
#######################################################
#                                                     #
#                        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   45 (  355),  selected    7 , name one
# Molecule2: number of CA atoms    7 (   56),  selected    7 , 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:     7       5_B - 11_B        1.71     1.71
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       5_B - 11_B        1.71     1.71
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       6_B - 10_B        0.86     2.57
  LCS_AVERAGE:     63.27

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:    7
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     E     5_B     E     5_B      3    7    7      3    3    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     M     6_B     M     6_B      5    7    7      3    4    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     T     7_B     T     7_B      5    7    7      3    4    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     L     8_B     L     8_B      5    7    7      3    4    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     K     9_B     K     9_B      5    7    7      3    4    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     F    10_B     F    10_B      5    7    7      3    4    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     G    11_B     G    11_B      3    7    7      3    4    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:  87.76  (  63.27  100.00  100.00 )

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      4      5      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_AT  42.86  57.14  71.43  85.71 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.50   0.72   1.22   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71
GDT RMS_ALL_AT   2.23   2.18   2.37   2.34   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71

# Checking swapping
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  F    10_B      F    10_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E     5_B      E     5_B     2.233     0    0.623   0.931     4.566   70.714   62.434
LGA    M     6_B      M     6_B     2.450     0    0.593   0.901     4.224   60.119   51.012
LGA    T     7_B      T     7_B     1.181     0    0.079   0.110     3.599   81.786   68.231
LGA    L     8_B      L     8_B     0.744     0    0.129   1.375     6.369   88.452   65.536
LGA    K     9_B      K     9_B     1.640     0    0.114   0.830    11.596   71.429   39.788
LGA    F    10_B      F    10_B     2.078     0    0.334   1.517     9.587   88.810   40.260
LGA    G    11_B      G    11_B     0.798     0    0.477   0.477     4.281   70.714   70.714

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:        7      28     28  100.00      56     56  100.00                 7
SUMMARY(RMSD_GDC):     1.715          2.014                  3.279           76.003   56.854

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45    7    4.0      7    1.71    85.714    93.484     0.386

LGA_LOCAL      RMSD:   1.715  Number of atoms:    7  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.715  Number of assigned atoms:    7 
Std_ASGN_ATOMS RMSD:   1.715  Standard rmsd on all 7 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.050883 * X  +  -0.152220 * Y  +   0.987036 * Z  + -46.047478
  Y_new =   0.820208 * X  +  -0.570240 * Y  +  -0.045659 * Z  + -69.853584
  Z_new =   0.569798 * X  +   0.807252 * Y  +   0.153867 * Z  + -84.246078 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.632753 -0.606260  1.382449   [DEG:   93.5499  -34.7361   79.2085 ]
ZXZ:  1.524570  1.416315  0.614641   [DEG:   87.3514   81.1489   35.2163 ]
 
# END of job
