
#######################################################
#                                                     #
#                        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        1.69     1.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        1.69     1.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27       8_A - 34_A        0.99     1.79
  LCS_AVERAGE:     65.66

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   34   34      1    3    4    4    5    5   19   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A      3   34   34      1   14   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A      3   34   34      1   14   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A      3   34   34      0    3   21   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A      6   34   34      4    5    6   10   15   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A      6   34   34      5   13   23   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A      6   34   34      4    5   15   24   29   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     27   34   34      7   21   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     27   34   34      8   21   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     27   34   34      3    5   10   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     27   34   34      3    5    9   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     27   34   34      9   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     27   34   34      9   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     27   34   34      8   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     27   34   34      9   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     27   34   34      8   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     27   34   34      5   17   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     27   34   34     11   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     27   34   34     13   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     27   34   34      8   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     27   34   34      6   22   27   28   30   32   33   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_AVERAGE  LCS_A:  88.55  (  65.66  100.00  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     13     22     27     28     30     32     33     33     34     34     34     34     34     34     34     34     34     34     34     34 
GDT PERCENT_AT  38.24  64.71  79.41  82.35  88.24  94.12  97.06  97.06 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.59   0.82   0.90   1.10   1.33   1.46   1.46   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69
GDT RMS_ALL_AT   2.05   1.91   1.89   1.84   1.78   1.73   1.70   1.70   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69

# 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     5.310     0    0.513   0.572     6.985   47.381   36.032
LGA    G     2_B      G     2_A     1.743     0    0.631   0.631     1.845   72.857   72.857
LGA    P     3_B      P     3_A     2.409     0    0.566   0.529     3.975   70.952   60.068
LGA    N     4_B      N     4_A     1.639     0    0.338   1.256     8.392   61.905   40.774
LGA    G     5_B      G     5_A     3.583     0    0.632   0.632     3.583   61.429   61.429
LGA    G     6_B      G     6_A     2.154     0    0.068   0.068     3.290   59.167   59.167
LGA    V     7_B      V     7_A     3.422     0    0.071   1.054     6.763   57.262   44.558
LGA    C     8_B      C     8_A     0.870     0    0.191   0.217     1.754   86.071   86.032
LGA    P     9_B      P     9_A     0.805     0    0.667   0.709     2.282   84.048   82.993
LGA    V    10_B      V    10_A     2.573     0    0.261   1.220     4.633   57.262   54.762
LGA    L    11_B      L    11_A     2.288     3    0.088   0.105     2.566   68.810   41.548
LGA    I    12_B      I    12_A     0.591     0    0.260   1.151     2.661   83.810   80.714
LGA    Y    13_B      Y    13_A     0.870     0    0.080   0.568     4.640   92.857   66.349
LGA    L    14_B      L    14_A     0.431     0    0.028   0.934     3.859   95.238   84.762
LGA    C    15_B      C    15_A     0.305     0    0.061   0.135     0.674   97.619   98.413
LGA    R    16_B      R    16_A     0.589     0    0.158   0.775     3.152   90.476   72.381
LGA    R    17_B      R    17_A     0.708     0    0.040   1.155     7.678   92.857   66.364
LGA    D    18_B      D    18_A     0.342     0    0.037   0.332     1.148  100.000   95.298
LGA    S    19_B      S    19_A     0.294     0    0.077   0.652     2.400  100.000   94.127
LGA    D    20_B      D    20_A     0.626     0    0.034   0.695     2.278   92.857   85.119
LGA    C    21_B      C    21_A     0.732     0    0.039   0.648     2.378   92.857   87.778
LGA    P    22_B      P    22_A     1.251     0    0.027   0.098     2.240   81.429   76.599
LGA    G    23_B      G    23_A     1.252     0    0.065   0.065     1.252   83.690   83.690
LGA    E    24_B      E    24_A     1.233     0    0.157   0.315     1.944   81.429   76.667
LGA    C    25_B      C    25_A     1.090     0    0.043   0.159     1.196   81.429   82.937
LGA    I    26_B      I    26_A     1.125     0    0.022   0.091     2.497   88.333   78.571
LGA    C    27_B      C    27_A     0.289     0    0.043   0.116     0.529   97.619   96.825
LGA    L    28_B      L    28_A     0.438     0    0.059   0.179     1.875  100.000   89.702
LGA    G    29_B      G    29_A     0.617     0    0.110   0.110     1.352   88.333   88.333
LGA    N    30_B      N    30_A     1.800     0    0.208   0.725     3.293   81.548   72.321
LGA    G    31_B      G    31_A     0.813     0    0.098   0.098     1.148   88.214   88.214
LGA    Y    32_B      Y    32_A     0.482     0    0.064   0.100     1.153   92.857   90.516
LGA    C    33_B      C    33_A     0.685     0    0.055   0.086     0.773   90.476   90.476
LGA    G    34_B      G    34_A     0.845     0    0.697   0.697     3.386   78.095   78.095

# 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):     1.690          1.582                  2.222           82.328   75.426

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     33    1.46    86.029    92.982     2.114

LGA_LOCAL      RMSD:   1.461  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.703  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   1.690  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.479673 * X  +  -0.188684 * Y  +  -0.856920 * Z  +  -8.925696
  Y_new =  -0.767764 * X  +   0.382548 * Y  +  -0.513999 * Z  +  -4.194898
  Z_new =   0.424797 * X  +   0.904464 * Y  +   0.038633 * Z  + -16.565037 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.012366 -0.438737  1.528109   [DEG:  -58.0043  -25.1378   87.5542 ]
ZXZ: -1.030508  1.532154  0.439088   [DEG:  -59.0438   87.7860   25.1579 ]
 
# END of job
