
#######################################################
#                                                     #
#                        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        3.44     3.44
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.83     3.79
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.68     4.11
  LCS_AVERAGE:     82.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.40     4.29
  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   25   30   36   36 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   15   20   26   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3    6    7    7   31   33   34   35   35   35   35   35   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   35   35   36   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    3   10   23   28   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     24   31   31   31   31   31   31   32   32   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   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   35   35   36   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   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   35   35   36   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     23   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     23   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     26   31   31   31   31   31   31   32   33   34   35   35   35   35   35   36   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    4    4    6    9    9   32   32   32   33   35   35   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     26     31     31     31     31     31     31     32     33     34     35     35     35     35     35     36     36     36     36     36 
GDT PERCENT_AT  70.27  83.78  83.78  83.78  83.78  83.78  83.78  86.49  89.19  91.89  94.59  94.59  94.59  94.59  94.59  97.30  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.33   0.40   0.40   0.40   0.40   0.40   0.40   1.17   2.07   2.10   2.52   2.52   2.52   2.40   2.40   2.78   2.78   2.78   2.78   2.78
GDT RMS_ALL_AT   4.28   4.29   4.29   4.29   4.29   4.29   4.29   4.09   3.59   3.63   3.51   3.51   3.51   3.65   3.65   3.51   3.51   3.51   3.51   3.51

# Checking swapping
#   possible swapping detected:  E     3_C      E     3_B
#   possible swapping detected:  D     9_C      D     9_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    16.107     0    0.407   0.387    17.661    0.000    0.000
LGA    E     3_C      E     3_B    10.745     0    0.620   1.025    12.447    0.714    0.635
LGA    A     4_C      A     4_B     8.215     0    0.592   0.572     9.266    3.452    3.048
LGA    E     5_C      E     5_B     8.777     0    0.619   1.007    10.426    5.714    2.857
LGA    Q     6_C      Q     6_B     5.876     0    0.597   1.302    13.765   26.548   13.439
LGA    E     7_C      E     7_B     1.247     0    0.605   0.724     8.774   85.952   49.365
LGA    K     8_C      K     8_B     0.770     0    0.071   1.264     4.632   90.476   72.116
LGA    D     9_C      D     9_B     0.859     0    0.046   0.938     3.505   90.476   77.202
LGA    Q    10_C      Q    10_B     0.620     0    0.037   0.280     1.199   90.476   89.471
LGA    L    11_C      L    11_B     0.909     0    0.014   0.073     1.059   90.476   85.952
LGA    R    12_C      R    12_B     0.769     0    0.043   1.431     7.327   90.476   64.762
LGA    T    13_C      T    13_B     0.350     0    0.024   0.992     2.458  100.000   91.088
LGA    Q    14_C      Q    14_B     0.514     0    0.015   0.639     2.765   97.619   85.132
LGA    V    15_C      V    15_B     0.622     0    0.016   0.048     0.932   92.857   91.837
LGA    V    16_C      V    16_B     0.507     0    0.024   0.084     0.702   97.619   94.558
LGA    R    17_C      R    17_B     0.278     0    0.022   1.726     7.714  100.000   67.489
LGA    L    18_C      L    18_B     0.255     0    0.017   0.106     0.367  100.000  100.000
LGA    Q    19_C      Q    19_B     0.273     0    0.019   0.187     0.842  100.000   98.942
LGA    A    20_C      A    20_B     0.277     0    0.019   0.019     0.369  100.000  100.000
LGA    E    21_C      E    21_B     0.289     0    0.016   0.116     0.865  100.000   96.825
LGA    K    22_C      K    22_B     0.273     0    0.034   0.073     0.622  100.000   97.884
LGA    A    23_C      A    23_B     0.199     0    0.004   0.011     0.287  100.000  100.000
LGA    D    24_C      D    24_B     0.304     0    0.010   0.204     1.373  100.000   95.298
LGA    L    25_C      L    25_B     0.169     0    0.009   0.026     0.564  100.000   97.619
LGA    L    26_C      L    26_B     0.465     0    0.037   0.041     0.672   95.238   92.857
LGA    G    27_C      G    27_B     0.696     0    0.085   0.085     0.696   95.238   95.238
LGA    I    28_C      I    28_B     0.291     0    0.017   0.080     0.861  100.000   97.619
LGA    V    29_C      V    29_B     0.338     0    0.022   0.052     0.497  100.000  100.000
LGA    S    30_C      S    30_B     0.609     0    0.030   0.099     0.942   92.857   92.063
LGA    E    31_C      E    31_B     0.658     0    0.033   1.035     6.327   95.238   64.127
LGA    L    32_C      L    32_B     0.318     0    0.000   0.035     0.882  100.000   96.429
LGA    Q    33_C      Q    33_B     0.595     0    0.042   1.069     3.839   97.619   85.450
LGA    L    34_C      L    34_B     0.397     0    0.047   0.180     1.198  100.000   94.107
LGA    K    35_C      K    35_B     0.191     0    0.035   0.546     2.573   97.619   92.116
LGA    L    36_C      L    36_B     0.603     0    0.108   0.130     0.986   95.238   92.857
LGA    N    37_C      N    37_B     0.404     0    0.442   0.855     6.695   74.405   54.405
LGA    S    38_C      S    38_B     7.408     0    0.514   0.804    11.042   10.833    7.698

# 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):     3.437          3.368                  3.894           81.544   74.067

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     32    1.17    87.838    86.503     2.521

LGA_LOCAL      RMSD:   1.169  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.087  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.437  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.033267 * X  +   0.744719 * Y  +   0.666548 * Z  + -37.689095
  Y_new =   0.035011 * X  +  -0.665640 * Y  +   0.745451 * Z  +  46.780876
  Z_new =   0.998833 * X  +   0.048135 * Y  +  -0.003930 * Z  + -40.504570 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.330654 -1.522483  1.652254   [DEG:  133.5366  -87.2318   94.6672 ]
ZXZ:  2.412017  1.574726  1.522642   [DEG:  138.1984   90.2252   87.2410 ]
 
# END of job
