
#######################################################
#                                                     #
#                        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        1.88     1.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       5_B - 11_B        1.88     1.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       6_B - 10_B        0.71     2.81
  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    4    5    6    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    5    6    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      4    4    5    5    6    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      4    4    5    5    6    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      4    4    5    5    6    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      4    4    5    5    6    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    3    4    5    6    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      4      4      5      5      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_AT  57.14  57.14  71.43  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
GDT RMS_LOCAL    0.37   0.37   0.71   0.71   1.44   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88
GDT RMS_ALL_AT   2.71   2.71   2.81   2.81   2.80   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88

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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E     5_B      E     5_B     1.458     0    0.585   1.081     4.884   60.119   54.709
LGA    M     6_B      M     6_B     1.301     0    0.395   1.084     5.326   77.262   65.536
LGA    T     7_B      T     7_B     2.362     0    0.134   0.179     6.573   61.429   43.197
LGA    L     8_B      L     8_B     1.768     0    0.114   1.375     8.163   77.381   48.095
LGA    K     9_B      K     9_B     2.519     0    0.112   0.148    13.603   63.214   32.646
LGA    F    10_B      F    10_B     2.066     0    0.550   0.413     7.222   77.381   44.156
LGA    G    11_B      G    11_B     1.229     0    0.697   0.697     2.720   69.048   69.048

# 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):     1.876          2.098                  3.644           69.405   51.055

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45    7    4.0      7    1.88    82.143    91.541     0.354

LGA_LOCAL      RMSD:   1.876  Number of atoms:    7  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.876  Number of assigned atoms:    7 
Std_ASGN_ATOMS RMSD:   1.876  Standard rmsd on all 7 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.664972 * X  +   0.135796 * Y  +   0.734419 * Z  +   8.651388
  Y_new =   0.083857 * X  +  -0.963539 * Y  +   0.254089 * Z  + 137.010193
  Z_new =   0.742145 * X  +   0.230549 * Y  +   0.629339 * Z  + -87.329514 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  3.016148 -0.836266  0.351152   [DEG:  172.8126  -47.9145   20.1195 ]
ZXZ:  1.903879  0.890094  1.269596   [DEG:  109.0843   50.9986   72.7425 ]
 
# END of job
