
#######################################################
#                                                     #
#                        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   34 (  315),  selected   26 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   26 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      12_F - 33_F        4.97     7.41
  LCS_AVERAGE:     82.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.70    12.44
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.52    12.98
  LCS_AVERAGE:     38.31

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   26
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     L     8_D     L     8_F      3    3   19      0    3    3    3    3    3   10   14   14   15   17   17   18   19   19   21   22   24   25   25 
LCS_GDT     Q     9_D     Q     9_F      4    4   19      3    3    5    6    6   10   12   14   14   15   17   17   18   19   20   23   23   24   25   25 
LCS_GDT     K    10_D     K    10_F      4    4   19      3    4    5    6    6    6    7   11   13   15   15   15   17   19   19   20   21   23   25   25 
LCS_GDT     L    11_D     L    11_F      4   12   20      3    4    5    7    9   11   12   14   14   15   17   17   18   19   20   23   23   24   25   25 
LCS_GDT     N    12_D     N    12_F     10   12   22      3    8   10   11   11   11   12   14   14   15   17   18   19   20   21   23   23   24   25   25 
LCS_GDT     S    13_D     S    13_F     10   12   22      4    8   10   11   11   11   12   14   14   15   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     W    14_D     W    14_F     10   12   22      4    8   10   11   11   11   12   14   14   15   17   18   18   20   21   23   23   24   25   25 
LCS_GDT     D    15_D     D    15_F     10   12   22      5    8   10   11   11   11   12   14   14   15   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     V    16_D     V    16_F     10   12   22      5    8   10   11   11   12   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     F    17_D     F    17_F     10   12   22      5    8   10   11   11   11   12   14   14   15   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     G    18_D     G    18_F     10   12   22      5    8   10   11   11   11   12   14   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     N    19_D     N    19_F     10   12   22      5    8   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     W    20_D     W    20_F     10   12   22      3    8   10   11   11   11   12   14   15   15   17   17   18   19   20   22   23   24   25   25 
LCS_GDT     F    21_D     F    21_F     10   13   22      3    7   10   11   11   11   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     D    22_D     D    22_F     12   13   22      9   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     L    23_D     L    23_F     12   13   22      9   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     A    24_D     A    24_F     12   13   22      9   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     S    25_D     S    25_F     12   13   22      9   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     W    26_D     W    26_F     12   13   22      9   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     I    27_D     I    27_F     12   13   22      9   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     K    28_D     K    28_F     12   13   22      9   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     Y    29_D     Y    29_F     12   13   22      9   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     I    30_D     I    30_F     12   13   22      9   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     Q    31_D     Q    31_F     12   13   22      8   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     R    32_D     R    32_F     12   13   22      6   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_GDT     R    33_D     R    33_F     12   13   22      3   12   12   13   13   13   14   15   15   16   17   19   19   20   21   23   23   24   25   25 
LCS_AVERAGE  LCS_A:  55.23  (  38.31   44.38   82.99 )

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      9     12     12     13     13     13     14     15     15     16     17     19     19     20     21     23     23     24     25     25 
GDT PERCENT_AT  34.62  46.15  46.15  50.00  50.00  50.00  53.85  57.69  57.69  61.54  65.38  73.08  73.08  76.92  80.77  88.46  88.46  92.31  96.15  96.15
GDT RMS_LOCAL    0.23   0.52   0.52   0.95   0.95   0.95   1.75   2.26   2.26   2.72   3.22   4.14   4.14   4.45   4.74   5.44   5.37   5.69   6.01   6.01
GDT RMS_ALL_AT  12.72  12.98  12.98  11.98  11.98  11.98  11.84  10.57  10.57   9.84   9.45   8.09   8.09   7.49   7.25   6.50   6.89   6.53   6.30   6.30

# Checking swapping
#   possible swapping detected:  F    17_D      F    17_F
#   possible swapping detected:  D    22_D      D    22_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    26.027     0    0.293   0.418    28.441    0.000    0.000
LGA    Q     9_D      Q     9_F    20.701     0    0.610   0.567    22.910    0.000    0.000
LGA    K    10_D      K    10_F    21.600     0    0.069   0.371    27.172    0.000    0.000
LGA    L    11_D      L    11_F    17.801     0    0.599   0.788    19.258    0.000    0.000
LGA    N    12_D      N    12_F    14.454     0    0.661   0.722    16.625    0.000    0.000
LGA    S    13_D      S    13_F    13.841     0    0.024   0.159    16.277    0.000    0.000
LGA    W    14_D      W    14_F    15.516     0    0.019   1.382    23.850    0.000    0.000
LGA    D    15_D      D    15_F    11.012     0    0.041   0.557    15.266    4.524    2.262
LGA    V    16_D      V    16_F     4.819     0    0.059   0.075     7.179   25.000   29.456
LGA    F    17_D      F    17_F     9.338     0    0.025   1.257    18.016    4.524    1.645
LGA    G    18_D      G    18_F     7.040     0    0.195   0.195     7.806   26.071   26.071
LGA    N    19_D      N    19_F     1.473     0    0.193   0.990     6.971   58.690   44.107
LGA    W    20_D      W    20_F     6.265     0    0.133   1.240    16.131   20.595    6.224
LGA    F    21_D      F    21_F     4.535     0    0.604   1.228    11.873   44.405   19.307
LGA    D    22_D      D    22_F     2.719     0    0.575   1.380     7.933   62.976   39.940
LGA    L    23_D      L    23_F     2.257     0    0.097   0.969     4.722   66.786   60.655
LGA    A    24_D      A    24_F     1.961     0    0.046   0.043     2.235   72.976   71.333
LGA    S    25_D      S    25_F     1.747     0    0.145   0.728     2.381   79.405   77.302
LGA    W    26_D      W    26_F     1.390     0    0.049   0.278     2.626   83.690   70.238
LGA    I    27_D      I    27_F     0.614     0    0.032   0.121     1.360   95.238   91.786
LGA    K    28_D      K    28_F     0.368     0    0.104   0.430     4.158   97.619   76.772
LGA    Y    29_D      Y    29_F     0.238     0    0.024   0.340     1.328   97.619   90.635
LGA    I    30_D      I    30_F     1.163     0    0.068   0.655     2.726   81.548   75.298
LGA    Q    31_D      Q    31_F     1.815     0    0.033   1.244     6.243   72.976   54.656
LGA    R    32_D      R    32_F     1.532     0    0.381   0.951     6.167   72.976   62.771
LGA    R    33_D      R    33_F     1.426     0    0.587   0.455     9.207   79.405   40.779

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       26     104    104  100.00     234    234  100.00                26
SUMMARY(RMSD_GDC):     6.259          6.107                  8.106           44.116   36.201

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.26    60.577    54.769     0.635

LGA_LOCAL      RMSD:   2.264  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.570  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   6.259  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.148145 * X  +  -0.239695 * Y  +   0.959479 * Z  +  40.969376
  Y_new =  -0.642067 * X  +  -0.761225 * Y  +  -0.091032 * Z  + -68.780182
  Z_new =   0.752199 * X  +  -0.602564 * Y  +  -0.266672 * Z  +  -4.750206 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.344034 -0.851393 -1.987448   [DEG:  -77.0075  -48.7812 -113.8724 ]
ZXZ:  1.476203  1.840734  2.246189   [DEG:   84.5802  105.4663  128.6971 ]
 
# END of job
