
#######################################################
#                                                     #
#                        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        3.38     3.38
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       4_A - 34_A        1.87     3.59
  LCS_AVERAGE:     84.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27       8_A - 34_A        0.98     3.79
  LCS_AVERAGE:     66.00

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      5    7   34      4    5    6    6    6    8    9    9    9   15   16   22   32   32   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A      5    7   34      4    5    6    6    6    8    9    9    9   15   16   22   32   32   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A      5    7   34      4    5    6    6    6    8    9    9   10   15   18   27   32   32   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A      5   31   34      4    5    6    6   16   26   27   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A      5   31   34      4    5    6    7    8   28   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A      4   31   34      4    9   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A      5   31   34      4    5   14   24   28   29   29   29   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     27   31   34      4   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     27   31   34      8   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     27   31   34      3    5    6   25   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     27   31   34      3    5   12   21   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     27   31   34      9   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     27   31   34      6   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     27   31   34     13   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     27   31   34     11   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     27   31   34     13   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     27   31   34      4   22   25   26   28   29   29   30   30   31   31   31   31   32   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     27   31   34      4   11   25   26   28   29   29   30   30   31   31   31   31   32   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     27   31   34      9   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     27   31   34     14   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     27   31   34      9   22   25   26   28   29   29   30   30   31   31   31   32   32   34   34   34   34   34   34 
LCS_AVERAGE  LCS_A:  83.65  (  66.00   84.95  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     22     25     26     28     29     29     30     30     31     31     31     32     32     34     34     34     34     34     34 
GDT PERCENT_AT  41.18  64.71  73.53  76.47  82.35  85.29  85.29  88.24  88.24  91.18  91.18  91.18  94.12  94.12 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.53   0.71   0.77   1.02   1.20   1.20   1.70   1.51   1.87   1.87   1.87   3.40   2.63   3.38   3.38   3.38   3.38   3.38   3.38
GDT RMS_ALL_AT   3.74   3.73   3.76   3.81   3.82   3.94   3.94   3.54   3.76   3.59   3.59   3.59   3.40   3.44   3.38   3.38   3.38   3.38   3.38   3.38

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A     9.271     0    0.317   0.933    12.465    0.357    4.762
LGA    G     2_B      G     2_A    10.638     0    0.048   0.048    10.638    1.429    1.429
LGA    P     3_B      P     3_A    10.819     0    0.363   0.622    14.076    0.476    0.272
LGA    N     4_B      N     4_A     5.577     0    0.204   1.088     8.642   29.643   21.250
LGA    G     5_B      G     5_A     3.477     0    0.152   0.152     3.890   54.048   54.048
LGA    G     6_B      G     6_A     2.826     0    0.084   0.084     2.968   63.214   63.214
LGA    V     7_B      V     7_A     4.967     0    0.095   0.990     8.648   37.262   25.578
LGA    C     8_B      C     8_A     1.968     0    0.208   0.800     3.143   67.143   71.905
LGA    P     9_B      P     9_A     1.607     0    0.657   0.595     2.422   72.976   71.769
LGA    V    10_B      V    10_A     2.824     0    0.246   0.246     3.684   55.357   52.109
LGA    L    11_B      L    11_A     2.470     3    0.106   0.155     2.992   68.810   41.548
LGA    I    12_B      I    12_A     0.703     0    0.220   0.702     2.513   88.214   84.048
LGA    Y    13_B      Y    13_A     0.923     0    0.093   0.976     6.499   90.476   63.095
LGA    L    14_B      L    14_A     0.652     0    0.077   0.182     1.110   90.476   89.345
LGA    C    15_B      C    15_A     0.270     0    0.037   0.090     0.377  100.000  100.000
LGA    R    16_B      R    16_A     0.663     0    0.175   1.401     7.403   90.476   60.606
LGA    R    17_B      R    17_A     0.558     0    0.048   1.272     7.412   95.238   66.494
LGA    D    18_B      D    18_A     0.130     0    0.040   0.072     0.746  100.000   97.619
LGA    S    19_B      S    19_A     0.396     0    0.110   0.589     1.737   97.619   92.302
LGA    D    20_B      D    20_A     0.389     0    0.030   0.210     0.809   97.619   96.429
LGA    C    21_B      C    21_A     0.449     0    0.029   0.101     1.009   92.976   95.317
LGA    P    22_B      P    22_A     1.210     0    0.035   0.037     1.592   90.595   84.218
LGA    G    23_B      G    23_A     0.886     0    0.058   0.058     1.366   85.952   85.952
LGA    E    24_B      E    24_A     1.057     0    0.163   0.464     3.819   88.214   70.423
LGA    C    25_B      C    25_A     0.454     0    0.050   0.089     0.491  100.000  100.000
LGA    I    26_B      I    26_A     0.599     0    0.043   1.085     2.921   90.476   78.929
LGA    C    27_B      C    27_A     0.598     0    0.048   0.074     0.639   90.476   90.476
LGA    L    28_B      L    28_A     0.608     0    0.059   1.393     3.527   90.476   76.667
LGA    G    29_B      G    29_A     1.531     0    0.095   0.095     1.950   75.000   75.000
LGA    N    30_B      N    30_A     1.723     0    0.215   0.885     3.960   79.405   67.500
LGA    G    31_B      G    31_A     0.450     0    0.075   0.075     0.923   97.619   97.619
LGA    Y    32_B      Y    32_A     0.468     0    0.052   0.121     2.763   95.238   80.556
LGA    C    33_B      C    33_A     0.491     0    0.052   0.135     0.647   97.619   95.238
LGA    G    34_B      G    34_A     0.860     0    0.096   0.096     0.860   90.476   90.476

# 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):     3.383          3.300                  3.634           75.452   69.006

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     30    1.70    82.353    84.356     1.671

LGA_LOCAL      RMSD:   1.695  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.544  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   3.383  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.823321 * X  +   0.044969 * Y  +  -0.565792 * Z  +  -7.942798
  Y_new =  -0.495331 * X  +   0.543629 * Y  +  -0.677580 * Z  +  -3.986114
  Z_new =   0.277111 * X  +   0.838120 * Y  +   0.469856 * Z  + -17.270828 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.541614 -0.280786  1.059846   [DEG:  -31.0322  -16.0879   60.7247 ]
ZXZ: -0.695732  1.081669  0.319319   [DEG:  -39.8625   61.9751   18.2957 ]
 
# END of job
