
#######################################################
#                                                     #
#                        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        4.50     4.50
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_A - 34_A        1.19     5.15
  LCS_AVERAGE:     80.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       7_A - 34_A        0.79     5.19
  LCS_AVERAGE:     71.54

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      4    8   34      3    4    4    5    7    9   10   11   11   12   12   12   13   15   17   17   17   17   26   33 
LCS_GDT     G     2_B     G     2_A      4    8   34      3    4    4    6    8    9   10   11   11   12   12   12   13   15   17   17   17   21   26   27 
LCS_GDT     P     3_B     P     3_A      4    8   34      3    4    4    6    8    9   10   11   11   12   12   12   13   15   17   18   18   31   31   33 
LCS_GDT     N     4_B     N     4_A      4    8   34      3    4    4    6    9   16   23   27   29   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     G     5_B     G     5_A      3   30   34      4   10   24   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     G     6_B     G     6_A     24   30   34      3   11   18   28   28   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     V     7_B     V     7_A     28   30   34      8   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     C     8_B     C     8_A     28   30   34      9   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     P     9_B     P     9_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     V    10_B     V    10_A     28   30   34     11   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     L    11_B     L    11_A     28   30   34      6   20   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     I    12_B     I    12_A     28   30   34      8   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     Y    13_B     Y    13_A     28   30   34     16   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     L    14_B     L    14_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     C    15_B     C    15_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     R    16_B     R    16_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     R    17_B     R    17_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     D    18_B     D    18_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     S    19_B     S    19_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     D    20_B     D    20_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     C    21_B     C    21_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     P    22_B     P    22_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     G    23_B     G    23_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     E    24_B     E    24_A     28   30   34     11   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     C    25_B     C    25_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     I    26_B     I    26_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     C    27_B     C    27_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     L    28_B     L    28_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     G    29_B     G    29_A     28   30   34     16   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     N    30_B     N    30_A     28   30   34      3   13   24   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     G    31_B     G    31_A     28   30   34      4   23   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     Y    32_B     Y    32_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     C    33_B     C    33_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_GDT     G    34_B     G    34_A     28   30   34     18   24   27   28   29   29   30   30   30   30   30   30   31   31   31   31   31   31   31   33 
LCS_AVERAGE  LCS_A:  84.05  (  71.54   80.62  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     18     24     27     28     29     29     30     30     30     30     30     30     31     31     31     31     31     31     31     33 
GDT PERCENT_AT  52.94  70.59  79.41  82.35  85.29  85.29  88.24  88.24  88.24  88.24  88.24  88.24  91.18  91.18  91.18  91.18  91.18  91.18  91.18  97.06
GDT RMS_LOCAL    0.35   0.55   0.71   0.79   0.98   0.98   1.19   1.19   1.19   1.19   1.19   1.19   2.01   2.01   2.01   2.01   2.01   2.01   2.01   3.89
GDT RMS_ALL_AT   5.21   5.21   5.23   5.19   5.04   5.04   5.15   5.15   5.15   5.15   5.15   5.15   4.89   4.89   4.89   4.89   4.89   4.89   4.89   4.54

# Checking swapping
#   possible swapping detected:  Y    13_B      Y    13_A
#   possible swapping detected:  E    24_B      E    24_A
#   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    14.601     0    0.237   0.756    17.042    0.000    0.000
LGA    G     2_B      G     2_A    16.780     0    0.058   0.058    16.780    0.000    0.000
LGA    P     3_B      P     3_A    16.426     0    0.502   0.491    18.696    0.000    0.000
LGA    N     4_B      N     4_A     9.737     0    0.049   1.251    12.104    3.095    2.679
LGA    G     5_B      G     5_A     3.303     0    0.394   0.394     5.561   44.881   44.881
LGA    G     6_B      G     6_A     3.514     0    0.564   0.564     3.514   59.524   59.524
LGA    V     7_B      V     7_A     1.332     0    0.189   1.242     3.795   79.524   71.293
LGA    C     8_B      C     8_A     0.937     0    0.069   0.098     1.167   90.595   90.556
LGA    P     9_B      P     9_A     0.671     0    0.033   0.109     1.227   95.238   89.320
LGA    V    10_B      V    10_A     0.679     0    0.086   0.134     1.385   90.595   89.252
LGA    L    11_B      L    11_A     1.737     3    0.108   0.144     1.855   75.000   46.607
LGA    I    12_B      I    12_A     1.013     0    0.024   1.062     2.470   88.333   80.714
LGA    Y    13_B      Y    13_A     0.353     0    0.085   0.945     5.804   97.619   69.087
LGA    L    14_B      L    14_A     0.472     0    0.067   0.808     2.050   95.238   88.631
LGA    C    15_B      C    15_A     0.415     0    0.074   0.143     0.703   95.238   95.238
LGA    R    16_B      R    16_A     0.557     0    0.176   0.889     3.678   95.238   80.909
LGA    R    17_B      R    17_A     0.991     0    0.034   1.169     7.200   90.476   64.589
LGA    D    18_B      D    18_A     0.928     0    0.035   0.079     1.223   88.214   84.821
LGA    S    19_B      S    19_A     1.140     0    0.072   0.629     1.687   85.952   84.524
LGA    D    20_B      D    20_A     0.685     0    0.026   0.096     0.933   92.857   91.667
LGA    C    21_B      C    21_A     0.094     0    0.047   0.108     0.525   97.619   98.413
LGA    P    22_B      P    22_A     0.382     0    0.045   0.286     0.658  100.000   98.639
LGA    G    23_B      G    23_A     0.183     0    0.028   0.028     0.371  100.000  100.000
LGA    E    24_B      E    24_A     0.651     0    0.200   0.927     4.144   97.619   74.815
LGA    C    25_B      C    25_A     0.136     0    0.020   0.063     0.348  100.000  100.000
LGA    I    26_B      I    26_A     0.574     0    0.046   1.089     3.721   92.857   76.548
LGA    C    27_B      C    27_A     0.630     0    0.022   0.080     0.656   90.476   90.476
LGA    L    28_B      L    28_A     0.635     0    0.030   0.979     3.739   95.238   82.619
LGA    G    29_B      G    29_A     0.270     0    0.107   0.107     1.217   92.976   92.976
LGA    N    30_B      N    30_A     1.882     0    0.253   1.036     2.606   79.286   73.214
LGA    G    31_B      G    31_A     1.120     0    0.081   0.081     1.186   85.952   85.952
LGA    Y    32_B      Y    32_A     0.145     0    0.067   0.222     1.161   97.619   95.278
LGA    C    33_B      C    33_A     0.373     0    0.045   0.045     0.602  100.000   96.825
LGA    G    34_B      G    34_A     0.312     0    0.655   0.655     1.974   93.214   93.214

# 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):     4.502          4.387                  4.392           79.132   73.331

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     30    1.19    83.088    83.855     2.333

LGA_LOCAL      RMSD:   1.186  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.149  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   4.502  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.796739 * X  +   0.049683 * Y  +   0.602277 * Z  + -49.575653
  Y_new =   0.379450 * X  +   0.734537 * Y  +  -0.562559 * Z  + -45.417240
  Z_new =  -0.470345 * X  +   0.676747 * Y  +   0.566383 * Z  + -53.303623 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.444470  0.489681  0.873946   [DEG:   25.4663   28.0567   50.0734 ]
ZXZ:  0.819482  0.968686 -0.607368   [DEG:   46.9529   55.5016  -34.7996 ]
 
# END of job
