20   20   21   21 
LCS_GDT     S    30_A     S    30_A      3    6   13      3    3    4    5    6    8    9   10   10   10   11   12   12   12   14   16   19   20   21   21 
LCS_GDT     I    31_A     I    31_A      3    5   13      0    3    3    5    6    8    9   10   10   10   11   12   12   12   13   14   14   17   19   20 
LCS_AVERAGE  LCS_A:  30.76  (  12.53   21.07   58.68 )

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      3      5      6      7      8     10     12     13     14     14     16     16     18     19     20     20     20     20     21     21 
GDT PERCENT_AT   9.09  15.15  18.18  21.21  24.24  30.30  36.36  39.39  42.42  42.42  48.48  48.48  54.55  57.58  60.61  60.61  60.61  60.61  63.64  63.64
GDT RMS_LOCAL    0.03   0.57   0.94   1.12   1.72   2.28   2.58   2.91   3.10   3.10   4.07   4.07   4.61   4.77   4.96   4.96   4.96   4.96   5.47   5.47
GDT RMS_ALL_AT   8.93  12.13  11.48  12.11   7.05   7.84   7.92   9.41   7.85   7.85   6.98   6.98   6.51   6.54   6.37   6.37   6.37   6.37   6.22   6.22

# Checking swapping
#   possible swapping detected:  F    10_A      F    10_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  F    26_A      F    26_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    F    10_A      F    10_A     9.941     0    0.664   1.144    14.130    0.595    0.346
LGA    G    11_A      G    11_A    12.950     0    0.190   0.190    12.950    0.000    0.000
LGA    G    12_A      G    12_A    12.680     0    0.246   0.246    13.009    0.714    0.714
LGA    L    13_A      L    13_A     7.544     0    0.044   1.405     9.678    6.429    5.119
LGA    G    14_A      G    14_A     3.744     0    0.229   0.229     4.577   43.690   43.690
LGA    G    15_A      G    15_A     2.099     0    0.677   0.677     3.894   59.405   59.405
LGA    G    16_A      G    16_A     3.144     0    0.639   0.639     3.395   53.571   53.571
LGA    S    17_A      S    17_A     3.035     0    0.197   0.649     7.231   48.571   39.286
LGA    V    18_A      V    18_A     3.161     0    0.150   1.076     5.601   65.357   51.020
LGA    R    19_A      R    19_A     3.706     0    0.186   1.211    12.247   45.000   22.338
LGA    F    20_A      F    20_A     2.649     0    0.076   0.530     3.871   60.952   56.753
LGA    G    21_A      G    21_A     2.036     0    0.095   0.095     2.334   73.095   73.095
LGA    P    22_A      P    22_A     0.630     0    0.117   0.118     2.092   86.071   80.476
LGA    G    23_A      G    23_A     1.946     0    0.616   0.616     4.400   64.405   64.405
LGA    V    24_A      V    24_A     3.827     0    0.651   0.631     7.426   57.619   38.844
LGA    A    25_A      A    25_A     2.640     0    0.171   0.218     5.034   47.619   49.524
LGA    F    26_A      F    26_A     3.477     0    0.236   1.190     5.789   38.690   68.355
LGA    R    27_A      R    27_A     9.791     0    0.650   1.303    21.765    2.619    0.952
LGA    A    28_A      A    28_A    14.644     0    0.216   0.256    16.705    0.000    0.000
LGA    P    29_A      P    29_A    15.173     0    0.108   0.404    19.348    0.000    0.000
LGA    S    30_A      S    30_A    19.506     0    0.562   0.735    22.431    0.000    0.000
LGA    I    31_A      I    31_A    20.788     0    0.065   0.121    22.290    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       22      88     88  100.00     149    149  100.00                33
SUMMARY(RMSD_GDC):     6.148          6.120                  7.722           22.861   21.451

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   22   33    4.0     13    2.91    34.091    31.624     0.431

LGA_LOCAL      RMSD:   2.913  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.409  Number of assigned atoms:   22 
Std_ASGN_ATOMS RMSD:   6.148  Standard rmsd on all 22 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.753611 * X  +  -0.412080 * Y  +   0.512114 * Z  + -67.464279
  Y_new =   0.090127 * X  +  -0.706958 * Y  +  -0.701490 * Z  +  83.568588
  Z_new =   0.651113 * X  +   0.574806 * Y  +  -0.495632 * Z  + -24.481136 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.119028 -0.709050  2.282365   [DEG:    6.8198  -40.6256  130.7699 ]
ZXZ:  0.630603  2.089358  0.847563   [DEG:   36.1309  119.7114   48.5618 ]
 
# END of job
