
#######################################################
#                                                     #
#                        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   35 (  259),  selected   12 , name one
# Molecule2: number of CA atoms  260 ( 2048),  selected   12 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      46_B - 57_B        4.06     4.06
  LCS_AVERAGE:      4.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      46_B - 54_B        1.95     5.48
  LONGEST_CONTINUOUS_SEGMENT:     9      47_B - 55_B        1.49     4.73
  LONGEST_CONTINUOUS_SEGMENT:     9      48_B - 56_B        1.89     4.49
  LCS_AVERAGE:      3.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      47_B - 53_B        0.97     5.62
  LONGEST_CONTINUOUS_SEGMENT:     7      48_B - 54_B        0.94     4.97
  LCS_AVERAGE:      2.24

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   12
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     N    46_A     N    46_B      4    9   12      3    3    5    5    6    6    8    8   10   10   10   11   11   11   11   11   11   12   12   12 
LCS_GDT     P    47_A     P    47_B      7    9   12      3    4    7    7    8    9    9   10   10   10   10   11   11   11   11   11   11   12   12   12 
LCS_GDT     D    48_A     D    48_B      7    9   12      4    5    7    8    8    9    9   10   10   10   10   11   11   11   11   11   11   12   12   12 
LCS_GDT     G    49_A     G    49_B      7    9   12      4    5    7    8    8    9    9   10   10   10   10   11   11   11   11   11   11   12   12   12 
LCS_GDT     T    50_A     T    50_B      7    9   12      3    5    7    8    8    9    9   10   10   10   10   11   11   11   11   11   11   12   12   12 
LCS_GDT     L    51_A     L    51_B      7    9   12      4    5    7    8    8    9    9   10   10   10   10   11   11   11   11   11   11   12   12   12 
LCS_GDT     T    52_A     T    52_B      7    9   12      4    5    7    8    8    9    9   10   10   10   10   11   11   11   11   11   11   12   12   12 
LCS_GDT     I    53_A     I    53_B      7    9   12      4    5    7    8    8    9    9   10   10   10   10   11   11   11   11   11   11   12   12   12 
LCS_GDT     T    54_A     T    54_B      7    9   12      0    5    7    8    8    9    9   10   10   10   10   11   11   11   11   11   11   12   12   12 
LCS_GDT     F    55_A     F    55_B      4    9   12      0    3    7    8    8    9    9   10   10   10   10   11   11   11   11   11   11   12   12   12 
LCS_GDT     D    56_A     D    56_B      3    9   12      0    3    3    4    5    7    9   10   10   10   10   11   11   11   11   11   11   12   12   12 
LCS_GDT     D    57_A     D    57_B      3    3   12      0    3    3    3    3    5    5    6    7    8    9    9    9   10   10   10   10   12   12   12 
LCS_AVERAGE  LCS_A:   3.38  (   2.24    3.27    4.62 )

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      7      8      8      9      9     10     10     10     10     11     11     11     11     11     11     12     12     12 
GDT PERCENT_AT   1.54   1.92   2.69   3.08   3.08   3.46   3.46   3.85   3.85   3.85   3.85   4.23   4.23   4.23   4.23   4.23   4.23   4.62   4.62   4.62
GDT RMS_LOCAL    0.21   0.36   0.94   1.16   1.16   1.49   1.49   2.26   2.11   2.11   2.11   2.80   2.80   2.80   2.80   2.80   2.80   4.06   4.06   4.06
GDT RMS_ALL_AT   5.10   5.13   4.97   4.65   4.65   4.73   4.73   4.30   4.97   4.97   4.97   4.36   4.36   4.36   4.36   4.36   4.36   4.06   4.06   4.06

# Checking swapping
#   possible swapping detected:  D    48_A      D    48_B
#   possible swapping detected:  F    55_A      F    55_B
#   possible swapping detected:  D    56_A      D    56_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    N    46_A      N    46_B     6.616     0    0.620   0.700    12.071   22.976   11.845
LGA    P    47_A      P    47_B     3.620     0    0.564   0.566     6.284   55.119   44.150
LGA    D    48_A      D    48_B     1.372     0    0.303   0.883     4.545   65.595   57.083
LGA    G    49_A      G    49_B     0.705     0    0.322   0.322     2.025   79.524   79.524
LGA    T    50_A      T    50_B     1.791     0    0.169   1.141     3.629   79.286   68.912
LGA    L    51_A      L    51_B     0.718     0    0.220   0.518     3.492   92.976   77.202
LGA    T    52_A      T    52_B     1.170     0    0.000   0.140     2.068   81.548   76.667
LGA    I    53_A      I    53_B     1.746     0    0.177   1.125     3.715   70.833   68.155
LGA    T    54_A      T    54_B     1.830     0    0.669   0.542     4.059   61.905   66.599
LGA    F    55_A      F    55_B     1.218     0    0.722   1.215     3.423   69.405   72.944
LGA    D    56_A      D    56_B     4.735     0    0.667   0.888     7.915   22.976   22.381
LGA    D    57_A      D    57_B    11.278     0    0.674   1.276    13.578    0.714    0.357

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       12      48     48  100.00      91     91  100.00               260
SUMMARY(RMSD_GDC):     4.057          4.116                  4.844            2.703    2.484

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35  260    4.0     10    2.26     3.269     3.380     0.425

LGA_LOCAL      RMSD:   2.256  Number of atoms:   10  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.300  Number of assigned atoms:   12 
Std_ASGN_ATOMS RMSD:   4.057  Standard rmsd on all 12 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.840757 * X  +   0.129965 * Y  +  -0.525582 * Z  + 322.267456
  Y_new =   0.541071 * X  +   0.236148 * Y  +  -0.807140 * Z  +  27.175241
  Z_new =   0.019216 * X  +  -0.962987 * Y  +  -0.268864 * Z  + 150.108780 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.569763 -0.019217 -1.843061   [DEG:  147.2366   -1.1010 -105.5996 ]
ZXZ: -0.577194  1.843009  3.121641   [DEG:  -33.0708  105.5967  178.8569 ]
 
# END of job
