
#######################################################
#                                                     #
#                        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   34 (  238),  selected   34 , name one
# Molecule2: number of CA atoms   34 (  235),  selected   34 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       2_A - 34_A        4.33     5.21
  LCS_AVERAGE:     95.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_A - 34_A        1.44     5.91
  LCS_AVERAGE:     80.28

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       6_A - 34_A        0.91     6.18
  LCS_AVERAGE:     74.83

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   34
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     S     1_B     S     1_A      3    5   14      3    3    3    4    5    5    6    6    7    8    8    8    9   11   12   16   19   20   20   20 
LCS_GDT     G     2_B     G     2_A      3    5   33      3    3    3    4    5    5    6    8    9   10   11   15   15   17   19   21   25   27   32   33 
LCS_GDT     P     3_B     P     3_A      6    9   33      3    5    6    7    8    9    9   10   10   13   16   16   22   28   29   31   32   32   32   33 
LCS_GDT     N     4_B     N     4_A      6    9   33      0    5    6    7    8    9   12   18   24   25   27   30   31   31   31   31   32   32   32   33 
LCS_GDT     G     5_B     G     5_A      6   30   33      4    5    9   14   23   26   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     G     6_B     G     6_A     29   30   33      4    4   19   25   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     V     7_B     V     7_A     29   30   33      4   24   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     C     8_B     C     8_A     29   30   33      7   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     P     9_B     P     9_A     29   30   33      9   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     V    10_B     V    10_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     L    11_B     L    11_A     29   30   33      3   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     I    12_B     I    12_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     Y    13_B     Y    13_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     L    14_B     L    14_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     C    15_B     C    15_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     R    16_B     R    16_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     R    17_B     R    17_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     D    18_B     D    18_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     S    19_B     S    19_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     D    20_B     D    20_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     C    21_B     C    21_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     P    22_B     P    22_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     G    23_B     G    23_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     E    24_B     E    24_A     29   30   33      9   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     C    25_B     C    25_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     I    26_B     I    26_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     C    27_B     C    27_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     L    28_B     L    28_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     G    29_B     G    29_A     29   30   33     12   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     N    30_B     N    30_A     29   30   33      4   11   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     G    31_B     G    31_A     29   30   33     15   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     Y    32_B     Y    32_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     C    33_B     C    33_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_GDT     G    34_B     G    34_A     29   30   33     20   26   28   28   29   29   29   30   30   30   30   30   31   31   31   31   32   32   32   33 
LCS_AVERAGE  LCS_A:  83.51  (  74.83   80.28   95.42 )

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     20     26     28     28     29     29     29     30     30     30     30     30     31     31     31     31     32     32     32     33 
GDT PERCENT_AT  58.82  76.47  82.35  82.35  85.29  85.29  85.29  88.24  88.24  88.24  88.24  88.24  91.18  91.18  91.18  91.18  94.12  94.12  94.12  97.06
GDT RMS_LOCAL    0.32   0.51   0.66   0.66   0.91   0.91   0.91   1.44   1.44   1.44   1.44   1.44   2.41   2.41   2.41   2.41   3.44   3.44   3.44   4.33
GDT RMS_ALL_AT   6.18   6.28   6.32   6.32   6.18   6.18   6.18   5.91   5.91   5.91   5.91   5.91   5.60   5.60   5.60   5.60   5.35   5.35   5.35   5.21

# Checking swapping
#   possible swapping detected:  Y    32_B      Y    32_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A    19.923     0    0.181   0.610    23.378    0.000    0.000
LGA    G     2_B      G     2_A    18.232     0    0.707   0.707    18.232    0.000    0.000
LGA    P     3_B      P     3_A    16.173     0    0.348   0.425    16.638    0.000    0.000
LGA    N     4_B      N     4_A    11.578     0    0.194   0.767    13.418    0.714    0.536
LGA    G     5_B      G     5_A     5.620     0    0.554   0.554     7.715   28.810   28.810
LGA    G     6_B      G     6_A     2.464     0    0.166   0.166     3.514   61.667   61.667
LGA    V     7_B      V     7_A     2.512     0    0.034   1.083     5.708   64.881   49.932
LGA    C     8_B      C     8_A     1.759     0    0.036   0.071     2.216   72.976   74.365
LGA    P     9_B      P     9_A     1.299     0    0.015   0.061     1.504   85.952   82.789
LGA    V    10_B      V    10_A     0.321     0    0.010   0.035     1.096   95.238   90.612
LGA    L    11_B      L    11_A     1.126     3    0.059   0.088     1.927   90.595   54.405
LGA    I    12_B      I    12_A     0.525     0    0.164   0.656     2.487   92.857   89.643
LGA    Y    13_B      Y    13_A     0.503     0    0.025   0.343     2.294   95.238   83.333
LGA    L    14_B      L    14_A     0.354     0    0.034   1.353     3.733  100.000   81.310
LGA    C    15_B      C    15_A     0.366     0    0.029   0.032     0.603   97.619   96.825
LGA    R    16_B      R    16_A     0.348     0    0.058   0.374     2.942  100.000   82.511
LGA    R    17_B      R    17_A     0.356     0    0.024   0.240     1.889  100.000   89.177
LGA    D    18_B      D    18_A     0.239     0    0.019   0.119     0.879  100.000   96.429
LGA    S    19_B      S    19_A     0.355     0    0.032   0.106     0.819  100.000   98.413
LGA    D    20_B      D    20_A     0.356     0    0.056   0.162     0.868  100.000   96.429
LGA    C    21_B      C    21_A     0.586     0    0.030   0.066     0.717   90.476   92.063
LGA    P    22_B      P    22_A     0.971     0    0.043   0.184     1.104   85.952   85.306
LGA    G    23_B      G    23_A     1.305     0    0.029   0.029     1.448   81.429   81.429
LGA    E    24_B      E    24_A     1.441     0    0.054   0.998     6.140   81.429   59.259
LGA    C    25_B      C    25_A     0.658     0    0.041   0.063     0.919   95.238   95.238
LGA    I    26_B      I    26_A     0.423     0    0.028   0.104     0.883   92.857   91.667
LGA    C    27_B      C    27_A     0.542     0    0.064   0.086     0.645   95.238   93.651
LGA    L    28_B      L    28_A     0.292     0    0.024   0.108     1.132   95.238   92.917
LGA    G    29_B      G    29_A     1.083     0    0.062   0.062     1.885   81.548   81.548
LGA    N    30_B      N    30_A     1.602     0    0.068   0.110     2.626   79.286   74.167
LGA    G    31_B      G    31_A     0.527     0    0.085   0.085     0.766   95.238   95.238
LGA    Y    32_B      Y    32_A     0.503     0    0.019   0.134     2.504   97.619   81.310
LGA    C    33_B      C    33_A     0.399     0    0.068   0.085     0.788   97.619   95.238
LGA    G    34_B      G    34_A     0.376     0    0.057   0.057     1.191   92.976   92.976

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       34     136    136  100.00     235    235  100.00                34
SUMMARY(RMSD_GDC):     5.165          5.031                  5.026           77.903   72.623

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     30    1.44    84.559    84.362     1.950

LGA_LOCAL      RMSD:   1.439  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.909  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   5.165  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.721763 * X  +  -0.691469 * Y  +  -0.030469 * Z  + -10.560131
  Y_new =   0.043337 * X  +   0.089084 * Y  +  -0.995081 * Z  +  -7.257574
  Z_new =   0.690782 * X  +   0.716893 * Y  +   0.094263 * Z  + -18.218233 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.059971 -0.762570  1.440058   [DEG:    3.4361  -43.6920   82.5092 ]
ZXZ: -0.030610  1.476393  0.766851   [DEG:   -1.7539   84.5911   43.9373 ]
 
# END of job
