
#######################################################
#                                                     #
#                        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        3.61     3.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.80     4.38
  LCS_AVERAGE:     80.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.57     4.64
  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   24   28   32   36 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   15   19   23   28   34   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   29   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3    3   37      3    3    3    4    6   10   15   23   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    4    8   17   26   29   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     21   30   31   31   31   31   31   31   32   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     18   26   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     20   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     21   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     20   30   31   31   31   31   31   31   33   34   34   34   35   35   36   36   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     18   30   31   31   31   31   31   31   33   34   34   34   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   34   35   36   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     21     30     31     31     31     31     31     31     33     34     34     34     35     35     36     36     36     36     36     36 
GDT PERCENT_AT  56.76  81.08  83.78  83.78  83.78  83.78  83.78  83.78  89.19  91.89  91.89  91.89  94.59  94.59  97.30  97.30  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.30   0.53   0.57   0.57   0.57   0.57   0.57   0.57   2.25   2.27   2.27   2.27   2.73   2.52   2.94   2.94   2.94   2.94   2.94   2.94
GDT RMS_ALL_AT   4.62   4.66   4.64   4.64   4.64   4.64   4.64   4.64   3.76   3.82   3.82   3.82   3.69   3.84   3.69   3.69   3.69   3.69   3.69   3.69

# Checking swapping
#   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    18.092     0    0.453   0.444    19.735    0.000    0.000
LGA    E     3_C      E     3_B    12.607     0    0.591   1.027    14.380    0.000    0.000
LGA    A     4_C      A     4_B     9.571     0    0.626   0.586    10.751    0.238    0.190
LGA    E     5_C      E     5_B    10.182     0    0.601   1.239    12.695    1.071    0.476
LGA    Q     6_C      Q     6_B     7.461     0    0.602   0.964    12.432   16.429    7.778
LGA    E     7_C      E     7_B     0.467     0    0.581   0.954     8.676   86.905   50.688
LGA    K     8_C      K     8_B     0.680     0    0.065   1.083     6.150   90.476   68.307
LGA    D     9_C      D     9_B     1.236     0    0.052   0.191     2.913   88.214   76.548
LGA    Q    10_C      Q    10_B     0.771     0    0.045   0.280     2.352   92.857   85.661
LGA    L    11_C      L    11_B     0.461     0    0.010   0.061     1.009   97.619   92.917
LGA    R    12_C      R    12_B     0.769     0    0.021   0.298     2.594   90.476   77.186
LGA    T    13_C      T    13_B     0.487     0    0.029   0.937     2.804  100.000   89.864
LGA    Q    14_C      Q    14_B     0.680     0    0.012   1.028     4.051   92.857   74.497
LGA    V    15_C      V    15_B     0.563     0    0.023   0.061     0.983   97.619   94.558
LGA    V    16_C      V    16_B     0.274     0    0.015   0.105     0.741  100.000   98.639
LGA    R    17_C      R    17_B     0.278     0    0.049   1.951     9.698  100.000   61.255
LGA    L    18_C      L    18_B     0.457     0    0.018   0.086     1.045  100.000   94.107
LGA    Q    19_C      Q    19_B     0.325     0    0.019   0.258     0.925  100.000   97.884
LGA    A    20_C      A    20_B     0.221     0    0.078   0.087     0.311  100.000  100.000
LGA    E    21_C      E    21_B     0.447     0    0.014   0.102     1.089   95.238   91.587
LGA    K    22_C      K    22_B     0.581     0    0.023   0.115     0.948   90.476   90.476
LGA    A    23_C      A    23_B     0.470     0    0.029   0.038     0.497  100.000  100.000
LGA    D    24_C      D    24_B     0.356     0    0.034   0.217     1.228  100.000   96.488
LGA    L    25_C      L    25_B     0.486     0    0.011   0.061     0.628  100.000   95.238
LGA    L    26_C      L    26_B     0.462     0    0.035   0.096     0.820  100.000   95.238
LGA    G    27_C      G    27_B     0.513     0    0.092   0.092     0.513   95.238   95.238
LGA    I    28_C      I    28_B     0.470     0    0.019   0.113     0.697   97.619   94.048
LGA    V    29_C      V    29_B     0.296     0    0.033   0.052     0.516  100.000   98.639
LGA    S    30_C      S    30_B     0.341     0    0.040   0.586     1.888  100.000   95.476
LGA    E    31_C      E    31_B     0.367     0    0.019   0.925     4.949  100.000   76.349
LGA    L    32_C      L    32_B     0.202     0    0.009   0.039     0.560  100.000   98.810
LGA    Q    33_C      Q    33_B     0.607     0    0.036   1.052     3.114   92.857   84.074
LGA    L    34_C      L    34_B     0.730     0    0.063   0.216     1.074   90.476   89.345
LGA    K    35_C      K    35_B     0.599     0    0.020   0.470     2.112   90.476   89.735
LGA    L    36_C      L    36_B     0.782     0    0.038   0.064     0.898   90.476   94.048
LGA    N    37_C      N    37_B     0.999     0    0.295   0.875     7.358   71.667   49.702
LGA    S    38_C      S    38_B     6.971     0    0.631   0.557     9.167   15.595   11.111

# 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):     3.606          3.488                  4.133           80.672   73.410

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    0.57    86.486    85.457     4.600

LGA_LOCAL      RMSD:   0.574  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.638  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.606  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.007359 * X  +  -0.245912 * Y  +  -0.969264 * Z  + -11.888451
  Y_new =  -0.999671 * X  +  -0.025629 * Y  +  -0.001088 * Z  +  29.487478
  Z_new =  -0.024573 * X  +   0.968953 * Y  +  -0.246020 * Z  + -38.239929 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.563435  0.024576  1.819445   [DEG:  -89.5782    1.4081  104.2465 ]
ZXZ: -1.569674  1.819368 -0.025355   [DEG:  -89.9357  104.2421   -1.4528 ]
 
# END of job
