
#######################################################
#                                                     #
#                        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   20 (  160),  selected   20 , name one
# Molecule2: number of CA atoms   81 (  640),  selected   20 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      60_B - 79_B        4.14     4.14
  LCS_AVERAGE:     24.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      63_B - 79_B        1.91     4.82
  LCS_AVERAGE:     18.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      66_B - 79_B        0.46     5.99
  LCS_AVERAGE:     13.95

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   20
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     R    60_B     R    60_B      5    6   20      4    5    5    5    5    6    8    9    9   10   10   12   13   14   16   16   20   20   20   20 
LCS_GDT     E    61_B     E    61_B      5    6   20      4    5    5    5    5    7    8    9    9   11   12   12   15   16   19   19   20   20   20   20 
LCS_GDT     L    62_B     L    62_B      5    6   20      4    5    5    5    5    7    9   11   14   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     L    63_B     L    63_B      5   17   20      5    5    5    9   13   15   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     P    64_B     P    64_B      5   17   20      5    5    5    9   13   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     A    65_B     A    65_B      5   17   20      5    5    5    9   13   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     K    66_B     K    66_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     A    67_B     A    67_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     E    68_B     E    68_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     I    69_B     I    69_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     I    70_B     I    70_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     D    71_B     D    71_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     A    72_B     A    72_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     L    73_B     L    73_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     R    74_B     R    74_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     E    75_B     E    75_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     E    76_B     E    76_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     A    77_B     A    77_B     14   17   20      7   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     E    78_B     E    78_B     14   17   20     10   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_GDT     K    79_B     K    79_B     14   17   20      7   14   14   14   14   16   17   17   17   17   17   18   18   18   19   19   20   20   20   20 
LCS_AVERAGE  LCS_A:  19.20  (  13.95   18.95   24.69 )

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     14     14     14     14     16     17     17     17     17     17     18     18     18     19     19     20     20     20     20 
GDT PERCENT_AT  12.35  17.28  17.28  17.28  17.28  19.75  20.99  20.99  20.99  20.99  20.99  22.22  22.22  22.22  23.46  23.46  24.69  24.69  24.69  24.69
GDT RMS_LOCAL    0.33   0.46   0.46   0.46   0.46   1.67   1.91   1.91   1.91   1.91   1.91   2.77   2.77   2.77   3.58   3.58   4.14   4.14   4.14   4.14
GDT RMS_ALL_AT   5.88   5.99   5.99   5.99   5.99   5.06   4.82   4.82   4.82   4.82   4.82   4.43   4.43   4.43   4.18   4.18   4.14   4.14   4.14   4.14

# Checking swapping
#   possible swapping detected:  D    71_B      D    71_B
#   possible swapping detected:  E    75_B      E    75_B
#   possible swapping detected:  E    78_B      E    78_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    R    60_B      R    60_B    12.161     0    0.006   1.758    14.309    0.714    0.260
LGA    E    61_B      E    61_B    12.554     0    0.022   0.895    20.479    0.000    0.000
LGA    L    62_B      L    62_B     9.813     0    0.031   0.101    14.656    7.738    3.869
LGA    L    63_B      L    63_B     3.764     0    0.529   0.680     8.990   46.667   31.786
LGA    P    64_B      P    64_B     2.977     0    0.157   0.213     5.220   61.190   48.503
LGA    A    65_B      A    65_B     3.019     0    0.065   0.071     3.825   55.476   53.048
LGA    K    66_B      K    66_B     1.798     0    0.330   1.188     7.933   75.238   49.312
LGA    A    67_B      A    67_B     2.035     0    0.016   0.015     2.149   68.810   68.000
LGA    E    68_B      E    68_B     1.960     0    0.038   0.872     2.207   72.857   71.058
LGA    I    69_B      I    69_B     1.409     0    0.072   0.161     1.811   79.286   78.214
LGA    I    70_B      I    70_B     1.517     0    0.024   0.659     2.428   79.405   74.107
LGA    D    71_B      D    71_B     1.467     0    0.014   0.409     2.892   79.286   72.083
LGA    A    72_B      A    72_B     1.181     0    0.026   0.032     1.317   85.952   85.048
LGA    L    73_B      L    73_B     0.249     0    0.060   0.097     0.741   92.857   94.048
LGA    R    74_B      R    74_B     1.230     0    0.032   0.984     2.371   85.952   76.926
LGA    E    75_B      E    75_B     0.641     0    0.060   0.751     4.386   90.476   75.979
LGA    E    76_B      E    76_B     1.011     0    0.073   0.902     4.087   81.548   70.370
LGA    A    77_B      A    77_B     1.693     0    0.031   0.037     2.028   72.976   72.952
LGA    E    78_B      E    78_B     1.032     0    0.062   0.719     2.788   81.429   74.180
LGA    K    79_B      K    79_B     1.978     0    0.020   0.682     4.809   65.357   52.116

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       20      80     80  100.00     160    160  100.00                81
SUMMARY(RMSD_GDC):     4.137          3.926                  5.451           15.842   14.220

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   20   81    4.0     17    1.91    19.753    19.639     0.846

LGA_LOCAL      RMSD:   1.911  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.816  Number of assigned atoms:   20 
Std_ASGN_ATOMS RMSD:   4.137  Standard rmsd on all 20 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.854943 * X  +  -0.438325 * Y  +  -0.277387 * Z  +  59.739475
  Y_new =  -0.263175 * X  +  -0.094285 * Y  +   0.960130 * Z  +  35.426666
  Z_new =  -0.447003 * X  +   0.893857 * Y  +  -0.034748 * Z  + -18.860487 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.842970  0.463412  1.609651   [DEG: -162.8902   26.5515   92.2262 ]
ZXZ: -2.860345  1.605551 -0.463714   [DEG: -163.8857   91.9913  -26.5688 ]
 
# END of job
