
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        3.82     3.82
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21       1_A - 21_A        1.92     4.40
  LONGEST_CONTINUOUS_SEGMENT:    21       2_A - 22_A        1.92     4.37
  LCS_AVERAGE:     31.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       4_A - 20_A        0.87     4.22
  LCS_AVERAGE:     22.81

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     D     1_A     D     1_A      9   21   60      3    4    7   20   25   34   36   38   38   46   53   56   58   58   59   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     15   21   60      5   16   24   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     15   21   60      5   11   23   31   34   35   36   44   48   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     17   21   60      5   16   28   31   34   35   38   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     17   21   60      5   12   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     17   21   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     17   21   60     12   19   26   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A      4   21   60      3    4    4    9   18   29   33   39   47   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A      4   21   60      4    4    4    9   14   20   25   36   46   48   53   54   58   58   59   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      4   19   60      4    4    7   13   23   30   34   43   47   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A      4    5   60      4    4    4    5    6    9   20   29   38   43   50   54   58   58   59   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A      4   16   60      4    4    7   11   20   29   34   43   47   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     14   16   60      3   10   14   14   15   25   31   46   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     14   16   60      8   13   14   15   28   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     14   16   60     11   13   14   22   28   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     14   16   60      8   13   14   16   28   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     14   16   60     11   13   14   22   28   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     14   16   60     11   13   14   22   28   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     14   16   60     11   13   14   22   28   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     14   16   60     11   13   14   19   28   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     14   16   60     11   13   14   22   28   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     14   16   60     11   13   14   22   28   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     14   16   60     11   13   14   22   28   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     14   16   60     11   13   14   15   24   33   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     14   16   60     11   13   14   17   24   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     14   16   60     11   13   14   22   28   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A      4   16   60      3    3    4    6   15   18   25   31   48   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A      4   16   60      3    3    4    6   10   14   18   27   31   38   49   53   57   58   59   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A      4   19   60      3    3    8   13   19   25   31   46   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     12   19   60      3    3   11   16   22   25   36   38   38   42   50   53   58   58   59   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     14   19   60      4    8   14   18   23   35   36   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     15   19   60      5   14   18   23   34   35   40   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     15   19   60      4   14   18   23   34   35   40   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     15   19   60      7   15   24   31   34   35   40   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     15   19   60      8   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     15   19   60      8   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     15   19   60      8   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     15   19   60      8   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     15   19   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     15   19   60     12   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     15   19   60      8   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     15   19   60      7   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     15   19   60      9   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     15   19   60      9   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     15   19   60      8   19   28   31   34   35   36   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     15   19   60      5   19   28   31   34   35   41   47   49   52   55   56   58   58   59   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     14   19   60      3    3    3    9   15   31   35   38   40   49   55   56   58   58   59   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  51.30  (  22.81   31.08  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     12     19     28     31     34     35     41     47     49     52     55     56     58     58     59     60     60     60     60     60 
GDT PERCENT_AT  20.00  31.67  46.67  51.67  56.67  58.33  68.33  78.33  81.67  86.67  91.67  93.33  96.67  96.67  98.33 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.61   0.98   1.10   1.32   1.45   2.35   2.74   2.89   3.11   3.31   3.40   3.58   3.58   3.69   3.82   3.82   3.82   3.82   3.82
GDT RMS_ALL_AT   4.12   4.28   4.63   4.67   4.77   4.76   4.16   4.00   3.99   3.90   3.86   3.85   3.83   3.83   3.82   3.82   3.82   3.82   3.82   3.82

# Checking swapping
#   possible swapping detected:  D     8_A      D     8_A
#   possible swapping detected:  E    23_A      E    23_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  F    45_A      F    45_A
#   possible swapping detected:  D    53_A      D    53_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     7.480     0    0.164   0.454     9.636    7.738    9.107
LGA    D     2_A      D     2_A     3.737     0    0.148   0.196     4.845   42.024   47.917
LGA    K     3_A      K     3_A     4.683     0    0.064   1.382     6.551   37.262   30.741
LGA    A     4_A      A     4_A     4.098     0    0.029   0.035     4.832   47.262   44.095
LGA    A     5_A      A     5_A     2.376     0    0.069   0.067     2.996   71.190   68.381
LGA    C     6_A      C     6_A     1.368     0    0.067   0.135     3.142   77.143   70.556
LGA    A     7_A      A     7_A     1.858     0    0.038   0.053     2.209   72.857   71.238
LGA    D     8_A      D     8_A     1.303     0    0.045   0.979     3.634   81.429   73.512
LGA    G     9_A      G     9_A     0.889     0    0.054   0.054     1.215   85.952   85.952
LGA    I    10_A      I    10_A     1.458     0    0.031   1.265     5.246   79.286   68.452
LGA    A    11_A      A    11_A     1.382     0    0.045   0.052     1.455   81.429   81.429
LGA    A    12_A      A    12_A     1.050     0    0.044   0.050     1.136   83.690   83.238
LGA    V    13_A      V    13_A     0.751     0    0.058   0.132     1.099   88.214   90.544
LGA    K    14_A      K    14_A     1.363     0    0.029   0.823     4.264   77.143   61.746
LGA    A    15_A      A    15_A     1.664     0    0.055   0.057     1.834   72.857   72.857
LGA    R    16_A      R    16_A     1.362     0    0.052   1.582     4.297   79.286   68.398
LGA    V    17_A      V    17_A     1.598     0    0.040   0.100     1.891   75.000   76.531
LGA    E    18_A      E    18_A     1.769     0    0.112   0.401     2.665   70.833   70.212
LGA    K    19_A      K    19_A     1.506     0    0.189   0.751     2.524   77.143   72.116
LGA    L    20_A      L    20_A     1.685     0    0.084   0.954     5.480   53.810   48.631
LGA    A    21_A      A    21_A     6.056     0    0.038   0.046     7.387   31.310   27.048
LGA    P    22_A      P    22_A     7.934     0    0.635   0.615    12.022   13.452    7.687
LGA    E    23_A      E    23_A     6.245     0    0.161   0.802     9.193   13.452   11.005
LGA    A    24_A      A    24_A     8.468     0    0.282   0.283    10.138    6.667    5.333
LGA    V    25_A      V    25_A     5.996     0    0.593   0.627     8.650   18.571   15.374
LGA    P    26_A      P    26_A     4.724     0    0.666   0.748     5.614   42.024   39.728
LGA    Q    27_A      Q    27_A     2.834     0    0.077   1.354     3.428   53.571   58.413
LGA    K    28_A      K    28_A     3.556     0    0.051   0.791     6.645   45.000   34.497
LGA    L    29_A      L    29_A     3.676     0    0.056   0.952     3.742   43.333   52.381
LGA    K    30_A      K    30_A     3.210     0    0.048   0.657     5.389   50.000   44.709
LGA    R    31_A      R    31_A     3.081     0    0.024   1.208    10.761   50.000   30.216
LGA    A    32_A      A    32_A     3.355     0    0.046   0.046     3.642   50.000   48.667
LGA    L    33_A      L    33_A     3.567     0    0.036   1.212     5.834   46.667   39.345
LGA    K    34_A      K    34_A     3.336     0    0.044   0.932     3.493   50.000   66.243
LGA    I    35_A      I    35_A     3.081     0    0.028   0.104     3.344   50.000   50.893
LGA    A    36_A      A    36_A     3.424     0    0.058   0.077     3.755   50.000   48.667
LGA    E    37_A      E    37_A     3.640     0    0.055   0.916     6.994   46.667   34.762
LGA    R    38_A      R    38_A     3.218     0    0.101   1.352     5.903   53.571   55.108
LGA    E    39_A      E    39_A     2.800     0    0.614   1.029     5.440   53.571   44.603
LGA    Q    40_A      Q    40_A     6.228     0    0.420   1.225    11.062   18.452    9.841
LGA    G    41_A      G    41_A     8.987     0    0.124   0.124     9.104    4.048    4.048
LGA    E    42_A      E    42_A     6.195     0    0.689   0.978     7.207   25.000   18.677
LGA    G    43_A      G    43_A     7.825     0    0.648   0.648     7.825   12.976   12.976
LGA    E    44_A      E    44_A     5.138     0    0.306   0.686     9.626   27.976   17.407
LGA    F    45_A      F    45_A     3.991     0    0.068   1.424     8.344   41.786   29.481
LGA    D    46_A      D    46_A     3.833     0    0.047   1.038     4.366   45.000   42.619
LGA    E    47_A      E    47_A     3.501     0    0.089   0.782     6.348   48.452   38.889
LGA    C    48_A      C    48_A     2.655     0    0.069   0.132     2.986   60.952   59.683
LGA    L    49_A      L    49_A     1.671     0    0.047   1.448     4.286   72.976   62.738
LGA    E    50_A      E    50_A     1.915     0    0.054   0.802     6.031   72.857   53.915
LGA    A    51_A      A    51_A     2.054     0    0.035   0.038     2.188   68.810   68.000
LGA    L    52_A      L    52_A     0.968     0    0.049   0.836     3.359   88.214   79.881
LGA    D    53_A      D    53_A     1.050     0    0.021   0.585     2.682   79.405   78.512
LGA    D    54_A      D    54_A     2.380     0    0.041   0.889     5.144   62.976   50.476
LGA    A    55_A      A    55_A     2.939     0    0.034   0.050     3.347   55.357   55.714
LGA    K    56_A      K    56_A     2.438     0    0.041   0.681     3.205   59.167   65.026
LGA    R    57_A      R    57_A     3.098     0    0.157   1.102     6.981   46.905   41.732
LGA    A    58_A      A    58_A     4.085     0    0.198   0.199     5.311   35.952   36.190
LGA    L    59_A      L    59_A     2.936     0    0.572   1.023     3.878   48.452   57.857
LGA    P    60_A      P    60_A     6.497     0    0.662   0.667     9.781   24.048   15.442

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     3.816          3.722                  4.265           52.153   48.491

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     47    2.74    65.417    59.394     1.654

LGA_LOCAL      RMSD:   2.741  Number of atoms:   47  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.002  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   3.816  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.374599 * X  +  -0.789875 * Y  +  -0.485564 * Z  +  34.341621
  Y_new =   0.891156 * X  +  -0.451294 * Y  +   0.046626 * Z  +   6.816766
  Z_new =  -0.255961 * X  +  -0.415247 * Y  +   0.872957 * Z  +  12.046388 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.968724  0.258842 -0.444002   [DEG:  112.7996   14.8305  -25.4395 ]
ZXZ: -1.666527  0.509565 -2.589197   [DEG:  -95.4850   29.1959 -148.3501 ]
 
# END of job
