
#######################################################
#                                                     #
#                        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   30 (  246),  selected   30 , name one
# Molecule2: number of CA atoms  198 ( 1543),  selected   30 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      48_A - 65_A        4.80    19.51
  LONGEST_CONTINUOUS_SEGMENT:    18      49_A - 66_A        4.93    17.25
  LONGEST_CONTINUOUS_SEGMENT:    18      50_A - 67_A        4.89    15.75
  LONGEST_CONTINUOUS_SEGMENT:    18      52_A - 69_A        4.94    14.38
  LCS_AVERAGE:      8.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      69_A - 77_A        1.27    19.72
  LCS_AVERAGE:      3.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8      70_A - 77_A        0.93    19.99
  LCS_AVERAGE:      2.79

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   30
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    48_A     E    48_A      3    3   18      0    3    4    6    6    6    9   10   12   14   15   15   17   17   17   17   17   18   18   19 
LCS_GDT     T    49_A     T    49_A      3    3   18      0    3    4    6    6    6    9   10   12   14   15   15   17   18   19   19   21   21   21   21 
LCS_GDT     F    50_A     F    50_A      3    8   18      2    3    5    6    6    7    9   10   12   14   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     K    51_A     K    51_A      4    8   18      2    4    4    5    7    7    8    9   10   14   15   15   17   18   19   19   21   21   21   21 
LCS_GDT     K    52_A     K    52_A      4    8   18      1    4    5    6    7    7    8   10   12   14   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     G    53_A     G    53_A      5    8   18      4    5    5    6    7    7    8   10   12   14   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     V    54_A     V    54_A      5    8   18      4    5    5    6    7    7    9   10   12   14   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     F    55_A     F    55_A      5    8   18      4    5    5    6    7    7    9   10   12   14   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     P    56_A     P    56_A      5    8   18      4    5    5    6    7    7    8   10   12   14   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     N    57_A     N    57_A      5    8   18      3    5    5    6    7    7    8   10   10   14   15   15   17   17   19   19   21   21   21   21 
LCS_GDT     N    58_A     N    58_A      3    5   18      3    3    4    6    6    7    9   10   12   14   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     K    59_A     K    59_A      4    7   18      3    3    5    5    7    8    9   10   12   14   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     R    60_A     R    60_A      4    7   18      3    3    5    5    7    8    9   10   12   14   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     E    61_A     E    61_A      4    7   18      3    3    5    5    7    9   10   10   12   14   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     K    62_A     K    62_A      4    7   18      3    3    5    6    7    9   10   10   12   13   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     S    63_A     S    63_A      5    8   18      3    4    7    8    8    9   10   10   12   13   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     D    64_A     D    64_A      6    8   18      3    5    7    8    8    9   10   10   12   13   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     I    65_A     I    65_A      6    8   18      3    5    7    8    8    9   10   10   11   13   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     L    66_A     L    66_A      6    8   18      3    5    7    8    8    9   10   10   11   13   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     V    67_A     V    67_A      6    8   18      3    5    7    8    8    9   10   10   11   13   15   16   17   18   19   19   21   21   21   21 
LCS_GDT     F    68_A     F    68_A      6    8   18      3    5    7    8    8    9   10   10   10   12   13   15   17   18   18   19   21   21   21   21 
LCS_GDT     H    69_A     H    69_A      6    9   18      3    5    7    9    9    9   10   10   10   12   13   15   17   18   18   19   21   21   21   21 
LCS_GDT     N    70_A     N    70_A      8    9   14      4    7    7    9    9    9   10   10   10   11   12   13   13   13   14   16   17   19   21   21 
LCS_GDT     G    71_A     G    71_A      8    9   14      6    7    7    9    9    9    9   10   10   11   12   13   13   13   14   16   17   18   20   21 
LCS_GDT     E    72_A     E    72_A      8    9   14      6    7    7    9    9    9    9   10   10   11   11   12   12   13   13   14   14   14   16   18 
LCS_GDT     V    73_A     V    73_A      8    9   14      6    7    7    9    9    9    9    9   10   11   11   12   12   12   12   13   13   14   15   16 
LCS_GDT     K    74_A     K    74_A      8    9   13      6    7    7    9    9    9    9    9   10   11   11   12   12   12   12   13   13   14   14   16 
LCS_GDT     T    75_A     T    75_A      8    9   13      3    4    7    9    9    9    9    9   10   11   11   11   11   12   12   13   13   14   14   16 
LCS_GDT     E    76_A     E    76_A      8    9   13      6    7    7    9    9    9    9    9   10   11   11   11   11   12   12   13   13   14   14   16 
LCS_GDT     T    77_A     T    77_A      8    9   13      6    7    7    9    9    9    9    9   10   11   11   11   11   11   12   13   13   14   14   16 
LCS_AVERAGE  LCS_A:   5.06  (   2.79    3.91    8.48 )

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      6      7      7      9      9      9     10     10     12     14     15     16     17     18     19     19     21     21     21     21 
GDT PERCENT_AT   3.03   3.54   3.54   4.55   4.55   4.55   5.05   5.05   6.06   7.07   7.58   8.08   8.59   9.09   9.60   9.60  10.61  10.61  10.61  10.61
GDT RMS_LOCAL    0.27   0.49   0.49   1.27   1.27   1.27   2.30   2.30   3.12   3.63   3.77   4.30   4.28   4.86   5.11   5.11   5.65   5.65   5.65   5.65
GDT RMS_ALL_AT  20.33  20.83  20.83  19.72  19.72  19.72  19.68  19.68  21.29  21.73  21.45  15.19  20.43  14.38  16.34  16.34  15.22  15.22  15.22  15.22

# Checking swapping
#   possible swapping detected:  E    48_A      E    48_A
#   possible swapping detected:  D    64_A      D    64_A
#   possible swapping detected:  F    68_A      F    68_A
#   possible swapping detected:  E    72_A      E    72_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E    48_A      E    48_A    10.483     0    0.569   1.112    13.573    0.119    3.757
LGA    T    49_A      T    49_A    12.762     0    0.623   0.575    14.771    0.000    0.000
LGA    F    50_A      F    50_A    16.402     0    0.634   1.350    20.873    0.000    0.000
LGA    K    51_A      K    51_A    22.078     0    0.599   1.308    24.496    0.000    0.000
LGA    K    52_A      K    52_A    26.365     0    0.611   1.046    33.172    0.000    0.000
LGA    G    53_A      G    53_A    28.288     0    0.643   0.643    28.750    0.000    0.000
LGA    V    54_A      V    54_A    26.888     0    0.008   1.306    27.123    0.000    0.000
LGA    F    55_A      F    55_A    25.285     0    0.062   1.345    34.652    0.000    0.000
LGA    P    56_A      P    56_A    20.677     0    0.612   0.598    22.126    0.000    0.000
LGA    N    57_A      N    57_A    21.673     0    0.586   1.559    24.664    0.000    0.000
LGA    N    58_A      N    58_A    20.308     0    0.297   0.370    24.009    0.000    0.000
LGA    K    59_A      K    59_A    15.503     0    0.041   0.682    21.307    0.000    0.000
LGA    R    60_A      R    60_A     9.889     0    0.287   0.950    14.474    5.952    2.165
LGA    E    61_A      E    61_A     2.846     0    0.111   1.301     5.500   52.143   51.217
LGA    K    62_A      K    62_A     2.516     0    0.229   0.926     8.084   61.190   35.820
LGA    S    63_A      S    63_A     1.558     0    0.618   0.791     3.807   67.857   64.365
LGA    D    64_A      D    64_A     3.298     0    0.024   0.870     8.393   67.262   38.750
LGA    I    65_A      I    65_A     1.140     0    0.097   0.138     7.646   75.476   50.595
LGA    L    66_A      L    66_A     2.076     0    0.095   1.430     8.677   65.595   38.988
LGA    V    67_A      V    67_A     1.849     0    0.080   1.058     6.478   84.048   59.524
LGA    F    68_A      F    68_A     2.835     0    0.024   0.793    10.347   57.619   25.108
LGA    H    69_A      H    69_A     2.133     0    0.582   1.270     9.775   79.524   38.333
LGA    N    70_A      N    70_A     1.906     0    0.464   0.997     6.403   52.143   44.048
LGA    G    71_A      G    71_A     8.135     0    0.070   0.070     9.848    8.214    8.214
LGA    E    72_A      E    72_A    14.570     0    0.054   0.836    18.402    0.000    0.000
LGA    V    73_A      V    73_A    20.399     0    0.097   1.072    23.334    0.000    0.000
LGA    K    74_A      K    74_A    27.875     0    0.305   0.303    30.623    0.000    0.000
LGA    T    75_A      T    75_A    31.995     0    0.051   0.095    34.987    0.000    0.000
LGA    E    76_A      E    76_A    38.822     0    0.016   1.086    40.774    0.000    0.000
LGA    T    77_A      T    77_A    45.096     0    0.733   1.020    47.913    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       30     120    120  100.00     246    246  100.00               198
SUMMARY(RMSD_GDC):    11.961         11.898                 12.969            3.420    2.328

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   30  198    4.0     10    2.30     5.682     5.316     0.416

LGA_LOCAL      RMSD:   2.302  Number of atoms:   10  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  19.684  Number of assigned atoms:   30 
Std_ASGN_ATOMS RMSD:  11.961  Standard rmsd on all 30 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.937789 * X  +  -0.330495 * Y  +   0.106416 * Z  + -12.735942
  Y_new =   0.316009 * X  +   0.939425 * Y  +   0.132740 * Z  +  -4.005859
  Z_new =  -0.143840 * X  +  -0.090853 * Y  +   0.985422 * Z  + -36.619263 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.325022  0.144340 -0.091938   [DEG:   18.6224    8.2701   -5.2676 ]
ZXZ:  2.465822  0.170961 -2.134148   [DEG:  141.2812    9.7954 -122.2777 ]
 
# END of job
