
#######################################################
#                                                     #
#                        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        0.88     0.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       5_B - 11_B        0.88     0.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       5_B - 11_B        0.88     0.88
  LCS_AVERAGE:    100.00

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      7    7    7      5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     M     6_B     M     6_B      7    7    7      5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     T     7_B     T     7_B      7    7    7      5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     L     8_B     L     8_B      7    7    7      5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     K     9_B     K     9_B      7    7    7      5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     F    10_B     F    10_B      7    7    7      3    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     G    11_B     G    11_B      7    7    7      3    5    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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      5      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_AT  71.43  85.71 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.60   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88
GDT RMS_ALL_AT   1.30   1.12   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88   0.88

# 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     0.644     0    0.635   1.112     7.653   79.643   54.497
LGA    M     6_B      M     6_B     0.996     0    0.083   1.495     4.126   92.857   74.702
LGA    T     7_B      T     7_B     0.121     0    0.094   0.986     2.460   97.619   89.728
LGA    L     8_B      L     8_B     0.678     0    0.025   1.432     5.802   97.619   73.333
LGA    K     9_B      K     9_B     0.497     0    0.112   1.006     5.920   92.857   72.222
LGA    F    10_B      F    10_B     1.294     0    0.053   1.317     9.385   86.071   44.329
LGA    G    11_B      G    11_B     1.291     0    0.544   0.544     1.633   83.810   83.810

# 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):     0.884          0.869                  3.209           90.068   70.375

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45    7    4.0      7    0.88    96.429    98.872     0.711

LGA_LOCAL      RMSD:   0.884  Number of atoms:    7  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.884  Number of assigned atoms:    7 
Std_ASGN_ATOMS RMSD:   0.884  Standard rmsd on all 7 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.870744 * X  +  -0.127463 * Y  +   0.474929 * Z  + -25.442558
  Y_new =   0.489419 * X  +   0.130984 * Y  +  -0.862156 * Z  +  30.544605
  Z_new =   0.047685 * X  +   0.983156 * Y  +   0.176437 * Z  + -26.616499 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.512062 -0.047703  1.393227   [DEG:   29.3390   -2.7332   79.8260 ]
ZXZ:  0.503505  1.393431  0.048464   [DEG:   28.8487   79.8377    2.7768 ]
 
# END of job
