
#######################################################
#                                                     #
#                        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        1.67     1.67
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       5_B - 11_B        1.67     1.67
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       6_B - 10_B        0.97     2.88
  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    5    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      4    5    5    5    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      4    5    5    5    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      4    5    5    5    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      4    5    5    5    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    3    5    5    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    5    5    5    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      4      5      5      5      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_AT  57.14  71.43  71.43  71.43 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.42   0.64   0.64   0.64   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67
GDT RMS_ALL_AT   2.78   2.58   2.58   2.58   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67   1.67

# 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     1.370     0    0.636   1.184     5.458   64.048   56.296
LGA    M     6_B      M     6_B     2.135     0    0.594   1.247     4.891   58.690   59.940
LGA    T     7_B      T     7_B     1.010     0    0.168   0.217     3.996   75.833   63.878
LGA    L     8_B      L     8_B     0.863     0    0.242   1.428     6.630   84.048   62.083
LGA    K     9_B      K     9_B     2.251     0    0.108   0.119    13.258   65.238   34.286
LGA    F    10_B      F    10_B     2.432     0    0.315   1.531     9.948   81.786   35.801
LGA    G    11_B      G    11_B     0.545     0    0.503   0.503     4.462   68.452   68.452

# 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):     1.668          2.197                  3.895           71.156   54.391

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45    7    4.0      7    1.67    85.714    93.609     0.396

LGA_LOCAL      RMSD:   1.668  Number of atoms:    7  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.668  Number of assigned atoms:    7 
Std_ASGN_ATOMS RMSD:   1.668  Standard rmsd on all 7 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.643840 * X  +  -0.053265 * Y  +   0.763304 * Z  +  -9.804035
  Y_new =  -0.291653 * X  +   0.939347 * Y  +  -0.180458 * Z  +  34.056576
  Z_new =  -0.707395 * X  +  -0.338806 * Y  +  -0.620324 * Z  + -34.749756 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.716255  0.785806 -2.641690   [DEG: -155.6299   45.0234 -151.3577 ]
ZXZ:  1.338642  2.239953 -2.017462   [DEG:   76.6985  128.3398 -115.5920 ]
 
# END of job
