
#######################################################
#                                                     #
#                        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        3.62     3.62
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.99     4.01
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.79     4.37
  LCS_AVERAGE:     82.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.47     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    8    9   10   11   13   14   16   22   23   25   28   32   36 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   16   20   25   30   35   35   35   36   36   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3    6    6    8   30   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3   33   37      3    3    3    4    6   10   15   23   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    4    8   16   27   30   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     22   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     22   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     23   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     22   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     22   31   31   31   31   31   31   31   32   34   34   35   35   35   36   36   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    4    4    7    7   10   21   32   32   32   34   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     23     31     31     31     31     31     31     31     32     34     34     35     35     35     36     36     36     36     36     36 
GDT PERCENT_AT  62.16  83.78  83.78  83.78  83.78  83.78  83.78  83.78  86.49  91.89  91.89  94.59  94.59  94.59  97.30  97.30  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.28   0.47   0.47   0.47   0.47   0.47   0.47   0.47   1.32   2.26   2.26   2.71   2.71   2.71   2.95   2.95   2.95   2.95   2.95   2.95
GDT RMS_ALL_AT   4.57   4.61   4.61   4.61   4.61   4.61   4.61   4.61   4.36   3.83   3.83   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70   3.70

# Checking swapping
#   possible swapping detected:  E     5_C      E     5_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    17.980     0    0.444   0.436    19.599    0.000    0.000
LGA    E     3_C      E     3_B    12.461     0    0.609   1.026    14.254    0.000    0.000
LGA    A     4_C      A     4_B     9.490     0    0.629   0.584    10.681    0.476    0.381
LGA    E     5_C      E     5_B    10.172     0    0.608   0.667    12.994    1.190    0.529
LGA    Q     6_C      Q     6_B     7.376     0    0.598   0.918    12.299   16.429    7.989
LGA    E     7_C      E     7_B     0.319     0    0.580   0.954     8.638   89.286   52.116
LGA    K     8_C      K     8_B     0.518     0    0.065   1.059     5.763   92.857   72.169
LGA    D     9_C      D     9_B     0.961     0    0.053   0.170     2.586   90.476   77.679
LGA    Q    10_C      Q    10_B     0.655     0    0.042   0.279     2.058   92.857   86.667
LGA    L    11_C      L    11_B     0.430     0    0.011   0.059     0.886  100.000   95.238
LGA    R    12_C      R    12_B     0.613     0    0.019   0.304     2.148   97.619   83.550
LGA    T    13_C      T    13_B     0.414     0    0.025   0.934     2.671  100.000   88.639
LGA    Q    14_C      Q    14_B     0.587     0    0.013   1.059     3.920   97.619   77.302
LGA    V    15_C      V    15_B     0.419     0    0.021   0.052     0.784  100.000   95.918
LGA    V    16_C      V    16_B     0.271     0    0.016   0.099     0.657  100.000   98.639
LGA    R    17_C      R    17_B     0.235     0    0.055   1.926     9.703  100.000   61.255
LGA    L    18_C      L    18_B     0.274     0    0.015   0.073     0.768  100.000   96.429
LGA    Q    19_C      Q    19_B     0.214     0    0.017   0.160     0.601  100.000   98.942
LGA    A    20_C      A    20_B     0.196     0    0.049   0.057     0.268  100.000  100.000
LGA    E    21_C      E    21_B     0.304     0    0.014   0.123     0.869  100.000   96.825
LGA    K    22_C      K    22_B     0.498     0    0.024   0.133     0.809   97.619   94.709
LGA    A    23_C      A    23_B     0.458     0    0.013   0.023     0.487  100.000  100.000
LGA    D    24_C      D    24_B     0.331     0    0.062   0.811     3.162  100.000   83.988
LGA    L    25_C      L    25_B     0.414     0    0.013   0.052     0.518  100.000   98.810
LGA    L    26_C      L    26_B     0.365     0    0.048   0.100     0.729  100.000   96.429
LGA    G    27_C      G    27_B     0.469     0    0.095   0.095     0.469  100.000  100.000
LGA    I    28_C      I    28_B     0.426     0    0.022   0.098     0.596  100.000   97.619
LGA    V    29_C      V    29_B     0.233     0    0.029   0.050     0.398  100.000  100.000
LGA    S    30_C      S    30_B     0.309     0    0.028   0.123     0.787  100.000   98.413
LGA    E    31_C      E    31_B     0.394     0    0.018   0.912     4.975  100.000   75.344
LGA    L    32_C      L    32_B     0.222     0    0.004   0.059     0.715  100.000   98.810
LGA    Q    33_C      Q    33_B     0.590     0    0.035   1.053     3.263   92.857   84.074
LGA    L    34_C      L    34_B     0.635     0    0.073   0.214     1.103   90.476   89.345
LGA    K    35_C      K    35_B     0.416     0    0.031   0.451     1.971  100.000   95.926
LGA    L    36_C      L    36_B     0.634     0    0.040   0.062     0.702   90.476   94.048
LGA    N    37_C      N    37_B     0.745     0    0.322   0.861     7.151   72.024   51.369
LGA    S    38_C      S    38_B     7.213     0    0.612   0.781     9.154   13.690    9.841

# 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):     3.621          3.517                  4.102           82.053   74.567

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    0.47    87.162    86.182     5.434

LGA_LOCAL      RMSD:   0.471  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.607  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.621  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.900021 * X  +  -0.355631 * Y  +   0.251971 * Z  + -11.925632
  Y_new =  -0.115827 * X  +  -0.362169 * Y  +  -0.924888 * Z  +  33.576149
  Z_new =   0.420175 * X  +  -0.861603 * Y  +   0.284768 * Z  + -36.897991 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.013602 -0.433638 -1.251590   [DEG: -172.6667  -24.8456  -71.7108 ]
ZXZ:  0.265980  1.282032  2.687860   [DEG:   15.2395   73.4550  154.0031 ]
 
# END of job
