
#######################################################
#                                                     #
#                        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   65 (  516),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40       6_C - 45_C        4.48     8.28
  LCS_AVERAGE:     71.47

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       7_C - 22_C        1.93     8.62
  LCS_AVERAGE:     21.61

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       9_C - 19_C        0.65     8.28
  LCS_AVERAGE:     11.42

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C      5   15   40      3    5    6   10   15   18   22   24   31   32   33   33   34   38   38   40   42   43   44   46 
LCS_GDT     T     7_C     T     7_C      5   16   40      4    5    9   13   17   20   24   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     K     8_C     K     8_C      5   16   40      4    5    7   13   17   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     I     9_C     I     9_C     11   16   40      4   12   13   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     L    10_C     L    10_C     11   16   40      5   12   13   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     P    11_C     P    11_C     11   16   40      7   12   13   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     C    12_C     C    12_C     11   16   40      7   12   13   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     P    13_C     P    13_C     11   16   40      7   12   13   14   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     R    14_C     R    14_C     11   16   40      7   12   13   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     C    15_C     C    15_C     11   16   40      7   12   13   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     N    16_C     N    16_C     11   16   40      7   12   13   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     S    17_C     S    17_C     11   16   40      7   12   13   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     M    18_C     M    18_C     11   16   40      7   12   13   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     E    19_C     E    19_C     11   16   40      4   12   13   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     T    20_C     T    20_C      5   16   40      0    3    5    6   13   17   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     K    21_C     K    21_C      5   16   40      4    4    8   11   13   20   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     F    22_C     F    22_C      5   16   40      4    4    6   12   14   20   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     C    23_C     C    23_C      5   15   40      4    4    5    6   14   20   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     Y    24_C     Y    24_C      5    9   40      4    4    6    6   11   20   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     Y    25_C     Y    25_C      4    9   40      3    4    6    7   14   20   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     N    26_C     N    26_C      4    9   40      3    4   13   13   17   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     N    27_C     N    27_C      4    9   40      3    3    6    9   16   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     Y    28_C     Y    28_C      4    9   40      3    3    6    6    7    8   11   20   25   29   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     N    29_C     N    29_C      4    9   40      3    4    5    6    7    8   10   18   24   28   31   35   37   38   40   41   42   43   44   46 
LCS_GDT     V    30_C     V    30_C      4    6   40      3    4    4    5    5    7   10   13   17   21   23   34   37   38   40   41   42   43   44   46 
LCS_GDT     N    31_C     N    31_C      4    6   40      3    4    4    5    6   13   18   22   28   29   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     Q    32_C     Q    32_C      5   10   40      4    4    6   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     P    33_C     P    33_C      5   10   40      4    4   12   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     R    34_C     R    34_C      5   10   40      4    4    7    9   17   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     H    35_C     H    35_C      5   10   40      4    4   12   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     F    36_C     F    36_C      5   10   40      3    4    7   11   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     C    37_C     C    37_C      5   10   40      5   12   13   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     K    38_C     K    38_C      5   10   40      5    5    8   15   18   21   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     A    39_C     A    39_C      5   10   40      5    5    7    9   13   18   24   26   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     C    40_C     C    40_C      5   10   40      5    5    7   13   18   20   24   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     Q    41_C     Q    41_C      5   10   40      5    5    7   13   18   20   24   29   32   32   33   35   37   38   40   41   42   43   44   46 
LCS_GDT     R    42_C     R    42_C      3    4   40      3    3    3    4    8   16   25   30   32   32   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     Y    43_C     Y    43_C      3    4   40      1    3    3    4    4    5   12   14   16   20   26   35   37   38   40   41   42   43   44   46 
LCS_GDT     W    44_C     W    44_C      3    3   40      3    4    4    6    9   11   13   16   22   28   34   35   37   38   40   41   42   43   44   46 
LCS_GDT     T    45_C     T    45_C      3    6   40      3    3    4    5    9   11   12   15   17   21   23   28   37   38   40   41   42   43   44   46 
LCS_GDT     S    46_C     S    46_C      3    6   39      3    3    5    5    6    7   10   13   14   15   18   19   20   20   25   31   34   35   36   40 
LCS_GDT     G    47_C     G    47_C      3    6   22      0    3    5    5    6    9   12   13   15   17   18   22   25   28   30   32   34   36   40   44 
LCS_GDT     G    48_C     G    48_C      3    9   22      3    4    5    6    9   11   13   14   15   18   22   24   28   29   34   41   41   43   44   46 
LCS_GDT     T    49_C     T    49_C      4    9   22      3    4    5    6    9   11   13   14   20   24   27   31   37   38   40   41   42   43   44   46 
LCS_GDT     M    50_C     M    50_C      4    9   22      3    4    5    6    9   11   13   14   17   21   22   25   29   36   39   41   42   43   44   46 
LCS_GDT     R    51_C     R    51_C      5    9   22      3    5    5    5    9   11   13   14   17   21   23   30   34   37   39   41   42   43   44   46 
LCS_GDT     S    52_C     S    52_C      5    9   22      3    5    5    6    9   11   13   14   15   17   18   19   20   27   31   32   36   41   44   46 
LCS_GDT     V    53_C     V    53_C      5    9   22      3    5    5    6    9   11   13   14   19   22   22   24   26   33   36   37   40   42   44   46 
LCS_GDT     P    54_C     P    54_C      5    9   22      3    5    5    7    9   11   13   14   15   17   18   19   23   29   31   32   34   35   37   45 
LCS_GDT     I    55_C     I    55_C      5    9   22      3    5    5    7    9   11   13   14   15   17   18   19   20   29   31   37   40   41   44   45 
LCS_GDT     G    56_C     G    56_C      4    9   22      3    5    5    7    9   11   13   14   15   17   18   19   20   24   31   37   40   42   44   46 
LCS_AVERAGE  LCS_A:  34.83  (  11.42   21.61   71.47 )

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      7     12     13     15     18     21     25     30     32     32     34     35     37     38     40     41     42     43     44     46 
GDT PERCENT_AT  13.73  23.53  25.49  29.41  35.29  41.18  49.02  58.82  62.75  62.75  66.67  68.63  72.55  74.51  78.43  80.39  82.35  84.31  86.27  90.20
GDT RMS_LOCAL    0.28   0.66   0.85   1.25   1.50   2.05   2.50   2.78   2.90   2.90   3.51   3.56   3.89   4.00   4.62   4.95   5.01   5.18   5.45   6.16
GDT RMS_ALL_AT   8.32   8.29   8.36   8.82   8.85   8.65   8.92   8.64   8.68   8.68   8.43   8.46   8.44   8.43   8.00   7.57   7.59   7.56   7.43   7.12

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  Y    28_C      Y    28_C
#   possible swapping detected:  F    36_C      F    36_C
#   possible swapping detected:  Y    43_C      Y    43_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C     5.914     2    0.680   0.612     8.492   22.262   15.170
LGA    T     7_C      T     7_C     3.489     0    0.128   0.137     4.935   56.905   46.803
LGA    K     8_C      K     8_C     2.614     4    0.047   0.063     3.814   65.357   33.862
LGA    I     9_C      I     9_C     1.604     0    0.103   1.584     4.014   81.548   62.500
LGA    L    10_C      L    10_C     1.928     0    0.079   0.117     2.615   68.810   65.833
LGA    P    11_C      P    11_C     1.605     0    0.034   0.059     1.797   77.143   75.306
LGA    C    12_C      C    12_C     1.446     0    0.057   0.143     1.767   77.143   77.143
LGA    P    13_C      P    13_C     2.079     0    0.102   0.180     2.583   70.833   68.299
LGA    R    14_C      R    14_C     1.676     0    0.045   1.449     7.178   72.857   58.312
LGA    C    15_C      C    15_C     1.816     0    0.666   0.570     4.572   58.571   64.762
LGA    N    16_C      N    16_C     1.618     0    0.490   0.775     3.805   83.929   68.810
LGA    S    17_C      S    17_C     2.114     0    0.084   0.746     2.552   68.810   67.540
LGA    M    18_C      M    18_C     2.047     0    0.372   1.069     4.978   75.357   63.095
LGA    E    19_C      E    19_C     1.497     4    0.469   0.514     3.957   63.571   35.450
LGA    T    20_C      T    20_C     3.728     0    0.482   1.061     8.061   48.810   32.925
LGA    K    21_C      K    21_C     3.888     0    0.244   1.361     8.786   45.000   29.259
LGA    F    22_C      F    22_C     3.555     0    0.044   1.292     9.487   46.667   27.273
LGA    C    23_C      C    23_C     3.485     0    0.604   0.607     6.413   38.571   41.270
LGA    Y    24_C      Y    24_C     3.629     0    0.135   1.250    10.121   55.595   30.198
LGA    Y    25_C      Y    25_C     4.130     0    0.037   1.102    15.336   45.595   16.667
LGA    N    26_C      N    26_C     2.674     0    0.589   1.097     7.009   71.071   46.667
LGA    N    27_C      N    27_C     2.332     0    0.370   0.376     5.842   52.500   45.179
LGA    Y    28_C      Y    28_C     7.676     0    0.478   1.373    11.869    9.405    4.008
LGA    N    29_C      N    29_C     9.955     0    0.264   0.827    12.995    2.738    1.369
LGA    V    30_C      V    30_C    12.473     0    0.683   1.465    17.189    0.000    0.000
LGA    N    31_C      N    31_C     8.502     0    0.121   0.531    12.742   14.048    7.083
LGA    Q    32_C      Q    32_C     3.167     0    0.512   0.985     5.983   40.833   33.439
LGA    P    33_C      P    33_C     2.682     0    0.076   0.210     3.143   62.976   59.456
LGA    R    34_C      R    34_C     3.331     0    0.138   1.103    11.536   53.571   24.416
LGA    H    35_C      H    35_C     1.798     0    0.104   1.363     5.371   61.429   58.810
LGA    F    36_C      F    36_C     2.558     0    0.114   1.259    10.468   69.048   31.948
LGA    C    37_C      C    37_C     0.850     0    0.280   0.997     2.703   77.738   76.111
LGA    K    38_C      K    38_C     3.129     0    0.131   0.977     7.511   46.548   35.185
LGA    A    39_C      A    39_C     4.836     0    0.099   0.116     5.314   34.524   32.857
LGA    C    40_C      C    40_C     3.575     0    0.208   0.804     4.108   41.786   51.270
LGA    Q    41_C      Q    41_C     4.555     0    0.388   1.293     8.494   42.143   26.508
LGA    R    42_C      R    42_C     4.404     0    0.576   1.694    12.879   28.929   14.589
LGA    Y    43_C      Y    43_C     7.826     0    0.601   1.432    14.567   10.714    3.730
LGA    W    44_C      W    44_C     8.059     0    0.590   0.885    13.396    3.333    2.755
LGA    T    45_C      T    45_C    11.379     0    0.608   1.038    14.802    0.119    0.068
LGA    S    46_C      S    46_C    18.357     0    0.625   0.750    20.956    0.000    0.000
LGA    G    47_C      G    47_C    19.858     0    0.700   0.700    20.038    0.000    0.000
LGA    G    48_C      G    48_C    17.230     0    0.595   0.595    17.856    0.000    0.000
LGA    T    49_C      T    49_C    12.559     0    0.129   1.076    13.647    0.000    0.068
LGA    M    50_C      M    50_C    13.041     0    0.038   0.303    16.506    0.000    0.000
LGA    R    51_C      R    51_C    13.642     0    0.641   0.670    16.392    0.000    0.000
LGA    S    52_C      S    52_C    16.896     0    0.037   0.136    20.657    0.000    0.000
LGA    V    53_C      V    53_C    13.633     0    0.075   1.197    15.317    0.000    0.068
LGA    P    54_C      P    54_C    17.383     0    0.034   0.106    18.786    0.000    0.000
LGA    I    55_C      I    55_C    15.781     0    0.054   1.518    17.532    0.000    0.000
LGA    G    56_C      G    56_C    17.098     0    0.553   0.553    18.165    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     7.045          7.002                  7.831           38.172   30.119

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     30    2.78    48.039    42.304     1.043

LGA_LOCAL      RMSD:   2.777  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.642  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   7.045  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.515207 * X  +   0.851676 * Y  +   0.095964 * Z  + -29.436243
  Y_new =  -0.628394 * X  +  -0.451512 * Y  +   0.633449 * Z  + -22.382441
  Z_new =   0.582822 * X  +   0.266055 * Y  +   0.767811 * Z  + -20.763748 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.257542 -0.622198  0.333563   [DEG: -129.3476  -35.6493   19.1118 ]
ZXZ:  2.991242  0.695380  1.142555   [DEG:  171.3855   39.8423   65.4636 ]
 
# END of job
