
#######################################################
#                                                     #
#                        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:    34       1_A - 34_A        4.78     4.78
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       6_A - 34_A        1.51     5.71
  LCS_AVERAGE:     75.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      10_A - 34_A        0.78     5.63
  LCS_AVERAGE:     56.40

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   34      3    3    4    4    5    5    5    6    7    7    7   10   11   11   12   12   13   16   16   18 
LCS_GDT     G     2_B     G     2_A      3    5   34      3    3    4    4    5    5    6    6    7    7   10   11   12   13   13   15   23   26   32   33 
LCS_GDT     P     3_B     P     3_A      3    5   34      3    4    4    4    5    5    8    9   12   15   21   27   29   32   32   32   32   32   32   33 
LCS_GDT     N     4_B     N     4_A      3    6   34      3    3    4    5    5    6    7    8   12   18   25   28   31   32   32   32   32   32   32   33 
LCS_GDT     G     5_B     G     5_A      3    6   34      1    3    4    5    5    6   22   26   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     G     6_B     G     6_A      3   29   34      1    4    9   15   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     V     7_B     V     7_A      3   29   34      2    4    9   12   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     C     8_B     C     8_A      3   29   34      0    7   21   24   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     P     9_B     P     9_A      3   29   34      3    4    8    8   15   17   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     V    10_B     V    10_A     25   29   34      3   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     L    11_B     L    11_A     25   29   34      4   17   23   25   26   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     I    12_B     I    12_A     25   29   34     11   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     Y    13_B     Y    13_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     L    14_B     L    14_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     C    15_B     C    15_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     R    16_B     R    16_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     R    17_B     R    17_A     25   29   34     11   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     D    18_B     D    18_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     S    19_B     S    19_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     D    20_B     D    20_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     C    21_B     C    21_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     P    22_B     P    22_A     25   29   34     13   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     G    23_B     G    23_A     25   29   34     10   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     E    24_B     E    24_A     25   29   34     10   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     C    25_B     C    25_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     I    26_B     I    26_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     C    27_B     C    27_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     L    28_B     L    28_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     G    29_B     G    29_A     25   29   34      4   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     N    30_B     N    30_A     25   29   34      4   14   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     G    31_B     G    31_A     25   29   34      5   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     Y    32_B     Y    32_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     C    33_B     C    33_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_GDT     G    34_B     G    34_A     25   29   34     14   21   24   25   27   28   29   29   29   29   30   30   31   32   32   32   32   32   32   33 
LCS_AVERAGE  LCS_A:  77.16  (  56.40   75.09  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     14     21     24     25     27     28     29     29     29     29     30     30     31     32     32     32     32     32     32     33 
GDT PERCENT_AT  41.18  61.76  70.59  73.53  79.41  82.35  85.29  85.29  85.29  85.29  88.24  88.24  91.18  94.12  94.12  94.12  94.12  94.12  94.12  97.06
GDT RMS_LOCAL    0.25   0.53   0.71   0.78   1.23   1.29   1.51   1.51   1.51   1.51   2.03   2.03   2.79   3.40   3.40   3.40   3.40   3.40   3.40   4.16
GDT RMS_ALL_AT   5.71   5.70   5.64   5.63   5.62   5.61   5.71   5.71   5.71   5.71   5.41   5.41   5.13   4.92   4.92   4.92   4.92   4.92   4.92   4.81

# Checking swapping
#   possible swapping detected:  Y    13_B      Y    13_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A    17.451     0    0.209   0.578    20.337    0.000    0.000
LGA    G     2_B      G     2_A    17.341     0    0.140   0.140    17.341    0.000    0.000
LGA    P     3_B      P     3_A    14.425     0    0.340   0.559    18.154    0.000    0.000
LGA    N     4_B      N     4_A    12.641     0    0.647   1.227    15.936    0.000    0.000
LGA    G     5_B      G     5_A     8.265     0    0.557   0.557     9.595   13.214   13.214
LGA    G     6_B      G     6_A     2.619     0    0.667   0.667     4.130   54.048   54.048
LGA    V     7_B      V     7_A     3.004     0    0.203   0.231     3.848   51.905   48.231
LGA    C     8_B      C     8_A     1.992     0    0.135   0.186     3.118   59.405   69.841
LGA    P     9_B      P     9_A     4.226     0    0.376   0.403     7.884   49.524   32.653
LGA    V    10_B      V    10_A     1.529     0    0.598   1.318     6.387   77.143   58.027
LGA    L    11_B      L    11_A     2.553     3    0.220   0.283     2.706   60.952   37.619
LGA    I    12_B      I    12_A     1.705     0    0.157   0.154     3.991   81.667   67.738
LGA    Y    13_B      Y    13_A     0.447     0    0.073   0.568     3.266   92.976   78.770
LGA    L    14_B      L    14_A     0.348     0    0.049   0.092     1.169  100.000   94.107
LGA    C    15_B      C    15_A     0.352     0    0.051   0.062     0.603  100.000   98.413
LGA    R    16_B      R    16_A     0.499     0    0.123   1.613     9.449  100.000   59.091
LGA    R    17_B      R    17_A     1.089     0    0.093   1.348     8.272   88.214   55.498
LGA    D    18_B      D    18_A     1.065     0    0.013   0.054     1.316   81.429   82.560
LGA    S    19_B      S    19_A     1.229     0    0.011   0.012     1.447   83.690   82.937
LGA    D    20_B      D    20_A     0.441     0    0.024   0.123     0.625   97.619   97.619
LGA    C    21_B      C    21_A     0.699     0    0.026   0.052     1.053   90.476   87.460
LGA    P    22_B      P    22_A     0.274     0    0.042   0.126     0.900   97.619   94.558
LGA    G    23_B      G    23_A     0.169     0    0.051   0.051     0.717   97.619   97.619
LGA    E    24_B      E    24_A     0.414     0    0.018   0.945     4.864  100.000   78.413
LGA    C    25_B      C    25_A     0.419     0    0.019   0.067     0.574  100.000   98.413
LGA    I    26_B      I    26_A     0.842     0    0.027   0.047     1.680   90.476   84.881
LGA    C    27_B      C    27_A     0.721     0    0.037   0.060     0.810   90.476   90.476
LGA    L    28_B      L    28_A     0.560     0    0.030   0.044     1.853   95.238   87.321
LGA    G    29_B      G    29_A     0.869     0    0.027   0.027     2.047   82.024   82.024
LGA    N    30_B      N    30_A     2.248     0    0.042   0.105     3.269   68.810   64.048
LGA    G    31_B      G    31_A     1.123     0    0.117   0.117     1.249   88.333   88.333
LGA    Y    32_B      Y    32_A     0.489     0    0.040   0.075     2.543   97.619   79.881
LGA    C    33_B      C    33_A     0.764     0    0.010   0.033     1.069   88.214   85.952
LGA    G    34_B      G    34_A     1.063     0    0.219   0.219     1.321   83.690   83.690

# 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):     4.780          4.606                  4.844           72.423   65.689

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     29    1.51    78.676    79.608     1.807

LGA_LOCAL      RMSD:   1.505  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.706  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   4.780  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.893270 * X  +   0.422917 * Y  +  -0.152347 * Z  +   2.561839
  Y_new =   0.298054 * X  +   0.810930 * Y  +   0.503545 * Z  +   7.855840
  Z_new =   0.336500 * X  +   0.404394 * Y  +  -0.850431 * Z  + -13.196560 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.819543 -0.343198  2.697723   [DEG:  161.5479  -19.6638  154.5681 ]
ZXZ: -2.847799  2.587601  0.694016   [DEG: -163.1669  148.2586   39.7642 ]
 
# END of job
