
#######################################################
#                                                     #
#                        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   53 (  410),  selected   49 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   49 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       7_F - 34_F        4.74    13.89
  LONGEST_CONTINUOUS_SEGMENT:    28       8_F - 35_F        4.67    13.84
  LCS_AVERAGE:     52.39

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      11_F - 28_F        1.96    15.29
  LCS_AVERAGE:     22.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      11_F - 25_F        0.86    16.67
  LCS_AVERAGE:     15.58

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   49
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     M     1_F     M     1_F      3    3    9      0    3    3    3    3    4    4    4    5    6    7    7   12   13   15   18   20   21   22   23 
LCS_GDT     G     2_F     G     2_F      3    4   11      0    3    3    4    4    5    8    8    9   10   12   12   13   15   16   19   21   22   23   24 
LCS_GDT     K     3_F     K     3_F      3    4   12      1    3    3    4    4    5    8    8    9   10   12   12   13   15   16   19   21   22   23   24 
LCS_GDT     I     4_F     I     4_F      3    4   12      1    3    3    4    4    5    8    8    9   10   12   12   13   15   16   19   21   22   23   27 
LCS_GDT     K     5_F     K     5_F      3    4   12      3    3    3    4    4    5    7    8    8   10   12   12   13   17   21   21   23   24   26   29 
LCS_GDT     R     6_F     R     6_F      3    3   12      3    3    3    3    3    5    6    6    7    8    9   11   12   15   18   19   23   25   27   29 
LCS_GDT     F     7_F     F     7_F      3    3   28      3    3    3    3    4    4    6    6    7    8   12   13   18   22   25   27   28   32   33   34 
LCS_GDT     F     8_F     F     8_F      3    4   28      1    3    3    3    8    8   10   13   19   21   23   24   26   27   30   33   34   36   37   37 
LCS_GDT     A     9_F     A     9_F      4    4   28      3    4    4    4    7    8   13   17   21   22   24   25   26   27   31   33   34   36   37   38 
LCS_GDT     K    10_F     K    10_F      4   17   28      4    5    6    9   12   15   18   20   22   23   24   25   26   27   30   32   33   36   37   38 
LCS_GDT     D    11_F     D    11_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     M    12_F     M    12_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     R    13_F     R    13_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     A    14_F     A    14_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     A    15_F     A    15_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     L    16_F     L    16_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     A    17_F     A    17_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     Q    18_F     Q    18_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     V    19_F     V    19_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     K    20_F     K    20_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     D    21_F     D    21_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     T    22_F     T    22_F     15   18   28      7   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     L    23_F     L    23_F     15   18   28      9   13   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     G    24_F     G    24_F     15   18   28      4    5   14   15   18   18   19   20   22   23   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     S    25_F     S    25_F     15   18   28      3    8   13   15   15   16   19   20   22   24   24   25   26   27   28   31   34   37   38   39 
LCS_GDT     D    26_F     D    26_F      6   18   28      3   10   14   15   18   18   19   21   22   24   24   25   26   27   32   34   35   37   38   39 
LCS_GDT     A    27_F     A    27_F      6   18   28      3    6    7   15   18   18   19   21   22   24   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     V    28_F     V    28_F      6   18   28      3    5    7   11   14   17   19   21   22   24   24   25   26   29   32   34   35   37   38   39 
LCS_GDT     I    29_F     I    29_F      6   13   28      3    5    7   11   18   18   19   21   22   24   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     M    30_F     M    30_F      6   13   28      3    5    6   11   14   17   19   21   22   24   24   25   26   29   30   33   34   36   38   39 
LCS_GDT     S    31_F     S    31_F      6    8   28      3    5    6   14   18   18   19   21   22   24   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     N    32_F     N    32_F      5    8   28      3    4    5    7   13   17   19   21   22   24   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     K    33_F     K    33_F      5    8   28      3    4    6   11   14   17   19   21   22   24   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     K    34_F     K    34_F      5    8   28      3    4    5    8   11   17   19   21   22   24   24   24   25   30   32   34   35   37   38   39 
LCS_GDT     V    35_F     V    35_F      4    7   28      3    4    4    5    6    6   19   21   22   24   24   24   24   30   32   34   35   37   38   39 
LCS_GDT     N    36_F     N    36_F      3    8   27      3    3    5    9   14   17   19   21   22   24   24   24   24   29   30   34   35   37   38   39 
LCS_GDT     G    37_F     G    37_F      5    8   27      3    4    5    6    6   10   15   21   22   24   24   24   24   25   28   32   34   37   38   39 
LCS_GDT     G    38_F     G    38_F      5    8   27      3    6    7    9   14   17   19   21   22   24   24   24   24   25   28   29   29   33   36   39 
LCS_GDT     I    39_F     I    39_F      5    8   27      3    6    7    9   14   17   19   21   22   24   24   24   24   29   30   34   35   37   38   39 
LCS_GDT     E    40_F     E    40_F      5    8   27      3    6    7   11   14   17   19   21   22   24   24   24   25   30   32   34   35   37   38   39 
LCS_GDT     I    41_F     I    41_F      5    8   27      3    6    7   11   14   17   19   21   22   24   24   25   26   30   32   34   35   37   38   39 
LCS_GDT     V    42_F     V    42_F      5    8   27      5    5    6    9   14   17   19   21   22   24   24   24   25   30   32   34   35   37   38   39 
LCS_GDT     A    43_F     A    43_F      5    8   27      5    5    6    8   10   16   19   20   22   24   24   24   26   30   32   34   35   37   38   39 
LCS_GDT     A    44_F     A    44_F      5    8   27      5    5    6   11   14   17   19   21   22   24   24   24   26   30   32   34   35   37   38   39 
LCS_GDT     V    45_F     V    45_F      5    8   27      5    5    5   11   14   17   19   20   22   24   24   24   24   30   32   34   35   37   38   39 
LCS_GDT     L    46_F     L    46_F      5    8   27      5    5    5    6   10   16   19   21   22   24   24   24   26   30   32   34   35   37   38   39 
LCS_GDT     E    47_F     E    47_F      3    8   27      2    3    5    7   13   17   19   21   22   24   24   24   26   30   32   34   35   37   38   39 
LCS_GDT     H    48_F     H    48_F      3    8   27      2    3    4    6    8   15   19   21   22   24   24   24   24   29   30   34   35   37   38   39 
LCS_GDT     H    49_F     H    49_F      3    8   27      0    4    4    6    8    8   10   11   13   16   18   22   26   30   32   34   35   37   38   39 
LCS_AVERAGE  LCS_A:  30.31  (  15.58   22.95   52.39 )

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     13     14     15     18     18     19     21     22     24     24     25     26     30     32     34     35     37     38     39 
GDT PERCENT_AT  18.37  26.53  28.57  30.61  36.73  36.73  38.78  42.86  44.90  48.98  48.98  51.02  53.06  61.22  65.31  69.39  71.43  75.51  77.55  79.59
GDT RMS_LOCAL    0.33   0.48   0.71   0.86   1.72   1.72   1.95   2.80   2.58   3.19   3.19   3.38   3.66   5.48   5.63   5.90   6.09   6.40   6.48   6.68
GDT RMS_ALL_AT  16.57  16.56  16.44  16.67  14.69  14.69  14.76  15.20  14.57  14.79  14.79  14.25  14.08  12.93  13.00  12.97  12.95  13.08  13.06  13.12

# Checking swapping
#   possible swapping detected:  F     7_F      F     7_F
#   possible swapping detected:  D    11_F      D    11_F
#   possible swapping detected:  D    21_F      D    21_F
#   possible swapping detected:  D    26_F      D    26_F
#   possible swapping detected:  E    40_F      E    40_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M     1_F      M     1_F    30.370     0    0.396   1.136    31.954    0.000    0.000
LGA    G     2_F      G     2_F    29.598     0    0.588   0.588    29.763    0.000    0.000
LGA    K     3_F      K     3_F    24.411     0    0.551   1.085    30.429    0.000    0.000
LGA    I     4_F      I     4_F    20.292     0    0.587   1.168    21.816    0.000    0.000
LGA    K     5_F      K     5_F    17.924     0    0.593   1.196    20.254    0.000    0.000
LGA    R     6_F      R     6_F    18.124     0    0.579   1.095    24.044    0.000    0.000
LGA    F     7_F      F     7_F    21.651     0    0.614   1.265    27.979    0.000    0.000
LGA    F     8_F      F     8_F    19.593     0    0.612   1.426    24.044    0.000    0.000
LGA    A     9_F      A     9_F    21.121     0    0.598   0.582    22.184    0.000    0.000
LGA    K    10_F      K    10_F    26.319     0    0.082   1.248    34.947    0.000    0.000
LGA    D    11_F      D    11_F    25.128     0    0.604   0.973    26.453    0.000    0.000
LGA    M    12_F      M    12_F    18.466     0    0.032   1.337    20.931    0.000    0.000
LGA    R    13_F      R    13_F    21.731     0    0.053   1.470    27.195    0.000    0.000
LGA    A    14_F      A    14_F    24.939     0    0.034   0.040    27.128    0.000    0.000
LGA    A    15_F      A    15_F    19.512     0    0.033   0.034    21.175    0.000    0.000
LGA    L    16_F      L    16_F    15.045     0    0.026   1.207    16.643    0.000    0.000
LGA    A    17_F      A    17_F    20.474     0    0.046   0.049    23.257    0.000    0.000
LGA    Q    18_F      Q    18_F    22.189     0    0.056   0.752    29.079    0.000    0.000
LGA    V    19_F      V    19_F    16.146     0    0.032   1.078    17.923    0.000    0.000
LGA    K    20_F      K    20_F    14.887     0    0.039   0.732    17.038    0.000    0.000
LGA    D    21_F      D    21_F    21.554     0    0.040   1.290    25.749    0.000    0.000
LGA    T    22_F      T    22_F    22.535     0    0.092   1.140    23.675    0.000    0.000
LGA    L    23_F      L    23_F    16.556     0    0.030   1.102    18.299    0.000    0.000
LGA    G    24_F      G    24_F    14.088     0    0.617   0.617    14.881    0.000    0.000
LGA    S    25_F      S    25_F     7.921     0    0.626   0.574    10.104    9.405    8.254
LGA    D    26_F      D    26_F     2.321     0    0.611   1.281     5.112   61.429   57.798
LGA    A    27_F      A    27_F     1.291     0    0.118   0.203     1.583   79.286   78.000
LGA    V    28_F      V    28_F     1.261     0    0.112   1.169     4.259   79.286   71.497
LGA    I    29_F      I    29_F     1.430     0    0.212   1.319     5.524   79.524   61.429
LGA    M    30_F      M    30_F     2.576     0    0.630   1.003     7.578   60.476   42.976
LGA    S    31_F      S    31_F     3.229     0    0.076   0.706     5.705   59.286   46.667
LGA    N    32_F      N    32_F     2.885     0    0.450   1.059     6.350   52.619   38.333
LGA    K    33_F      K    33_F     2.533     0    0.069   1.023    10.049   59.167   34.815
LGA    K    34_F      K    34_F     3.182     0    0.287   1.024    12.737   63.095   32.116
LGA    V    35_F      V    35_F     4.166     0    0.596   0.894     7.879   46.905   32.721
LGA    N    36_F      N    36_F     1.855     0    0.610   1.062     4.900   63.452   50.476
LGA    G    37_F      G    37_F     4.636     0    0.185   0.185     5.092   37.738   37.738
LGA    G    38_F      G    38_F     2.459     0    0.197   0.197     3.066   57.262   57.262
LGA    I    39_F      I    39_F     2.556     0    0.041   0.718     3.131   62.857   60.060
LGA    E    40_F      E    40_F     2.444     0    0.199   0.557     2.536   62.857   72.328
LGA    I    41_F      I    41_F     3.038     0    0.129   1.130     7.227   51.905   36.310
LGA    V    42_F      V    42_F     3.003     0    0.634   0.658     4.734   49.405   51.769
LGA    A    43_F      A    43_F     4.547     0    0.054   0.099     7.086   42.024   35.619
LGA    A    44_F      A    44_F     2.077     0    0.047   0.068     4.044   52.262   56.381
LGA    V    45_F      V    45_F     4.294     0    0.046   0.942     9.072   39.167   25.034
LGA    L    46_F      L    46_F     2.723     0    0.552   1.376     8.285   62.976   39.405
LGA    E    47_F      E    47_F     2.067     0    0.614   0.739     8.337   61.429   38.042
LGA    H    48_F      H    48_F     4.070     0    0.601   0.519     7.970   30.595   48.667
LGA    H    49_F      H    49_F    10.078     0    0.601   1.474    13.913    1.786    0.714

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       49     196    196  100.00     370    370  100.00                49
SUMMARY(RMSD_GDC):    12.109         12.025                 12.688           27.065   22.743

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     21    2.80    42.347    37.119     0.725

LGA_LOCAL      RMSD:   2.797  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.204  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:  12.109  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.612203 * X  +  -0.741915 * Y  +   0.273440 * Z  +  57.436611
  Y_new =   0.730010 * X  +   0.397473 * Y  +  -0.555968 * Z  + -99.719566
  Z_new =   0.303796 * X  +   0.539980 * Y  +   0.784940 * Z  + -74.346428 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.872944 -0.308674  0.602576   [DEG:   50.0160  -17.6857   34.5251 ]
ZXZ:  0.457088  0.668198  0.512470   [DEG:   26.1892   38.2849   29.3624 ]
 
# END of job
