
#######################################################
#                                                     #
#                        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   45 (  355),  selected    7 , name one
# Molecule2: number of CA atoms    7 (   56),  selected    7 , 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:     7       5_B - 11_B        1.89     1.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       5_B - 11_B        1.89     1.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       6_B - 10_B        0.88     2.60
  LONGEST_CONTINUOUS_SEGMENT:     5       7_B - 11_B        0.97     2.58
  LCS_AVERAGE:     67.35

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:    7
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     E     5_B     E     5_B      3    7    7      3    3    3    4    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     M     6_B     M     6_B      5    7    7      3    5    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     T     7_B     T     7_B      5    7    7      3    5    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     L     8_B     L     8_B      5    7    7      3    4    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     K     9_B     K     9_B      5    7    7      3    5    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     F    10_B     F    10_B      5    7    7      3    5    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     G    11_B     G    11_B      5    7    7      3    5    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:  89.12  (  67.35  100.00  100.00 )

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      5      5      6      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_AT  42.86  71.43  71.43  85.71  85.71 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.08   0.70   0.70   1.02   1.02   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89
GDT RMS_ALL_AT   6.94   2.52   2.52   2.55   2.55   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E     5_B      E     5_B     2.681     0    0.624   1.044     9.565   63.333   35.979
LGA    M     6_B      M     6_B     1.841     0    0.627   1.132     8.862   79.405   48.214
LGA    T     7_B      T     7_B     2.136     0    0.149   0.212     6.174   69.048   50.136
LGA    L     8_B      L     8_B     1.943     0    0.172   0.327     8.426   86.429   51.488
LGA    K     9_B      K     9_B     1.839     0    0.152   0.217    10.035   81.548   46.825
LGA    F    10_B      F    10_B     1.443     0    0.029   1.354     8.880   85.952   45.758
LGA    G    11_B      G    11_B     0.735     0    0.646   0.646     2.369   81.786   81.786

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:        7      28     28  100.00      56     56  100.00                 7
SUMMARY(RMSD_GDC):     1.887          1.630                  3.753           78.214   51.455

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45    7    4.0      7    1.89    89.286    93.672     0.352

LGA_LOCAL      RMSD:   1.887  Number of atoms:    7  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.887  Number of assigned atoms:    7 
Std_ASGN_ATOMS RMSD:   1.887  Standard rmsd on all 7 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.250332 * X  +   0.823730 * Y  +   0.508727 * Z  +  -2.261625
  Y_new =  -0.934231 * X  +  -0.067634 * Y  +  -0.350198 * Z  +  38.141518
  Z_new =  -0.254061 * X  +  -0.562934 * Y  +   0.786484 * Z  + -29.065920 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.832601  0.256877 -0.621225   [DEG: -105.0003   14.7180  -35.5936 ]
ZXZ:  0.967911  0.665700 -2.717645   [DEG:   55.4572   38.1418 -155.7096 ]
 
# END of job
