
#######################################################
#                                                     #
#                        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   25 (  210),  selected   25 , name one
# Molecule2: number of CA atoms  105 (  864),  selected   25 , 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:    25      63_A - 87_A        2.04     2.04
  LCS_AVERAGE:     23.81

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      63_A - 86_A        1.75     2.11
  LCS_AVERAGE:     22.21

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      63_A - 77_A        0.99     2.19
  LCS_AVERAGE:     11.47

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   25
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     K    63_A     K    63_A     15   24   25      6   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     C    64_A     C    64_A     15   24   25      8   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     N    65_A     N    65_A     15   24   25      8   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     F    66_A     F    66_A     15   24   25      8   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     C    67_A     C    67_A     15   24   25      5    9   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     D    68_A     D    68_A     15   24   25      5    7   14   19   21   22   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     Y    69_A     Y    69_A     15   24   25      6   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     M    70_A     M    70_A     15   24   25      6   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     C    71_A     C    71_A     15   24   25      6   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     K    72_A     K    72_A     15   24   25      5   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     G    73_A     G    73_A     15   24   25      8   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     I    74_A     I    74_A     15   24   25      8   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     R    75_A     R    75_A     15   24   25      8   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     N    76_A     N    76_A     15   24   25      6   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     I    77_A     I    77_A     15   24   25      8   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     R    78_A     R    78_A     12   24   25      6   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     L    79_A     L    79_A     12   24   25      6    9   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     H    80_A     H    80_A      9   24   25      5    6   10   17   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     H    81_A     H    81_A      7   24   25      5    6    8   18   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     K    82_A     K    82_A      7   24   25      5    6    8   12   14   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     K    83_A     K    83_A      7   24   25      5    6    8   12   14   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     S    84_A     S    84_A      7   24   25      5    7   10   17   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     H    85_A     H    85_A      7   24   25      8   15   17   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     P    86_A     P    86_A      5   24   25      3    4   16   19   21   23   24   24   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     D    87_A     D    87_A      3    7   25      3    4   13   15   18   20   23   23   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_AVERAGE  LCS_A:  19.16  (  11.47   22.21   23.81 )

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      8     15     17     19     21     23     24     24     25     25     25     25     25     25     25     25     25     25     25     25 
GDT PERCENT_AT   7.62  14.29  16.19  18.10  20.00  21.90  22.86  22.86  23.81  23.81  23.81  23.81  23.81  23.81  23.81  23.81  23.81  23.81  23.81  23.81
GDT RMS_LOCAL    0.36   0.74   0.96   1.10   1.29   1.71   1.75   1.75   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04
GDT RMS_ALL_AT   2.16   2.16   2.06   2.09   2.08   2.12   2.11   2.11   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04

# Checking swapping
#   possible swapping detected:  D    68_A      D    68_A
#   possible swapping detected:  Y    69_A      Y    69_A
#   possible swapping detected:  D    87_A      D    87_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    63_A      K    63_A     1.226     0    0.114   1.225     7.499   83.810   56.614
LGA    C    64_A      C    64_A     0.243     0    0.047   0.077     0.693  100.000   98.413
LGA    N    65_A      N    65_A     0.787     0    0.265   1.097     4.983   81.786   64.345
LGA    F    66_A      F    66_A     0.720     0    0.256   1.350     8.471   88.214   52.554
LGA    C    67_A      C    67_A     1.651     0    0.560   0.808     2.532   75.476   73.254
LGA    D    68_A      D    68_A     2.300     0    0.099   0.543     5.306   68.810   53.214
LGA    Y    69_A      Y    69_A     1.306     0    0.054   1.414    10.158   83.690   45.476
LGA    M    70_A      M    70_A     1.406     0    0.000   0.771     5.745   79.286   66.667
LGA    C    71_A      C    71_A     1.010     0    0.055   0.810     1.565   85.952   83.016
LGA    K    72_A      K    72_A     0.890     0    0.618   0.879     3.462   78.095   71.058
LGA    G    73_A      G    73_A     0.722     0    0.149   0.149     1.062   85.952   85.952
LGA    I    74_A      I    74_A     1.011     0    0.024   1.271     4.090   83.690   70.952
LGA    R    75_A      R    75_A     1.043     0    0.030   0.707     2.032   85.952   78.442
LGA    N    76_A      N    76_A     1.154     0    0.036   0.445     2.169   83.690   81.607
LGA    I    77_A      I    77_A     0.948     0    0.099   0.581     1.440   88.214   85.952
LGA    R    78_A      R    78_A     0.534     0    0.089   1.466     5.497   92.857   76.320
LGA    L    79_A      L    79_A     1.121     0    0.128   0.925     2.467   83.690   75.238
LGA    H    80_A      H    80_A     2.354     0    0.072   1.307    10.100   70.833   36.762
LGA    H    81_A      H    81_A     3.009     0    0.047   0.461     8.029   59.167   34.476
LGA    K    82_A      K    82_A     3.674     0    0.059   0.970    13.337   48.452   26.190
LGA    K    83_A      K    83_A     3.506     0    0.019   0.638     8.280   51.905   34.497
LGA    S    84_A      S    84_A     2.481     0    0.068   0.660     2.933   66.905   66.270
LGA    H    85_A      H    85_A     1.235     0    0.479   1.061     4.070   70.476   73.714
LGA    P    86_A      P    86_A     1.676     0    0.069   0.415     3.960   65.952   61.293
LGA    D    87_A      D    87_A     6.173     0    0.668   1.087     9.624   16.429    9.702

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       25     100    100  100.00     210    210  100.00               105
SUMMARY(RMSD_GDC):     2.039          2.112                  3.823           17.898   14.876

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   25  105    4.0     24    1.75    19.762    21.217     1.297

LGA_LOCAL      RMSD:   1.750  Number of atoms:   24  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.113  Number of assigned atoms:   25 
Std_ASGN_ATOMS RMSD:   2.039  Standard rmsd on all 25 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.054091 * X  +   0.779912 * Y  +   0.623548 * Z  + -233.397141
  Y_new =   0.742163 * X  +   0.449174 * Y  +  -0.497431 * Z  + -141.692215
  Z_new =  -0.668033 * X  +   0.435867 * Y  +  -0.603118 * Z  +  84.229149 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.643551  0.731563  2.515800   [DEG:   94.1685   41.9155  144.1447 ]
ZXZ:  0.897433  2.218200 -0.992692   [DEG:   51.4191  127.0935  -56.8770 ]
 
# END of job
