
#######################################################
#                                                     #
#                        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        3.68     3.68
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.83     4.39
  LCS_AVERAGE:     80.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.52     4.61
  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   10   10   12   14   17   18   23   24   27   31   35 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    4   15   21   25   30   34   35   35   35   36   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3    6    6    7   28   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3    3   37      3    3    3    4    6    8   12   22   28   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    4   10   17   27   30   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     22   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   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   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   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   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     19   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     19   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     22   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     19   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     15   31   31   31   31   31   31   31   33   34   34   34   35   35   35   36   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    3    4    5    7    9   21   26   32   32   33   35   36   36   36   36   36 
LCS_AVERAGE  LCS_A:  83.98  (  71.51   80.42  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     23     31     31     31     31     31     31     31     33     34     34     34     35     35     35     36     36     36     36     36 
GDT PERCENT_AT  62.16  83.78  83.78  83.78  83.78  83.78  83.78  83.78  89.19  91.89  91.89  91.89  94.59  94.59  94.59  97.30  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.31   0.52   0.52   0.52   0.52   0.52   0.52   0.52   1.90   2.28   2.28   2.28   2.73   2.73   2.57   2.99   2.99   2.99   2.99   2.99
GDT RMS_ALL_AT   4.55   4.61   4.61   4.61   4.61   4.61   4.61   4.61   4.06   3.89   3.89   3.89   3.76   3.76   3.92   3.76   3.76   3.76   3.76   3.76

# Checking swapping
#   possible swapping detected:  E     5_C      E     5_B
#   possible swapping detected:  D     9_C      D     9_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B    18.020     0    0.427   0.422    19.643    0.000    0.000
LGA    E     3_C      E     3_B    12.398     0    0.584   1.017    14.272    0.000    0.000
LGA    A     4_C      A     4_B     9.281     0    0.620   0.587    10.479    0.476    0.476
LGA    E     5_C      E     5_B    10.189     0    0.611   0.737    13.299    1.190    0.529
LGA    Q     6_C      Q     6_B     7.466     0    0.611   1.071    12.911   15.119    7.196
LGA    E     7_C      E     7_B     0.529     0    0.582   0.975     8.224   84.524   52.011
LGA    K     8_C      K     8_B     0.369     0    0.065   1.075     5.667   95.238   73.228
LGA    D     9_C      D     9_B     0.890     0    0.054   0.152     2.442   90.476   81.726
LGA    Q    10_C      Q    10_B     0.719     0    0.040   0.661     2.251   90.476   83.651
LGA    L    11_C      L    11_B     0.480     0    0.013   0.059     0.947  100.000   95.238
LGA    R    12_C      R    12_B     0.610     0    0.016   0.140     2.673   95.238   81.255
LGA    T    13_C      T    13_B     0.457     0    0.017   0.929     2.737  100.000   88.639
LGA    Q    14_C      Q    14_B     0.481     0    0.006   0.976     3.546  100.000   80.899
LGA    V    15_C      V    15_B     0.403     0    0.023   0.050     0.752  100.000   95.918
LGA    V    16_C      V    16_B     0.413     0    0.015   0.096     0.801  100.000   95.918
LGA    R    17_C      R    17_B     0.295     0    0.046   1.921     8.815  100.000   66.926
LGA    L    18_C      L    18_B     0.285     0    0.003   0.073     0.774  100.000   96.429
LGA    Q    19_C      Q    19_B     0.355     0    0.018   0.276     0.953  100.000   95.767
LGA    A    20_C      A    20_B     0.304     0    0.063   0.072     0.472  100.000  100.000
LGA    E    21_C      E    21_B     0.227     0    0.011   0.891     3.046  100.000   83.598
LGA    K    22_C      K    22_B     0.474     0    0.019   0.123     0.619   97.619   94.709
LGA    A    23_C      A    23_B     0.495     0    0.028   0.036     0.526   97.619   96.190
LGA    D    24_C      D    24_B     0.386     0    0.033   0.237     1.336  100.000   96.488
LGA    L    25_C      L    25_B     0.418     0    0.011   0.055     0.542  100.000   98.810
LGA    L    26_C      L    26_B     0.349     0    0.052   0.107     0.734  100.000   96.429
LGA    G    27_C      G    27_B     0.577     0    0.084   0.084     0.577   95.238   95.238
LGA    I    28_C      I    28_B     0.482     0    0.025   0.111     0.768   97.619   94.048
LGA    V    29_C      V    29_B     0.228     0    0.032   0.053     0.364  100.000  100.000
LGA    S    30_C      S    30_B     0.382     0    0.030   0.113     0.807  100.000   98.413
LGA    E    31_C      E    31_B     0.525     0    0.026   1.055     5.890   97.619   68.571
LGA    L    32_C      L    32_B     0.237     0    0.012   0.037     0.643  100.000   98.810
LGA    Q    33_C      Q    33_B     0.604     0    0.054   1.044     3.163   92.857   84.074
LGA    L    34_C      L    34_B     0.758     0    0.054   0.206     1.203   90.476   88.214
LGA    K    35_C      K    35_B     0.435     0    0.041   0.487     2.221   92.857   91.852
LGA    L    36_C      L    36_B     0.768     0    0.170   0.186     0.991   90.476   90.476
LGA    N    37_C      N    37_B     0.994     0    0.423   0.904     7.367   68.095   48.571
LGA    S    38_C      S    38_B     7.360     0    0.645   0.805     9.452   12.262    8.651

# 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):     3.683          3.599                  4.133           81.229   73.755

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    0.52    87.162    85.611     5.032

LGA_LOCAL      RMSD:   0.516  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.611  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.683  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.526931 * X  +  -0.703422 * Y  +  -0.477013 * Z  + -42.464828
  Y_new =   0.518255 * X  +  -0.710764 * Y  +   0.475632 * Z  +  39.730190
  Z_new =  -0.673614 * X  +   0.003411 * Y  +   0.739076 * Z  + -109.110146 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.364495  0.739087  0.004615   [DEG:  135.4756   42.3466    0.2644 ]
ZXZ: -2.354745  0.739099 -1.565733   [DEG: -134.9169   42.3473  -89.7099 ]
 
# END of job
