
#######################################################
#                                                     #
#                        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        3.77     3.77
  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     4.53
  LCS_AVERAGE:     80.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.73     4.74
  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    9    9   11   13   16   18   21   25   25   28   30   31   36 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    7   16   20   24   28   32   35   36   36   36   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3   14   19   21   27   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3    3   37      3    3    3    4    5    8   12   17   27   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    6    8   15   23   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     15   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     18   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     31   33   37     16   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     19   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     18   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     17   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     18   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     16   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     11   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     12   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     12   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     11   30   30   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37      3    3    3   31   31   31   31   31   33   33   34   34   35   36   36   36   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    4    4    4    9   12   16   32   32   32   34   36   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     19     30     30     31     31     31     31     31     33     33     34     34     35     36     36     36     36     36     36     36 
GDT PERCENT_AT  51.35  81.08  81.08  83.78  83.78  83.78  83.78  83.78  89.19  89.19  91.89  91.89  94.59  97.30  97.30  97.30  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.29   0.56   0.56   0.73   0.73   0.73   0.73   0.73   2.08   2.08   2.50   2.50   2.93   3.13   3.13   3.13   3.13   3.13   3.13   3.13
GDT RMS_ALL_AT   4.70   4.79   4.79   4.74   4.74   4.74   4.74   4.74   4.16   4.16   3.97   3.97   3.84   3.84   3.84   3.84   3.84   3.84   3.84   3.84

# Checking swapping
#   possible swapping detected:  E     3_C      E     3_B
#   possible swapping detected:  E     7_C      E     7_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    18.123     0    0.471   0.482    19.736    0.000    0.000
LGA    E     3_C      E     3_B    12.837     0    0.632   1.046    14.558    0.000    0.000
LGA    A     4_C      A     4_B    10.193     0    0.620   0.577    11.302    0.000    0.000
LGA    E     5_C      E     5_B    10.865     0    0.602   0.995    12.911    0.714    0.317
LGA    Q     6_C      Q     6_B     7.532     0    0.598   1.308    15.028   14.048    6.772
LGA    E     7_C      E     7_B     0.469     0    0.580   0.961     8.518   84.524   51.481
LGA    K     8_C      K     8_B     0.851     0    0.064   1.103     4.676   92.857   76.402
LGA    D     9_C      D     9_B     0.585     0    0.045   0.175     1.795   95.238   88.393
LGA    Q    10_C      Q    10_B     0.510     0    0.036   0.290     1.754   95.238   90.635
LGA    L    11_C      L    11_B     0.339     0    0.011   0.074     0.822  100.000   96.429
LGA    R    12_C      R    12_B     0.350     0    0.029   1.497     5.157  100.000   73.723
LGA    T    13_C      T    13_B     0.156     0    0.027   0.981     2.362  100.000   89.932
LGA    Q    14_C      Q    14_B     0.379     0    0.012   0.636     3.567  100.000   81.905
LGA    V    15_C      V    15_B     0.589     0    0.018   0.049     0.865   92.857   91.837
LGA    V    16_C      V    16_B     0.569     0    0.030   0.093     0.824   97.619   94.558
LGA    R    17_C      R    17_B     0.258     0    0.018   1.729     7.701  100.000   67.489
LGA    L    18_C      L    18_B     0.353     0    0.022   0.111     0.555  100.000   98.810
LGA    Q    19_C      Q    19_B     0.508     0    0.018   0.195     0.943   92.857   95.767
LGA    A    20_C      A    20_B     0.534     0    0.016   0.018     0.597   90.476   90.476
LGA    E    21_C      E    21_B     0.522     0    0.012   0.104     0.857   90.476   90.476
LGA    K    22_C      K    22_B     0.480     0    0.026   0.073     0.823   97.619   94.709
LGA    A    23_C      A    23_B     0.450     0    0.006   0.011     0.483  100.000  100.000
LGA    D    24_C      D    24_B     0.588     0    0.006   0.201     1.596   95.238   89.524
LGA    L    25_C      L    25_B     0.399     0    0.002   0.021     0.826  100.000   96.429
LGA    L    26_C      L    26_B     0.207     0    0.041   0.043     0.464  100.000  100.000
LGA    G    27_C      G    27_B     0.628     0    0.082   0.082     0.628   97.619   97.619
LGA    I    28_C      I    28_B     0.241     0    0.021   0.080     1.095  100.000   95.298
LGA    V    29_C      V    29_B     0.356     0    0.031   0.063     0.533   97.619   98.639
LGA    S    30_C      S    30_B     0.613     0    0.027   0.097     0.907   92.857   92.063
LGA    E    31_C      E    31_B     0.462     0    0.027   1.049     6.059  100.000   69.153
LGA    L    32_C      L    32_B     0.627     0    0.012   0.054     1.223   90.595   88.274
LGA    Q    33_C      Q    33_B     1.302     0    0.006   1.066     4.305   81.548   72.804
LGA    L    34_C      L    34_B     1.203     0    0.040   0.151     1.793   81.429   80.357
LGA    K    35_C      K    35_B     0.809     0    0.031   0.566     2.989   90.476   84.815
LGA    L    36_C      L    36_B     0.575     0    0.670   0.619     2.368   86.429   83.988
LGA    N    37_C      N    37_B     2.505     0    0.076   0.820     6.871   60.952   43.333
LGA    S    38_C      S    38_B     6.630     0    0.291   0.601     8.977   12.619   10.556

# 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):     3.769          3.775                  4.184           79.241   72.513

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    0.73    86.486    85.208     3.729

LGA_LOCAL      RMSD:   0.731  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.743  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.769  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.037673 * X  +   0.847478 * Y  +   0.529491 * Z  + -33.547287
  Y_new =  -0.733642 * X  +  -0.383222 * Y  +   0.561169 * Z  +  51.230545
  Z_new =   0.678491 * X  +  -0.367316 * Y  +   0.636183 * Z  + -33.226597 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.622102 -0.745707 -0.523617   [DEG:  -92.9396  -42.7258  -30.0011 ]
ZXZ:  2.385231  0.881256  2.066991   [DEG:  136.6637   50.4922  118.4299 ]
 
# END of job
