
#######################################################
#                                                     #
#                        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    8 (   72),  selected    6 , name one
# Molecule2: number of CA atoms  353 ( 2869),  selected    6 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      34_A - 39_A        1.66     1.66
  LCS_AVERAGE:      1.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      34_A - 39_A        1.66     1.66
  LCS_AVERAGE:      1.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4      34_A - 37_A        0.68     3.49
  LONGEST_CONTINUOUS_SEGMENT:     4      36_A - 39_A        0.68     3.10
  LCS_AVERAGE:      1.13

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:    6
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     Q    34_A     Q    34_A      4    6    6      3    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     L    35_A     L    35_A      4    6    6      3    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     H    36_A     H    36_A      4    6    6      3    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     Y    37_A     Y    37_A      4    6    6      3    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     P    38_A     P    38_A      4    6    6      3    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     K    39_A     K    39_A      4    6    6      3    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   1.51  (   1.13    1.70    1.70 )

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      4      5      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_AT   0.85   1.13   1.13   1.42   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70
GDT RMS_LOCAL    0.10   0.68   0.68   1.23   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66
GDT RMS_ALL_AT   2.41   3.10   3.10   1.88   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66   1.66

# Checking swapping
#   possible swapping detected:  Y    37_A      Y    37_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q    34_A      Q    34_A     1.326     0    0.106   1.307     7.585   86.190   52.910
LGA    L    35_A      L    35_A     1.837     0    0.052   0.902     5.191   79.405   57.083
LGA    H    36_A      H    36_A     1.399     0    0.040   0.273     3.513   77.143   63.095
LGA    Y    37_A      Y    37_A     2.341     0    0.160   1.114     6.865   75.119   55.198
LGA    P    38_A      P    38_A     0.982     0    0.029   0.125     2.503   88.214   78.231
LGA    K    39_A      K    39_A     1.752     0    0.638   1.358     9.318   59.405   45.979

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:        6      24     24  100.00      55     55  100.00               353
SUMMARY(RMSD_GDC):     1.663          1.681                  2.894            1.319    0.999

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)    8  353    4.0      6    1.66     1.487     1.593     0.340

LGA_LOCAL      RMSD:   1.663  Number of atoms:    6  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.663  Number of assigned atoms:    6 
Std_ASGN_ATOMS RMSD:   1.663  Standard rmsd on all 6 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.771724 * X  +  -0.084885 * Y  +  -0.630267 * Z  + -22.583328
  Y_new =  -0.583241 * X  +  -0.489543 * Y  +  -0.648212 * Z  + -16.174078
  Z_new =  -0.253519 * X  +   0.867838 * Y  +  -0.427300 * Z  +  83.516243 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.647179  0.256317  2.028324   [DEG:  -37.0806   14.6859  116.2144 ]
ZXZ: -0.771363  2.012301 -0.284219   [DEG:  -44.1958  115.2963  -16.2845 ]
 
# END of job
