
#######################################################
#                                                     #
#                        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        2.20     2.20
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       5_B - 10_B        1.76     2.57
  LONGEST_CONTINUOUS_SEGMENT:     6       6_B - 11_B        1.51     2.64
  LCS_AVERAGE:     85.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       7_B - 10_B        0.23     2.50
  LONGEST_CONTINUOUS_SEGMENT:     4       8_B - 11_B        1.00     3.71
  LCS_AVERAGE:     53.06

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    6    7      3    5    5    5    5    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     M     6_B     M     6_B      3    6    7      3    3    3    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     T     7_B     T     7_B      4    6    7      4    5    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     L     8_B     L     8_B      4    6    7      4    5    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     K     9_B     K     9_B      4    6    7      4    5    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     F    10_B     F    10_B      4    6    7      4    5    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     G    11_B     G    11_B      4    6    7      3    3    4    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:  79.59  (  53.06   85.71  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      4      5      5      5      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_AT  57.14  71.43  71.43  71.43  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    0.23   0.66   0.66   0.66   1.51   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20
GDT RMS_ALL_AT   2.50   2.89   2.89   2.89   2.64   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.20

# Checking swapping
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  F    10_B      F    10_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E     5_B      E     5_B     2.274     0    0.613   0.465     6.030   59.524   45.132
LGA    M     6_B      M     6_B     2.769     0    0.560   1.101     5.043   55.476   51.131
LGA    T     7_B      T     7_B     2.210     0    0.218   0.274     5.460   63.452   49.048
LGA    L     8_B      L     8_B     0.859     0    0.090   1.135     6.560   86.429   60.595
LGA    K     9_B      K     9_B     0.931     0    0.121   0.152    11.392   82.143   46.243
LGA    F    10_B      F    10_B     2.912     0    0.567   1.508     9.524   71.071   32.987
LGA    G    11_B      G    11_B     2.457     0    0.729   0.729     3.512   63.929   63.929

# 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):     2.199          2.167                  3.619           68.861   49.866

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45    7    4.0      7    2.20    85.714    89.098     0.305

LGA_LOCAL      RMSD:   2.199  Number of atoms:    7  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.199  Number of assigned atoms:    7 
Std_ASGN_ATOMS RMSD:   2.199  Standard rmsd on all 7 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.727549 * X  +   0.443684 * Y  +  -0.523274 * Z  +   0.985721
  Y_new =   0.679276 * X  +  -0.358909 * Y  +   0.640132 * Z  +  11.121203
  Z_new =   0.096209 * X  +  -0.821175 * Y  +  -0.562508 * Z  +  -2.339198 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.751098 -0.096358 -2.171387   [DEG:   43.0347   -5.5209 -124.4113 ]
ZXZ: -2.456303  2.168213  3.024965   [DEG: -140.7358  124.2294  173.3177 ]
 
# END of job
