
#######################################################
#                                                     #
#                        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   18 (  156),  selected   18 , name one
# Molecule2: number of CA atoms  473 ( 3591),  selected   18 , 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:    18     523_A - 540_A       0.97     0.97
  LCS_AVERAGE:      3.81

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18     523_A - 540_A       0.97     0.97
  LCS_AVERAGE:      3.81

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18     523_A - 540_A       0.97     0.97
  LCS_AVERAGE:      3.81

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   18
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     Y   523_A     Y   523_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     C   524_A     C   524_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     R   525_A     R   525_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     Q   526_A     Q   526_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     E   527_A     E   527_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     G   528_A     G   528_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     K   529_A     K   529_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     D   530_A     D   530_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     R   531_A     R   531_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     I   532_A     I   532_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     I   533_A     I   533_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     F   534_A     F   534_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     V   535_A     V   535_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     T   536_A     T   536_A     18   18   18      4   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     K   537_A     K   537_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     E   538_A     E   538_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     D   539_A     D   539_A     18   18   18     14   17   17   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     H   540_A     H   540_A     18   18   18      3    3    4    4    4   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_AVERAGE  LCS_A:   3.81  (   3.81    3.81    3.81 )

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     14     17     17     17     17     18     18     18     18     18     18     18     18     18     18     18     18     18     18     18 
GDT PERCENT_AT   2.96   3.59   3.59   3.59   3.59   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.81
GDT RMS_LOCAL    0.30   0.43   0.43   0.43   0.43   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97
GDT RMS_ALL_AT   1.03   1.06   1.06   1.06   1.06   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97

# Checking swapping
#   possible swapping detected:  Y   523_A      Y   523_A
#   possible swapping detected:  E   527_A      E   527_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y   523_A      Y   523_A     0.354     0    0.149   1.092     4.288   97.619   78.254
LGA    C   524_A      C   524_A     0.733     0    0.082   0.661     2.193   90.476   86.190
LGA    R   525_A      R   525_A     0.732     0    0.032   1.283     2.967   95.238   85.108
LGA    Q   526_A      Q   526_A     0.306     0    0.038   0.213     0.694  100.000   97.884
LGA    E   527_A      E   527_A     0.414     0    0.022   0.901     4.690  100.000   81.587
LGA    G   528_A      G   528_A     0.159     0    0.030   0.030     0.392  100.000  100.000
LGA    K   529_A      K   529_A     0.498     0    0.063   0.156     1.368   97.619   91.640
LGA    D   530_A      D   530_A     0.766     0    0.020   0.087     0.881   90.476   90.476
LGA    R   531_A      R   531_A     0.612     0    0.042   0.963     2.386   95.238   81.905
LGA    I   532_A      I   532_A     0.391     0    0.037   0.088     0.698  100.000   97.619
LGA    I   533_A      I   533_A     0.325     0    0.021   0.225     0.758  100.000   98.810
LGA    F   534_A      F   534_A     0.221     0    0.075   0.107     1.111   97.619   94.026
LGA    V   535_A      V   535_A     0.464     0    0.092   1.335     2.756   92.976   82.381
LGA    T   536_A      T   536_A     1.256     0    0.229   0.462     2.331   77.262   76.599
LGA    K   537_A      K   537_A     0.507     0    0.192   1.534     7.238   92.857   68.730
LGA    E   538_A      E   538_A     0.458     4    0.161   0.200     0.772   97.619   53.439
LGA    D   539_A      D   539_A     0.349     0    0.024   0.893     4.848   86.190   72.440
LGA    H   540_A      H   540_A     3.413     0    0.659   1.451     9.243   61.190   30.952

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       18      72     72  100.00     152    152  100.00               473
SUMMARY(RMSD_GDC):     0.973          0.898                  2.099            3.536    3.104

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   18  473    4.0     18    0.97     3.700     3.744     1.678

LGA_LOCAL      RMSD:   0.973  Number of atoms:   18  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.973  Number of assigned atoms:   18 
Std_ASGN_ATOMS RMSD:   0.973  Standard rmsd on all 18 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.500427 * X  +   0.863362 * Y  +   0.064643 * Z  + -35.781395
  Y_new =   0.805479 * X  +   0.491650 * Y  +  -0.330884 * Z  +  15.067124
  Z_new =  -0.317454 * X  +  -0.113515 * Y  +  -0.941455 * Z  + -11.887141 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.126715  0.323044 -3.021598   [DEG:  121.8518   18.5090 -173.1248 ]
ZXZ:  0.192934  2.797716 -1.914207   [DEG:   11.0543  160.2973 -109.6760 ]
 
# END of job
