
#######################################################
#                                                     #
#                        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   40 (  327),  selected   32 , name one
# Molecule2: number of CA atoms   43 (  346),  selected   32 , 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:    20      16_B - 35_B        4.93     7.65
  LONGEST_CONTINUOUS_SEGMENT:    20      19_B - 38_B        4.96     8.35
  LONGEST_CONTINUOUS_SEGMENT:    20      20_B - 39_B        4.84     8.86
  LCS_AVERAGE:     45.93

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      16_B - 30_B        1.89     9.26
  LCS_AVERAGE:     25.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      16_B - 29_B        0.45    10.05
  LCS_AVERAGE:     22.53

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   32
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     T    16_B     T    16_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   16   19   24   27   30   30   30   30   30 
LCS_GDT     R    17_B     R    17_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   16   22   24   28   30   30   30   30   30 
LCS_GDT     R    18_B     R    18_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   16   22   24   28   30   30   30   30   30 
LCS_GDT     S    19_B     S    19_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   16   22   24   28   30   30   30   30   30 
LCS_GDT     N    20_B     N    20_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     Y    21_B     Y    21_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     A    22_B     A    22_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     A    23_B     A    23_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     S    24_B     S    24_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     L    25_B     L    25_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     R    26_B     R    26_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     L    27_B     L    27_B     14   15   20     12   14   14   14   14   14   15   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     E    28_B     E    28_B     14   15   20     11   14   14   14   14   14   15   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     G    29_B     G    29_B     14   15   20      4   14   14   14   14   14   15   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     F    30_B     F    30_B      4   15   20      3    3    4    5    6    7   10   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     K    31_B     K    31_B      4    6   20      3    3    4    4    6   12   15   16   16   16   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     V    32_B     V    32_B      8    9   20      5    7    8    8    9    9   10   11   13   15   16   16   18   21   26   30   30   30   30   30 
LCS_GDT     T    33_B     T    33_B      8    9   20      5    7    8    8    9    9   10   11   13   15   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     F    34_B     F    34_B      8    9   20      5    7    8    8    9    9   10   11   13   15   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     A    35_B     A    35_B      8    9   20      5    7    8    8    9    9   10   11   13   15   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     D    36_B     D    36_B      8    9   20      5    7    8    8    9    9   10   11   13   15   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     G    37_B     G    37_B      8    9   20      4    7    8    8    9    9   10   11   13   15   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     E    38_B     E    38_B      8    9   20      4    7    8    8    9    9   10   11   13   15   16   18   22   24   28   30   30   30   30   30 
LCS_GDT     R    39_B     R    39_B      8    9   20      4    6    8    8    9    9   10   11   12   15   16   17   20   23   28   30   30   30   30   30 
LCS_GDT     K    40_B     K    40_B      6    9   19      4    5    6    6    6    9    9   10   11   12   13   13   13   15   17   19   22   27   29   29 
LCS_GDT     M    41_B     M    41_B      6    7   19      5    5    6    6    9    9   10   11   13   15   16   16   19   24   28   30   30   30   30   30 
LCS_GDT     P    42_B     P    42_B      6    7   19      5    5    6    6    7    9   10   11   13   15   16   16   17   23   28   30   30   30   30   30 
LCS_GDT     T    43_B     T    43_B      6    7   19      5    5    6    6    6    7   10   11   13   15   16   16   22   24   28   30   30   30   30   30 
LCS_GDT     R    44_B     R    44_B      6    7   19      5    5    6    6    6    7   10   11   13   15   16   16   21   24   28   30   30   30   30   30 
LCS_GDT     E    45_B     E    45_B      6    7   19      5    5    6    6    6    7   10   11   13   15   16   16   21   23   28   30   30   30   30   30 
LCS_GDT     E    46_B     E    46_B      3    7   19      3    3    3    3    4    6   10   11   13   15   16   16   18   23   28   30   30   30   30   30 
LCS_GDT     V    47_B     V    47_B      3    3   19      3    3    3    3    3    3    4    5    7    8   13   16   16   17   17   18   21   22   23   25 
LCS_AVERAGE  LCS_A:  31.47  (  22.53   25.94   45.93 )

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     12     14     14     14     14     14     15     16     16     16     16     18     22     24     28     30     30     30     30     30 
GDT PERCENT_AT  27.91  32.56  32.56  32.56  32.56  32.56  34.88  37.21  37.21  37.21  37.21  41.86  51.16  55.81  65.12  69.77  69.77  69.77  69.77  69.77
GDT RMS_LOCAL    0.31   0.45   0.45   0.45   0.45   0.45   1.80   2.27   2.27   2.27   2.27   4.57   5.31   5.53   6.12   6.24   6.24   6.24   6.24   6.24
GDT RMS_ALL_AT  10.17  10.05  10.05  10.05  10.05  10.05   9.14   8.89   8.89   8.89   8.89   8.51   7.44   7.28   6.94   6.95   6.95   6.95   6.95   6.95

# Checking swapping
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  E    46_B      E    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T    16_B      T    16_B     1.007     0    0.169   1.067     3.545   81.429   75.986
LGA    R    17_B      R    17_B     1.662     0    0.068   1.162     8.788   72.857   44.156
LGA    R    18_B      R    18_B     1.623     0    0.017   0.871     6.252   75.000   50.476
LGA    S    19_B      S    19_B     0.902     0    0.019   0.694     3.134   88.214   82.222
LGA    N    20_B      N    20_B     0.584     0    0.060   0.327     1.819   90.476   86.012
LGA    Y    21_B      Y    21_B     1.382     0    0.023   1.174    10.133   81.429   43.571
LGA    A    22_B      A    22_B     1.874     0    0.020   0.021     2.175   72.857   71.238
LGA    A    23_B      A    23_B     1.372     0    0.039   0.037     1.502   79.286   79.714
LGA    S    24_B      S    24_B     0.502     0    0.080   0.090     0.976   92.857   92.063
LGA    L    25_B      L    25_B     1.455     0    0.066   0.063     2.919   79.405   71.131
LGA    R    26_B      R    26_B     2.498     0    0.019   0.892     8.903   64.881   40.043
LGA    L    27_B      L    27_B     2.018     0    0.059   0.184     2.495   70.833   68.810
LGA    E    28_B      E    28_B     0.660     0    0.024   0.574     2.058   88.214   84.709
LGA    G    29_B      G    29_B     1.586     0    0.620   0.620     1.586   79.286   79.286
LGA    F    30_B      F    30_B     5.478     0    0.065   1.198    11.873   31.786   12.121
LGA    K    31_B      K    31_B     4.715     0    0.177   0.958     8.909   17.619   23.862
LGA    V    32_B      V    32_B    11.146     0    0.645   1.165    15.020    0.714    0.408
LGA    T    33_B      T    33_B    11.148     0    0.009   0.017    12.296    0.000    0.000
LGA    F    34_B      F    34_B    12.481     0    0.035   1.316    16.347    0.000    0.000
LGA    A    35_B      A    35_B    13.921     0    0.071   0.078    14.641    0.000    0.000
LGA    D    36_B      D    36_B    12.513     0    0.091   0.965    12.806    0.000    0.000
LGA    G    37_B      G    37_B    12.086     0    0.102   0.102    12.357    0.000    0.000
LGA    E    38_B      E    38_B    13.277     0    0.146   1.270    18.003    0.000    0.000
LGA    R    39_B      R    39_B    14.368     0    0.573   1.510    18.261    0.000    0.000
LGA    K    40_B      K    40_B    16.232     0    0.604   0.995    22.138    0.000    0.000
LGA    M    41_B      M    41_B    11.354     0    0.073   0.674    13.362    0.000    0.774
LGA    P    42_B      P    42_B    11.017     0    0.041   0.044    11.285    0.833    0.476
LGA    T    43_B      T    43_B     9.355     0    0.035   0.062    11.899    1.429    0.816
LGA    R    44_B      R    44_B     8.059     0    0.588   1.012    15.116    3.690    1.775
LGA    E    45_B      E    45_B     8.985     0    0.479   1.168    11.918    2.500    3.598
LGA    E    46_B      E    46_B    10.845     0    0.588   1.081    15.332    0.119    0.053
LGA    V    47_B      V    47_B    17.240     0    0.475   1.390    18.905    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       32     128    128  100.00     260    260  100.00                43
SUMMARY(RMSD_GDC):     6.900          6.882                  7.954           27.342   23.565

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   40   43    4.0     16    2.27    43.023    35.750     0.674

LGA_LOCAL      RMSD:   2.274  Number of atoms:   16  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.888  Number of assigned atoms:   32 
Std_ASGN_ATOMS RMSD:   6.900  Standard rmsd on all 32 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.098177 * X  +  -0.941389 * Y  +   0.322719 * Z  +  23.003723
  Y_new =  -0.669680 * X  +   0.177379 * Y  +   0.721156 * Z  + -30.694534
  Z_new =  -0.736132 * X  +  -0.286919 * Y  +  -0.613015 * Z  +  60.772339 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.425230  0.827338 -2.703833   [DEG:  -81.6597   47.4030 -154.9182 ]
ZXZ:  2.720818  2.230667 -1.942449   [DEG:  155.8914  127.8078 -111.2941 ]
 
# END of job
