
#######################################################
#                                                     #
#                        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   31 (  282),  selected   24 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   24 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      11_F - 31_F        4.89     6.21
  LCS_AVERAGE:     80.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      11_F - 22_F        1.72    10.28
  LCS_AVERAGE:     40.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      12_F - 22_F        0.93    10.48
  LCS_AVERAGE:     35.74

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   24
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     L     8_D     L     8_F      3    3   20      0    3    3    3    3    3    4    8   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     Q     9_D     Q     9_F      3    4   20      3    3    4    6    6    9   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     K    10_D     K    10_F      3    4   20      3    4    5    6    6    6    8   10   11   12   15   15   15   17   20   20   23   23   24   24 
LCS_GDT     L    11_D     L    11_F      3   12   21      3    4    5    6    9   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     N    12_D     N    12_F     11   12   21      8    8   10   11   11   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     S    13_D     S    13_F     11   12   21      8    8   10   11   11   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     W    14_D     W    14_F     11   12   21      8    8   10   11   11   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     D    15_D     D    15_F     11   12   21      8    8   10   11   11   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     V    16_D     V    16_F     11   12   21      8    8   10   11   11   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     F    17_D     F    17_F     11   12   21      8    8   10   11   11   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     G    18_D     G    18_F     11   12   21      8    8   10   11   11   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     N    19_D     N    19_F     11   12   21      8    8   11   11   11   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     W    20_D     W    20_F     11   12   21      3    8   10   11   11   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     F    21_D     F    21_F     11   12   21      3    5   10   11   11   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     D    22_D     D    22_F     11   12   21     10   10   11   11   11   11   13   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     L    23_D     L    23_F     10   11   21     10   10   11   11   11   11   12   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     A    24_D     A    24_F     10   11   21     10   10   11   11   11   11   12   13   15   15   16   19   19   20   22   22   23   23   24   24 
LCS_GDT     S    25_D     S    25_F     10   11   21     10   10   11   11   11   11   12   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     W    26_D     W    26_F     10   11   21     10   10   11   11   11   11   12   13   15   16   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     I    27_D     I    27_F     10   11   21     10   10   11   11   11   11   12   13   15   15   16   17   19   20   22   22   23   23   24   24 
LCS_GDT     K    28_D     K    28_F     10   11   21     10   10   11   11   11   11   12   13   15   15   16   17   19   20   22   22   23   23   24   24 
LCS_GDT     Y    29_D     Y    29_F     10   11   21     10   10   11   11   11   11   12   13   15   15   18   19   19   20   22   22   23   23   24   24 
LCS_GDT     I    30_D     I    30_F     10   11   21     10   10   11   11   11   11   12   13   13   14   16   17   19   20   22   22   23   23   24   24 
LCS_GDT     Q    31_D     Q    31_F     10   11   21     10   10   11   11   11   11   12   13   13   14   16   17   18   19   21   21   21   22   24   24 
LCS_AVERAGE  LCS_A:  52.24  (  35.74   40.71   80.29 )

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     10     10     11     11     11     11     13     13     15     16     18     19     19     20     22     22     23     23     24     24 
GDT PERCENT_AT  38.46  38.46  42.31  42.31  42.31  42.31  50.00  50.00  57.69  61.54  69.23  73.08  73.08  76.92  84.62  84.62  88.46  88.46  92.31  92.31
GDT RMS_LOCAL    0.23   0.23   0.81   0.81   0.81   0.81   2.19   2.12   3.09   3.36   3.96   4.21   4.21   4.63   5.02   5.02   5.24   5.24   5.58   5.58
GDT RMS_ALL_AT  12.34  12.34  11.30  11.30  11.30  11.30  10.45  10.00   9.18   8.44   6.91   6.62   6.62   5.97   5.70   5.70   5.69   5.69   5.58   5.58

# Checking swapping
#   possible swapping detected:  F    17_D      F    17_F
#   possible swapping detected:  D    22_D      D    22_F
#   possible swapping detected:  Y    29_D      Y    29_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    25.022     0    0.284   0.303    27.685    0.000    0.000
LGA    Q     9_D      Q     9_F    18.562     0    0.585   0.533    21.022    0.000    0.000
LGA    K    10_D      K    10_F    19.287     0    0.040   0.662    25.354    0.000    0.000
LGA    L    11_D      L    11_F    16.284     0    0.591   0.600    17.844    0.000    0.000
LGA    N    12_D      N    12_F    12.503     0    0.568   0.560    15.792    0.714    0.357
LGA    S    13_D      S    13_F    11.292     0    0.034   0.103    13.464    0.000    0.000
LGA    W    14_D      W    14_F    13.873     0    0.075   0.180    19.946    0.000    0.000
LGA    D    15_D      D    15_F     9.654     0    0.025   0.168    14.715    8.810    4.405
LGA    V    16_D      V    16_F     3.519     0    0.015   0.038     5.693   34.881   39.864
LGA    F    17_D      F    17_F     8.750     0    0.051   1.618    17.576    6.786    2.468
LGA    G    18_D      G    18_F     6.578     0    0.176   0.176     7.263   29.167   29.167
LGA    N    19_D      N    19_F     1.633     0    0.230   0.365     7.231   56.548   41.012
LGA    W    20_D      W    20_F     6.571     0    0.165   1.299    16.109   18.690    5.544
LGA    F    21_D      F    21_F     4.564     0    0.559   1.232    11.968   44.405   19.307
LGA    D    22_D      D    22_F     2.663     0    0.572   1.405     8.081   64.881   39.643
LGA    L    23_D      L    23_F     2.013     0    0.086   1.067     4.603   70.952   63.750
LGA    A    24_D      A    24_F     1.594     0    0.016   0.021     1.885   77.143   76.286
LGA    S    25_D      S    25_F     1.678     0    0.144   0.705     2.412   79.405   77.302
LGA    W    26_D      W    26_F     0.985     0    0.028   0.356     2.909   88.214   75.714
LGA    I    27_D      I    27_F     0.291     0    0.023   0.101     1.116   95.238   94.107
LGA    K    28_D      K    28_F     0.773     0    0.120   0.591     5.582   88.452   65.556
LGA    Y    29_D      Y    29_F     0.529     0    0.031   0.365     1.123   90.595   92.183
LGA    I    30_D      I    30_F     1.173     0    0.334   1.875     4.702   83.690   71.190
LGA    Q    31_D      Q    31_F     1.661     0    0.617   1.397     7.460   75.000   51.852

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       24      96     96  100.00     212    212  100.00                26
SUMMARY(RMSD_GDC):     5.577          5.424                  7.323           38.984   32.681

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   31   26    4.0     13    2.12    53.846    50.932     0.586

LGA_LOCAL      RMSD:   2.120  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.997  Number of assigned atoms:   24 
Std_ASGN_ATOMS RMSD:   5.577  Standard rmsd on all 24 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.695231 * X  +  -0.328907 * Y  +  -0.639119 * Z  +  38.563713
  Y_new =  -0.717427 * X  +  -0.262874 * Y  +  -0.645132 * Z  + -61.201496
  Z_new =   0.044181 * X  +   0.907038 * Y  +  -0.418725 * Z  +   5.657149 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.801109 -0.044195  2.003288   [DEG:  -45.9002   -2.5322  114.7799 ]
ZXZ: -0.780716  2.002837  0.048671   [DEG:  -44.7317  114.7541    2.7886 ]
 
# END of job
