
#######################################################
#                                                     #
#                        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    5 (   35),  selected    5 , name one
# Molecule2: number of CA atoms   63 (  472),  selected    5 , 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:     5      39_A - 43_A        2.39     2.39
  LCS_AVERAGE:      7.94

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4      39_A - 42_A        1.50     3.61
  LONGEST_CONTINUOUS_SEGMENT:     4      40_A - 43_A        1.85     2.91
  LCS_AVERAGE:      6.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3      39_A - 41_A        0.55     5.75
  LONGEST_CONTINUOUS_SEGMENT:     3      40_A - 42_A        0.75     3.76
  LONGEST_CONTINUOUS_SEGMENT:     3      41_A - 43_A        0.07     6.06
  LCS_AVERAGE:      4.76

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:    5
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     G    39_A     G    39_A      3    4    5      0    3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     T    40_A     T    40_A      3    4    5      3    3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     Y    41_A     Y    41_A      3    4    5      3    3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     G    42_A     G    42_A      3    4    5      3    3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     N    43_A     N    43_A      3    4    5      3    3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   6.35  (   4.76    6.35    7.94 )

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      3      3      3      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_AT   4.76   4.76   4.76   4.76   6.35   7.94   7.94   7.94   7.94   7.94   7.94   7.94   7.94   7.94   7.94   7.94   7.94   7.94   7.94   7.94
GDT RMS_LOCAL    0.07   0.07   0.07   0.07   1.50   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39
GDT RMS_ALL_AT   6.06   6.06   6.06   6.06   3.61   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G    39_A      G    39_A     2.788     0    0.068   0.068     4.702   50.833   50.833
LGA    T    40_A      T    40_A     1.584     0    0.320   1.313     5.791   70.952   52.653
LGA    Y    41_A      Y    41_A     2.223     0    0.589   1.486     7.423   73.571   38.849
LGA    G    42_A      G    42_A     2.485     0    0.143   0.143     3.110   67.262   67.262
LGA    N    43_A      N    43_A     2.677     0    0.671   0.949     8.460   67.143   44.762

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:        5      20     20  100.00      35     35  100.00                63
SUMMARY(RMSD_GDC):     2.390          2.257                  3.389            5.234    4.037

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)    5   63    4.0      5    2.39     6.349     6.725     0.201

LGA_LOCAL      RMSD:   2.390  Number of atoms:    5  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.390  Number of assigned atoms:    5 
Std_ASGN_ATOMS RMSD:   2.390  Standard rmsd on all 5 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.775809 * X  +   0.279826 * Y  +  -0.565525 * Z  +   6.210752
  Y_new =   0.125735 * X  +  -0.809743 * Y  +  -0.573156 * Z  +  -6.978205
  Z_new =  -0.618314 * X  +  -0.515765 * Y  +   0.593021 * Z  + -32.677242 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.980920  0.666595 -0.715834   [DEG:  170.7941   38.1931  -41.0143 ]
ZXZ: -0.778697  0.935990 -2.266016   [DEG:  -44.6160   53.6283 -129.8331 ]
 
# END of job
