
#######################################################
#                                                     #
#                        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 (   46),  selected    5 , name one
# Molecule2: number of CA atoms   41 (  336),  selected    5 , 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:     5       4_B - 8_B         2.41     2.41
  LCS_AVERAGE:     12.20

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       4_B - 7_B         0.79     3.45
  LCS_AVERAGE:      9.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       4_B - 7_B         0.79     3.45
  LCS_AVERAGE:      9.27

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     Q     4_B     Q     4_B      4    4    5      3    3    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     R     5_B     R     5_B      4    4    5      3    3    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     L     6_B     L     6_B      4    4    5      3    3    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     F     7_B     F     7_B      4    4    5      3    3    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     V     8_B     V     8_B      3    3    5      3    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:  10.24  (   9.27    9.27   12.20 )

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      4      4      4      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_AT   7.32   7.32   9.76   9.76   9.76   9.76   9.76  12.20  12.20  12.20  12.20  12.20  12.20  12.20  12.20  12.20  12.20  12.20  12.20  12.20
GDT RMS_LOCAL    0.20   0.20   0.79   0.79   0.79   0.79   0.79   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41
GDT RMS_ALL_AT   3.77   3.77   3.45   3.45   3.45   3.45   3.45   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q     4_B      Q     4_B     1.743     0    0.420   1.091     6.155   57.738   47.460
LGA    R     5_B      R     5_B     1.994     0    0.106   0.887     9.887   72.976   38.052
LGA    L     6_B      L     6_B     1.060     0    0.586   1.146     4.868   77.619   73.512
LGA    F     7_B      F     7_B     2.922     0    0.596   1.446     9.672   62.976   31.818
LGA    V     8_B      V     8_B     3.533     0    0.092   1.155     7.188   40.595   28.503

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:        5      20     20  100.00      46     46  100.00                41
SUMMARY(RMSD_GDC):     2.415          2.681                  4.406            7.607    5.350

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)    5   41    4.0      5    2.41    10.366    10.276     0.199

LGA_LOCAL      RMSD:   2.415  Number of atoms:    5  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.415  Number of assigned atoms:    5 
Std_ASGN_ATOMS RMSD:   2.415  Standard rmsd on all 5 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.386009 * X  +  -0.117404 * Y  +  -0.914993 * Z  + -13.689305
  Y_new =  -0.844690 * X  +   0.443671 * Y  +   0.299423 * Z  + -35.308758
  Z_new =   0.370803 * X  +   0.888466 * Y  +  -0.270431 * Z  +  -3.719720 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.999442 -0.379873  1.866266   [DEG: -114.5596  -21.7651  106.9292 ]
ZXZ: -1.887053  1.844637  0.395375   [DEG: -108.1202  105.6899   22.6533 ]
 
# END of job
