
#######################################################
#                                                     #
#                        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   36 (  285),  selected   36 , name one
# Molecule2: number of CA atoms   37 (  291),  selected   36 , 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:    36       2_B - 37_B        3.76     3.76
  LCS_AVERAGE:     97.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       6_B - 37_B        1.67     4.58
  LCS_AVERAGE:     77.78

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.91     4.89
  LCS_AVERAGE:     73.27

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   36
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   36      0    3    3    3    3    4    4    4    9   11   11   13   14   17   20   22   24   27   29   32 
LCS_GDT     E     3_C     E     3_B      3    3   36      0    3    3    3    3    4    5   15   19   22   27   31   32   35   35   35   35   35   35   35 
LCS_GDT     A     4_C     A     4_B      3    3   36      3    3    3    3    6    6   17   26   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     E     5_C     E     5_B      3    3   36      3    3    3    3    7   12   15   22   28   32   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     Q     6_C     Q     6_B      3   32   36      3    3    3    6    8   14   20   26   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     E     7_C     E     7_B     31   32   36      9   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     K     8_C     K     8_B     31   32   36      9   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     D     9_C     D     9_B     31   32   36      9   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     Q    10_C     Q    10_B     31   32   36      8   19   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     L    11_C     L    11_B     31   32   36      9   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     R    12_C     R    12_B     31   32   36     13   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     T    13_C     T    13_B     31   32   36      9   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     Q    14_C     Q    14_B     31   32   36      9   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     V    15_C     V    15_B     31   32   36     10   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     V    16_C     V    16_B     31   32   36     10   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     R    17_C     R    17_B     31   32   36     13   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     L    18_C     L    18_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     Q    19_C     Q    19_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     A    20_C     A    20_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     E    21_C     E    21_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     K    22_C     K    22_B     31   32   36      9   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     A    23_C     A    23_B     31   32   36      9   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     D    24_C     D    24_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     L    25_C     L    25_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     L    26_C     L    26_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     G    27_C     G    27_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     I    28_C     I    28_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     V    29_C     V    29_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     S    30_C     S    30_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     E    31_C     E    31_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     L    32_C     L    32_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     Q    33_C     Q    33_B     31   32   36     14   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     L    34_C     L    34_B     31   32   36     10   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     K    35_C     K    35_B     31   32   36      7   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     L    36_C     L    36_B     31   32   36     12   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_GDT     N    37_C     N    37_B     31   32   36     12   24   30   31   31   31   31   31   33   33   34   34   34   35   35   35   35   35   35   35 
LCS_AVERAGE  LCS_A:  82.78  (  73.27   77.78   97.30 )

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     14     24     30     31     31     31     31     31     33     33     34     34     34     35     35     35     35     35     35     35 
GDT PERCENT_AT  37.84  64.86  81.08  83.78  83.78  83.78  83.78  83.78  89.19  89.19  91.89  91.89  91.89  94.59  94.59  94.59  94.59  94.59  94.59  94.59
GDT RMS_LOCAL    0.33   0.63   0.86   0.91   0.91   0.91   0.91   0.91   2.21   2.21   2.59   2.59   2.59   3.04   3.04   3.04   3.04   3.04   3.04   3.04
GDT RMS_ALL_AT   5.53   5.46   4.96   4.89   4.89   4.89   4.89   4.89   4.23   4.23   4.02   4.02   4.02   3.85   3.85   3.85   3.85   3.85   3.85   3.85

# Checking swapping
#   possible swapping detected:  D     9_C      D     9_B
#   possible swapping detected:  E    21_C      E    21_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B    19.001     0    0.491   0.474    20.794    0.000    0.000
LGA    E     3_C      E     3_B    13.400     0    0.546   1.051    15.252    0.000    0.000
LGA    A     4_C      A     4_B    10.160     0    0.604   0.586    11.398    0.000    0.000
LGA    E     5_C      E     5_B    11.028     0    0.663   0.654    13.905    0.000    0.000
LGA    Q     6_C      Q     6_B     8.443     0    0.626   1.366    15.987   10.000    4.497
LGA    E     7_C      E     7_B     1.122     0    0.597   0.729     6.498   74.167   57.460
LGA    K     8_C      K     8_B     0.713     0    0.031   1.193     6.326   90.476   72.593
LGA    D     9_C      D     9_B     1.183     0    0.013   0.115     2.591   83.690   76.310
LGA    Q    10_C      Q    10_B     1.740     0    0.063   1.051     6.863   79.286   54.656
LGA    L    11_C      L    11_B     1.125     0    0.055   1.100     2.037   85.952   79.583
LGA    R    12_C      R    12_B     0.369     0    0.031   0.131     3.186  100.000   79.437
LGA    T    13_C      T    13_B     0.351     0    0.047   0.955     2.911   97.619   87.279
LGA    Q    14_C      Q    14_B     0.619     0    0.086   0.732     4.392   92.857   72.751
LGA    V    15_C      V    15_B     0.513     0    0.020   0.104     0.799   92.857   91.837
LGA    V    16_C      V    16_B     0.647     0    0.061   0.902     2.847   90.476   83.197
LGA    R    17_C      R    17_B     0.924     0    0.031   1.157     8.613   88.214   56.623
LGA    L    18_C      L    18_B     0.844     0    0.032   0.118     0.964   90.476   90.476
LGA    Q    19_C      Q    19_B     0.640     0    0.027   0.152     0.797   90.476   92.593
LGA    A    20_C      A    20_B     0.891     0    0.082   0.089     1.304   85.952   85.048
LGA    E    21_C      E    21_B     1.171     0    0.037   1.119     4.459   79.286   65.873
LGA    K    22_C      K    22_B     1.122     0    0.018   0.080     1.673   81.429   82.487
LGA    A    23_C      A    23_B     1.069     0    0.019   0.022     1.114   81.429   81.429
LGA    D    24_C      D    24_B     1.143     0    0.000   0.208     2.278   81.429   78.274
LGA    L    25_C      L    25_B     1.065     0    0.026   0.167     1.830   85.952   82.619
LGA    L    26_C      L    26_B     0.489     0    0.034   0.075     0.875   97.619   94.048
LGA    G    27_C      G    27_B     0.728     0    0.072   0.072     0.803   90.476   90.476
LGA    I    28_C      I    28_B     0.822     0    0.025   0.085     1.500   90.476   88.214
LGA    V    29_C      V    29_B     0.387     0    0.036   0.067     0.636  100.000   98.639
LGA    S    30_C      S    30_B     0.268     0    0.040   0.628     2.210  100.000   94.127
LGA    E    31_C      E    31_B     0.504     0    0.044   0.947     5.058   95.238   72.646
LGA    L    32_C      L    32_B     0.174     0    0.041   1.372     3.453  100.000   83.095
LGA    Q    33_C      Q    33_B     0.520     0    0.072   1.020     2.831   92.857   86.931
LGA    L    34_C      L    34_B     1.098     0    0.067   0.133     1.954   81.548   80.417
LGA    K    35_C      K    35_B     1.185     0    0.000   1.073     5.013   81.429   71.058
LGA    L    36_C      L    36_B     1.161     0    0.027   1.398     3.913   81.429   71.548
LGA    N    37_C      N    37_B     1.291     0    0.503   1.119     6.438   55.357   47.738

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       36     144    144  100.00     285    285  100.00                37
SUMMARY(RMSD_GDC):     3.764          3.743                  4.228           73.742   66.323

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   36   37    4.0     31    0.91    81.757    82.934     3.073

LGA_LOCAL      RMSD:   0.909  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.894  Number of assigned atoms:   36 
Std_ASGN_ATOMS RMSD:   3.764  Standard rmsd on all 36 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.574433 * X  +  -0.021578 * Y  +   0.818267 * Z  + -213.615646
  Y_new =  -0.814287 * X  +  -0.086851 * Y  +  -0.573929 * Z  + 189.939270
  Z_new =   0.083452 * X  +  -0.995988 * Y  +   0.032320 * Z  + -55.694004 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.185166 -0.083549 -1.538358   [DEG: -125.2008   -4.7870  -88.1414 ]
ZXZ:  0.959135  1.538471  3.058000   [DEG:   54.9544   88.1479  175.2105 ]
 
# END of job
