
#######################################################
#                                                     #
#                        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   38 (  302),  selected   37 , name one
# Molecule2: number of CA atoms   37 (  291),  selected   37 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       2_B - 38_B        3.42     3.42
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.85     3.77
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.68     4.10
  LCS_AVERAGE:     82.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.48     4.28
  LCS_AVERAGE:     71.51

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   37
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     A     2_C     A     2_B      3    3   37      0    3    3    3    3    4    4    7    9    9   11   13   14   16   21   23   27   30   36   36 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   16   21   28   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3    6   25   26   31   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3   33   37      3    3    3    4    7   10   16   25   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    4   10   20   28   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     22   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     31   33   37     23   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     23   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     14   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37      6   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     21   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     21   31   31   31   31   31   31   32   33   34   35   35   35   36   36   36   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    4    4    6    6    9   32   32   32   34   36   36   36   36   36   36   36 
LCS_AVERAGE  LCS_A:  84.71  (  71.51   82.62  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     24     31     31     31     31     31     31     32     33     34     35     35     35     36     36     36     36     36     36     36 
GDT PERCENT_AT  64.86  83.78  83.78  83.78  83.78  83.78  83.78  86.49  89.19  91.89  94.59  94.59  94.59  97.30  97.30  97.30  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.32   0.48   0.48   0.48   0.48   0.48   0.48   1.20   1.75   2.11   2.53   2.53   2.53   2.77   2.77   2.77   2.77   2.77   2.77   2.77
GDT RMS_ALL_AT   4.31   4.28   4.28   4.28   4.28   4.28   4.28   4.07   3.78   3.61   3.49   3.49   3.49   3.50   3.50   3.50   3.50   3.50   3.50   3.50

# Checking swapping
#   possible swapping detected:  E     3_C      E     3_B
#   possible swapping detected:  E     7_C      E     7_B
#   possible swapping detected:  D     9_C      D     9_B
#   possible swapping detected:  E    21_C      E    21_B
#   possible swapping detected:  E    31_C      E    31_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B    16.027     0    0.408   0.388    17.562    0.000    0.000
LGA    E     3_C      E     3_B    10.666     0    0.621   1.040    12.370    0.714    0.476
LGA    A     4_C      A     4_B     8.212     0    0.592   0.573     9.231    3.452    3.048
LGA    E     5_C      E     5_B     8.782     0    0.620   1.011    10.418    5.714    2.857
LGA    Q     6_C      Q     6_B     5.902     0    0.596   1.301    13.807   26.548   12.963
LGA    E     7_C      E     7_B     1.214     0    0.592   0.966     9.873   85.952   46.296
LGA    K     8_C      K     8_B     0.760     0    0.070   1.263     4.621   90.476   72.116
LGA    D     9_C      D     9_B     0.806     0    0.046   0.940     3.425   90.476   78.036
LGA    Q    10_C      Q    10_B     0.546     0    0.035   0.285     1.092   92.857   90.529
LGA    L    11_C      L    11_B     0.841     0    0.013   0.072     0.986   90.476   90.476
LGA    R    12_C      R    12_B     0.710     0    0.043   1.429     7.304   90.476   64.762
LGA    T    13_C      T    13_B     0.302     0    0.024   0.992     2.410  100.000   91.088
LGA    Q    14_C      Q    14_B     0.445     0    0.014   0.641     2.809  100.000   86.190
LGA    V    15_C      V    15_B     0.551     0    0.016   0.048     0.840   95.238   93.197
LGA    V    16_C      V    16_B     0.488     0    0.025   0.083     0.660  100.000   95.918
LGA    R    17_C      R    17_B     0.274     0    0.016   1.720     7.717  100.000   67.489
LGA    L    18_C      L    18_B     0.226     0    0.017   0.098     0.248  100.000  100.000
LGA    Q    19_C      Q    19_B     0.300     0    0.021   0.186     0.860  100.000   98.942
LGA    A    20_C      A    20_B     0.319     0    0.021   0.022     0.423  100.000  100.000
LGA    E    21_C      E    21_B     0.275     0    0.015   0.905     3.055  100.000   81.005
LGA    K    22_C      K    22_B     0.255     0    0.029   0.067     0.549  100.000   97.884
LGA    A    23_C      A    23_B     0.210     0    0.000   0.007     0.295  100.000  100.000
LGA    D    24_C      D    24_B     0.342     0    0.010   0.201     1.342  100.000   95.298
LGA    L    25_C      L    25_B     0.150     0    0.014   0.038     0.580  100.000   97.619
LGA    L    26_C      L    26_B     0.336     0    0.030   0.047     0.562   97.619   97.619
LGA    G    27_C      G    27_B     0.752     0    0.099   0.099     0.752   92.857   92.857
LGA    I    28_C      I    28_B     0.498     0    0.024   0.076     1.116   97.619   92.917
LGA    V    29_C      V    29_B     0.182     0    0.022   0.061     0.627  100.000   97.279
LGA    S    30_C      S    30_B     0.866     0    0.141   0.698     3.316   85.952   80.714
LGA    E    31_C      E    31_B     1.255     0    0.103   0.998     7.636   79.286   52.328
LGA    L    32_C      L    32_B     0.765     0    0.276   1.374     3.219   86.071   74.940
LGA    Q    33_C      Q    33_B     0.682     0    0.041   1.071     3.841   92.857   83.333
LGA    L    34_C      L    34_B     0.555     0    0.022   0.175     1.284   90.476   89.345
LGA    K    35_C      K    35_B     0.573     0    0.022   0.559     2.982   92.857   85.873
LGA    L    36_C      L    36_B     0.644     0    0.117   0.162     0.948   90.476   90.476
LGA    N    37_C      N    37_B     0.662     0    0.446   0.856     6.813   75.714   53.631
LGA    S    38_C      S    38_B     7.178     0    0.514   0.804    10.922   12.857    9.048

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       37     148    148  100.00     291    291  100.00                37
SUMMARY(RMSD_GDC):     3.424          3.359                  3.962           80.190   72.069

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     32    1.20    87.838    86.633     2.455

LGA_LOCAL      RMSD:   1.203  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.071  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.424  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.327359 * X  +   0.876504 * Y  +   0.352954 * Z  + -35.024845
  Y_new =  -0.448529 * X  +  -0.472914 * Y  +   0.758402 * Z  +  48.344326
  Z_new =   0.831660 * X  +   0.089959 * Y  +   0.547950 * Z  + -40.117771 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.201275 -0.982090  0.162722   [DEG: -126.1238  -56.2696    9.3233 ]
ZXZ:  2.706013  0.990884  1.463047   [DEG:  155.0431   56.7735   83.8264 ]
 
# END of job
