
#######################################################
#                                                     #
#                        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        1.79     1.79
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       5_B - 11_B        1.79     1.79
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       6_B - 11_B        0.99     2.17
  LCS_AVERAGE:     79.59

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      0    3    3    3    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     M     6_B     M     6_B      6    7    7      4    4    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     T     7_B     T     7_B      6    7    7      4    4    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     L     8_B     L     8_B      6    7    7      4    4    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     K     9_B     K     9_B      6    7    7      4    4    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     F    10_B     F    10_B      6    7    7      3    4    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     G    11_B     G    11_B      6    7    7      0    4    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:  93.20  (  79.59  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      6      6      6      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_AT  57.14  57.14  85.71  85.71  85.71  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
GDT RMS_LOCAL    0.36   0.36   0.99   0.99   0.99   0.99   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79
GDT RMS_ALL_AT   2.97   2.97   2.17   2.17   2.17   2.17   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79   1.79

# 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     3.196     0    0.628   0.991     8.674   54.048   33.069
LGA    M     6_B      M     6_B     2.453     0    0.630   1.208     9.442   75.238   43.333
LGA    T     7_B      T     7_B     1.611     0    0.097   0.154     3.533   75.000   65.374
LGA    L     8_B      L     8_B     1.155     0    0.045   0.086     4.500   88.333   67.857
LGA    K     9_B      K     9_B     0.418     0    0.653   1.016     3.274   82.738   77.407
LGA    F    10_B      F    10_B     0.675     0    0.568   1.291     9.306   82.143   47.229
LGA    G    11_B      G    11_B     1.242     0    0.654   0.654     4.458   64.286   64.286

# 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):     1.786          2.005                  3.834           74.541   56.937

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45    7    4.0      7    1.79    85.714    92.732     0.371

LGA_LOCAL      RMSD:   1.786  Number of atoms:    7  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.786  Number of assigned atoms:    7 
Std_ASGN_ATOMS RMSD:   1.786  Standard rmsd on all 7 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.991691 * X  +   0.018175 * Y  +  -0.127354 * Z  +  -6.887753
  Y_new =   0.123520 * X  +   0.411132 * Y  +  -0.903168 * Z  +   8.394277
  Z_new =   0.035944 * X  +  -0.911395 * Y  +  -0.409961 * Z  + -12.907159 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  3.017675 -0.035952 -1.993498   [DEG:  172.9001   -2.0599 -114.2190 ]
ZXZ: -0.140084  1.993207  3.102174   [DEG:   -8.0262  114.2024  177.7415 ]
 
# END of job
