
#######################################################
#                                                     #
#                        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        1.86     1.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       5_B - 11_B        1.86     1.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       5_B - 8_B         0.98     3.86
  LONGEST_CONTINUOUS_SEGMENT:     4       7_B - 10_B        0.60     3.89
  LONGEST_CONTINUOUS_SEGMENT:     4       8_B - 11_B        0.96     4.77
  LCS_AVERAGE:     57.14

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      4    7    7      3    3    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     M     6_B     M     6_B      4    7    7      3    3    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      4    7    7      3    4    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      4    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      4    7    7      3    4    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      4    7    7      3    4    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      4    7    7      3    3    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:  85.71  (  57.14  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      4      5      6      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_AT  42.86  57.14  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    0.22   0.60   1.05   1.52   1.52   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86
GDT RMS_ALL_AT   5.73   3.89   3.45   3.16   3.16   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E     5_B      E     5_B     1.838     0    0.024   1.019     6.645   75.119   52.011
LGA    M     6_B      M     6_B     0.815     0    0.213   1.526     6.852   86.071   64.940
LGA    T     7_B      T     7_B     1.262     0    0.106   0.176     4.168   83.810   68.503
LGA    L     8_B      L     8_B     2.723     0    0.155   0.236     9.254   73.214   42.321
LGA    K     9_B      K     9_B     2.773     0    0.295   0.651    10.167   69.048   36.032
LGA    F    10_B      F    10_B     1.502     0    0.060   1.352     9.200   75.119   39.870
LGA    G    11_B      G    11_B     1.159     0    0.619   0.619     3.319   67.500   67.500

# 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):     1.865          1.707                  4.106           75.697   53.025

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45    7    4.0      7    1.86    85.714    92.544     0.356

LGA_LOCAL      RMSD:   1.865  Number of atoms:    7  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.865  Number of assigned atoms:    7 
Std_ASGN_ATOMS RMSD:   1.865  Standard rmsd on all 7 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.649273 * X  +   0.262232 * Y  +   0.713918 * Z  +  -9.793861
  Y_new =  -0.760180 * X  +   0.253248 * Y  +   0.598325 * Z  +  29.605299
  Z_new =  -0.023898 * X  +  -0.931182 * Y  +   0.363770 * Z  + -27.337299 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.863924  0.023901 -1.198372   [DEG:  -49.4992    1.3694  -68.6617 ]
ZXZ:  2.268333  1.198484 -3.115934   [DEG:  129.9659   68.6681 -178.5298 ]
 
# END of job
