
#######################################################
#                                                     #
#                        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        4.53     4.53
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        1.72     5.58
  LCS_AVERAGE:     74.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22       7_B - 28_B        0.97     5.72
  LCS_AVERAGE:     49.60

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    9   11   12   14   15   21   21   22   25   32   33   35   35 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3   10   12   12   12   15   16   19   22   25   28   30   33   34   35   35   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    4   10   12   12   13   15   19   24   27   30   32   33   34   34   35   35   36   36   36 
LCS_GDT     E     5_C     E     5_B      3    3   37      3    3    3    3    7   11   15   20   23   27   29   32   33   34   34   35   35   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   27   37      3    3    3    4   12   16   19   24   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     E     7_C     E     7_B     22   31   37      8   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     K     8_C     K     8_B     22   31   37      8   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     D     9_C     D     9_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     L    11_C     L    11_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     R    12_C     R    12_B     22   31   37      8   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     T    13_C     T    13_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     V    15_C     V    15_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     V    16_C     V    16_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     R    17_C     R    17_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     L    18_C     L    18_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     A    20_C     A    20_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     E    21_C     E    21_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     K    22_C     K    22_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     A    23_C     A    23_B     22   31   37      9   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     D    24_C     D    24_B     22   31   37      7   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     L    25_C     L    25_B     22   31   37      7   18   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     L    26_C     L    26_B     22   31   37      7   17   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     G    27_C     G    27_B     22   31   37      7   15   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     I    28_C     I    28_B     22   31   37      7   15   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     V    29_C     V    29_B     20   31   37      7   15   21   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     S    30_C     S    30_B     20   31   37      7   15   22   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     E    31_C     E    31_B     20   31   37      6   15   19   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     L    32_C     L    32_B     20   31   37      7   15   19   25   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     20   31   37      7   15   19   25   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     L    34_C     L    34_B     20   31   37      7   15   19   26   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     K    35_C     K    35_B     20   31   37      7   15   19   23   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     L    36_C     L    36_B     20   31   37      7   11   19   21   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     N    37_C     N    37_B     17   31   37      6   10   14   21   28   30   31   31   32   32   32   32   33   34   34   35   35   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   26   37      3    3    3    3    4    4    6   10   14   18   22   26   30   32   32   33   35   36   36   36 
LCS_AVERAGE  LCS_A:  74.85  (  49.60   74.95  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      9     18     22     26     28     30     31     31     32     32     32     32     33     34     34     35     35     36     36     36 
GDT PERCENT_AT  24.32  48.65  59.46  70.27  75.68  81.08  83.78  83.78  86.49  86.49  86.49  86.49  89.19  91.89  91.89  94.59  94.59  97.30  97.30  97.30
GDT RMS_LOCAL    0.16   0.57   0.89   1.23   1.44   1.63   1.72   1.72   2.18   2.18   2.18   2.18   2.90   3.32   3.32   3.69   3.69   3.94   3.94   3.94
GDT RMS_ALL_AT   6.84   6.07   5.71   5.58   5.56   5.56   5.58   5.58   5.33   5.33   5.33   5.33   4.93   4.73   4.73   4.60   4.60   4.61   4.61   4.61

# Checking swapping
#   possible swapping detected:  E     5_C      E     5_B
#   possible swapping detected:  E     7_C      E     7_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    19.655     0    0.529   0.556    21.665    0.000    0.000
LGA    E     3_C      E     3_B    14.311     0    0.606   1.317    16.110    0.000    0.000
LGA    A     4_C      A     4_B    12.820     0    0.584   0.559    13.729    0.000    0.000
LGA    E     5_C      E     5_B    12.693     0    0.585   1.218    17.103    0.000    0.000
LGA    Q     6_C      Q     6_B     8.312     0    0.585   0.988    13.925    8.810    4.233
LGA    E     7_C      E     7_B     1.867     0    0.587   0.802     7.962   59.881   41.323
LGA    K     8_C      K     8_B     2.826     0    0.073   1.209     7.604   60.952   46.402
LGA    D     9_C      D     9_B     2.069     0    0.052   1.037     5.771   70.952   52.857
LGA    Q    10_C      Q    10_B     0.551     0    0.036   0.925     4.683   90.595   78.254
LGA    L    11_C      L    11_B     1.196     0    0.047   0.884     4.574   83.690   70.119
LGA    R    12_C      R    12_B     1.935     0    0.033   1.413    11.085   72.857   37.922
LGA    T    13_C      T    13_B     1.627     0    0.046   1.218     3.752   77.143   67.823
LGA    Q    14_C      Q    14_B     0.539     0    0.044   0.599     2.596   92.857   80.159
LGA    V    15_C      V    15_B     0.587     0    0.027   0.097     1.740   95.238   88.095
LGA    V    16_C      V    16_B     1.004     0    0.051   0.077     1.800   83.690   80.272
LGA    R    17_C      R    17_B     1.737     0    0.048   0.960     7.156   75.000   47.922
LGA    L    18_C      L    18_B     1.617     0    0.038   1.009     4.665   75.000   63.929
LGA    Q    19_C      Q    19_B     1.160     0    0.033   1.045     4.426   79.286   69.312
LGA    A    20_C      A    20_B     1.993     0    0.030   0.042     2.396   68.810   68.000
LGA    E    21_C      E    21_B     2.653     0    0.050   0.529     4.532   62.857   53.704
LGA    K    22_C      K    22_B     2.015     0    0.020   0.881     2.876   68.810   65.767
LGA    A    23_C      A    23_B     1.539     0    0.029   0.039     1.685   72.857   74.571
LGA    D    24_C      D    24_B     2.067     0    0.042   0.143     2.682   68.810   65.833
LGA    L    25_C      L    25_B     2.291     0    0.036   1.484     6.689   68.810   49.167
LGA    L    26_C      L    26_B     1.315     0    0.030   1.442     4.252   83.810   67.619
LGA    G    27_C      G    27_B     0.809     0    0.037   0.037     0.873   90.476   90.476
LGA    I    28_C      I    28_B     0.751     0    0.038   1.127     2.684   90.476   78.929
LGA    V    29_C      V    29_B     0.643     0    0.022   0.997     3.096   90.476   81.020
LGA    S    30_C      S    30_B     0.637     0    0.047   0.063     1.049   92.857   90.556
LGA    E    31_C      E    31_B     1.275     0    0.029   0.453     2.194   81.429   78.677
LGA    L    32_C      L    32_B     1.599     0    0.029   0.077     2.615   75.000   71.964
LGA    Q    33_C      Q    33_B     1.338     0    0.032   0.765     4.047   79.286   68.307
LGA    L    34_C      L    34_B     0.713     0    0.079   0.944     3.386   88.214   78.869
LGA    K    35_C      K    35_B     2.161     0    0.067   1.144     6.236   66.786   55.608
LGA    L    36_C      L    36_B     3.044     0    0.159   1.400     4.929   52.024   53.393
LGA    N    37_C      N    37_B     2.751     0    0.106   1.404     6.205   49.048   40.833
LGA    S    38_C      S    38_B     8.581     0    0.174   0.513    12.206    5.714    3.810

# 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):     4.535          4.492                  4.952           64.392   55.830

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    1.72    74.324    76.856     1.708

LGA_LOCAL      RMSD:   1.715  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.576  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   4.535  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.715336 * X  +   0.481499 * Y  +  -0.506412 * Z  +  20.520531
  Y_new =  -0.678849 * X  +   0.306996 * Y  +  -0.667021 * Z  +  28.913469
  Z_new =  -0.165704 * X  +   0.820922 * Y  +   0.546470 * Z  + -54.888592 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.759233  0.166471  0.983478   [DEG:  -43.5009    9.5381   56.3491 ]
ZXZ: -0.649372  0.992653 -0.199174   [DEG:  -37.2063   56.8748  -11.4118 ]
 
# END of job
