
#######################################################
#                                                     #
#                        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   13 (   92),  selected   13 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   13 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        2.05     2.05
  LCS_AVERAGE:     26.53

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      21_F - 32_F        1.95     2.13
  LCS_AVERAGE:     24.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      22_F - 27_F        0.96     6.72
  LCS_AVERAGE:     10.83

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   13
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     D    21_F     D    21_F      5   12   13      3    5    7   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     T    22_F     T    22_F      6   12   13      3    5    7   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     L    23_F     L    23_F      6   12   13      3    5    7   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     G    24_F     G    24_F      6   12   13      3    5    7   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     S    25_F     S    25_F      6   12   13      3    5    7   10   11   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     D    26_F     D    26_F      6   12   13      4    5    7   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     A    27_F     A    27_F      6   12   13      4    5    7   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     V    28_F     V    28_F      5   12   13      4    5    7   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     I    29_F     I    29_F      5   12   13      4    5    7   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     M    30_F     M    30_F      5   12   13      4    5    7   10   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     S    31_F     S    31_F      5   12   13      3    4    5    8   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     N    32_F     N    32_F      4   12   13      3    5    7    8   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     K    33_F     K    33_F      4    9   13      3    4    7    8   12   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:  20.46  (  10.83   24.02   26.53 )

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      7     10     12     12     13     13     13     13     13     13     13     13     13     13     13     13     13     13 
GDT PERCENT_AT   8.16  10.20  14.29  20.41  24.49  24.49  26.53  26.53  26.53  26.53  26.53  26.53  26.53  26.53  26.53  26.53  26.53  26.53  26.53  26.53
GDT RMS_LOCAL    0.12   0.38   1.00   1.50   1.84   1.84   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05
GDT RMS_ALL_AT   7.92   7.93   2.55   3.02   2.11   2.11   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05

# Checking swapping
#   possible swapping detected:  D    26_F      D    26_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D    21_F      D    21_F     1.003     0    0.024   0.821     4.387   77.262   67.738
LGA    T    22_F      T    22_F     1.060     0    0.256   0.274     1.701   90.595   85.442
LGA    L    23_F      L    23_F     1.279     0    0.170   1.069     4.329   81.429   70.714
LGA    G    24_F      G    24_F     2.087     0    0.134   0.134     3.082   61.190   61.190
LGA    S    25_F      S    25_F     3.411     0    0.220   0.244     4.318   51.905   46.984
LGA    D    26_F      D    26_F     1.863     0    0.232   1.374     5.922   71.071   54.524
LGA    A    27_F      A    27_F     1.567     0    0.056   0.076     3.197   84.048   77.238
LGA    V    28_F      V    28_F     1.882     0    0.033   0.061     5.167   69.286   53.946
LGA    I    29_F      I    29_F     1.709     0    0.099   0.468     5.673   83.810   59.405
LGA    M    30_F      M    30_F     2.500     0    0.611   0.527     7.060   57.500   41.429
LGA    S    31_F      S    31_F     2.150     0    0.194   0.505     5.564   61.429   51.746
LGA    N    32_F      N    32_F     2.274     0    0.278   1.221     4.740   58.690   48.869
LGA    K    33_F      K    33_F     2.550     0    0.668   1.399    10.107   43.690   35.291

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       13      52     52  100.00      92     92  100.00                49
SUMMARY(RMSD_GDC):     2.051          2.327                  3.298           18.202   15.398

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   13   49    4.0     13    2.05    20.918    23.012     0.604

LGA_LOCAL      RMSD:   2.051  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.051  Number of assigned atoms:   13 
Std_ASGN_ATOMS RMSD:   2.051  Standard rmsd on all 13 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.905174 * X  +   0.319628 * Y  +  -0.280174 * Z  +  41.197834
  Y_new =   0.387261 * X  +  -0.891862 * Y  +   0.233690 * Z  + -70.562309
  Z_new =  -0.175183 * X  +  -0.320031 * Y  +  -0.931070 * Z  +   1.954645 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.404265  0.176092 -2.810520   [DEG:   23.1627   10.0893 -161.0310 ]
ZXZ: -2.265979  2.768131 -2.640752   [DEG: -129.8311  158.6022 -151.3039 ]
 
# END of job
