
#######################################################
#                                                     #
#                        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   46 (  368),  selected   46 , name one
# Molecule2: number of CA atoms  153 ( 1242),  selected   46 , 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:    26       1_C - 26_C        4.94     7.96
  LCS_AVERAGE:     15.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      14_C - 28_C        1.84    16.87
  LCS_AVERAGE:      8.65

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      28_C - 39_C        0.82    12.90
  LCS_AVERAGE:      4.85

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   46
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_C     M     1_C      3   14   26      2    5   10   18   21   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     H     2_C     H     2_C      7   14   26      4   10   18   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     C     3_C     C     3_C      7   14   26     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     P     4_C     P     4_C      7   14   26     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     F     5_C     F     5_C      7   14   26     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     C     6_C     C     6_C      7   14   26     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     F     7_C     F     7_C      7   14   26      5   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     A     8_C     A     8_C      7   14   26      4    7   15   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     V     9_C     V     9_C      6   14   26      3    5    7   10   14   24   25   26   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     D    10_C     D    10_C      6   14   26      5    9   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     T    11_C     T    11_C      6   14   26      5   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     K    12_C     K    12_C      6   14   26     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     V    13_C     V    13_C      6   14   26      8   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     I    14_C     I    14_C      8   15   26      5    9   19   22   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     D    15_C     D    15_C      8   15   26      3    7   11   13   14   15   23   26   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     S    16_C     S    16_C      8   15   26      3    7   11   13   14   15   18   22   28   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     R    17_C     R    17_C      8   15   26      4    7   11   13   14   15   18   18   19   20   24   27   32   35   36   38   40   41   43   45 
LCS_GDT     L    18_C     L    18_C      8   15   26      4    7   11   13   14   15   18   18   19   19   22   24   27   30   32   35   40   41   43   45 
LCS_GDT     V    19_C     V    19_C      8   15   26      4    7   11   13   14   15   18   18   19   19   22   24   27   30   32   35   40   41   43   45 
LCS_GDT     G    20_C     G    20_C      8   15   26      4    7   11   13   14   15   18   18   19   19   22   24   27   29   30   35   37   40   43   45 
LCS_GDT     E    21_C     E    21_C      8   15   26      3    3    8   13   14   15   18   18   19   19   20   23   27   29   30   33   35   39   42   45 
LCS_GDT     G    22_C     G    22_C      4   15   26      3    3    5   10   13   15   18   18   19   19   22   24   27   29   30   34   37   40   43   45 
LCS_GDT     S    23_C     S    23_C      4   15   26      3    3    6    8   13   13   15   18   19   19   20   22   27   29   30   31   34   38   41   44 
LCS_GDT     S    24_C     S    24_C      5   15   26      3    5   11   13   14   15   18   18   19   19   22   24   27   30   32   35   40   41   43   45 
LCS_GDT     V    25_C     V    25_C      5   15   26      3    5   11   13   14   15   18   18   19   19   24   26   29   34   36   38   40   41   43   45 
LCS_GDT     R    26_C     R    26_C      5   15   26      3    6   11   13   14   15   18   21   25   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     R    27_C     R    27_C      5   15   25      3    6   11   13   14   21   25   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     R    28_C     R    28_C     12   15   25      4   13   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     R    29_C     R    29_C     12   14   25      7   15   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     Q    30_C     Q    30_C     12   14   25     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     C    31_C     C    31_C     12   14   25     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     L    32_C     L    32_C     12   14   22     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     V    33_C     V    33_C     12   14   20     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     C    34_C     C    34_C     12   14   20     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     N    35_C     N    35_C     12   14   20     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     E    36_C     E    36_C     12   14   20      7   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     R    37_C     R    37_C     12   14   20     11   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     F    38_C     F    38_C     12   14   20      7   16   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     T    39_C     T    39_C     12   14   20      6   13   19   23   24   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     T    40_C     T    40_C      4   14   20      4    4   11   18   23   24   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     F    41_C     F    41_C      4   14   20      4    4    5   10   17   23   26   27   29   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     E    42_C     E    42_C      3    8   20      3    3    4    7   10   12   18   23   28   30   32   33   34   35   36   38   40   41   43   45 
LCS_GDT     V    43_C     V    43_C      3    3   20      3    3    3    3   10   11   14   18   22   25   29   33   34   35   36   38   40   41   43   45 
LCS_GDT     A    44_C     A    44_C      3    3   20      3    3    3    3    3    4    5    9   15   20   22   26   28   31   34   38   40   41   43   45 
LCS_GDT     E    45_C     E    45_C      3    3    8      3    3    3    4    5    7    9   12   16   19   24   26   28   31   34   38   40   41   43   45 
LCS_GDT     L    46_C     L    46_C      3    3    8      3    3    3    3    3    4    4    8   10   10   10   15   15   27   28   31   35   40   43   45 
LCS_AVERAGE  LCS_A:   9.61  (   4.85    8.65   15.33 )

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     11     16     19     23     24     24     26     27     29     30     32     33     34     35     36     38     40     41     43     45 
GDT PERCENT_AT   7.19  10.46  12.42  15.03  15.69  15.69  16.99  17.65  18.95  19.61  20.92  21.57  22.22  22.88  23.53  24.84  26.14  26.80  28.10  29.41
GDT RMS_LOCAL    0.37   0.55   0.73   1.15   1.17   1.17   1.61   1.92   2.37   2.49   3.10   3.37   3.66   3.98   4.35   4.99   5.50   5.69   6.18   6.51
GDT RMS_ALL_AT  14.32  14.26  14.15  13.58  13.68  13.68  13.07  12.45  11.80  11.94  10.86  10.36   9.84   9.44   8.96   8.00   7.41   7.18   6.80   6.68

# Checking swapping
#   possible swapping detected:  F     5_C      F     5_C
#   possible swapping detected:  D    15_C      D    15_C
#   possible swapping detected:  E    21_C      E    21_C
#   possible swapping detected:  E    36_C      E    36_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M     1_C      M     1_C     3.627     0    0.404   0.594    10.185   42.262   24.762
LGA    H     2_C      H     2_C     3.467     0    0.703   1.258    11.501   61.429   27.762
LGA    C     3_C      C     3_C     1.132     0    0.062   0.096     1.948   79.286   83.016
LGA    P     4_C      P     4_C     1.187     0    0.071   0.097     1.489   85.952   84.014
LGA    F     5_C      F     5_C     0.640     0    0.067   1.407     6.823   95.238   61.818
LGA    C     6_C      C     6_C     0.561     0    0.018   0.089     1.173   90.595   90.556
LGA    F     7_C      F     7_C     1.532     0    0.158   0.296     1.900   75.000   82.511
LGA    A     8_C      A     8_C     2.956     0    0.664   0.609     5.011   47.857   45.714
LGA    V     9_C      V     9_C     4.937     0    0.530   0.906     8.612   38.810   24.694
LGA    D    10_C      D    10_C     1.803     0    0.061   0.154     2.707   73.214   72.143
LGA    T    11_C      T    11_C     0.770     0    0.033   0.130     1.385   85.952   86.599
LGA    K    12_C      K    12_C     0.760     0    0.041   0.292     2.046   95.238   84.762
LGA    V    13_C      V    13_C     0.584     0    0.047   1.160     3.123   73.929   72.585
LGA    I    14_C      I    14_C     2.280     0    0.566   0.491     8.717   53.810   40.298
LGA    D    15_C      D    15_C     5.978     0    0.328   0.820    11.060   22.857   12.321
LGA    S    16_C      S    16_C     9.412     0    0.179   0.257    13.456    2.143    1.508
LGA    R    17_C      R    17_C    14.386     0    0.053   1.504    17.642    0.000    0.000
LGA    L    18_C      L    18_C    20.239     0    0.121   0.982    23.392    0.000    0.000
LGA    V    19_C      V    19_C    20.903     0    0.098   0.237    22.825    0.000    0.000
LGA    G    20_C      G    20_C    25.336     0    0.607   0.607    28.956    0.000    0.000
LGA    E    21_C      E    21_C    29.967     0    0.451   1.195    32.036    0.000    0.000
LGA    G    22_C      G    22_C    28.057     0    0.158   0.158    29.063    0.000    0.000
LGA    S    23_C      S    23_C    28.501     0    0.365   0.619    30.386    0.000    0.000
LGA    S    24_C      S    24_C    22.749     0    0.042   0.565    24.360    0.000    0.000
LGA    V    25_C      V    25_C    17.421     0    0.027   0.092    19.905    0.000    0.000
LGA    R    26_C      R    26_C    11.338     0    0.051   1.000    13.649    0.238    5.628
LGA    R    27_C      R    27_C     6.250     0    0.064   0.380    12.825   19.881    9.697
LGA    R    28_C      R    28_C     0.920     0    0.170   0.912     7.432   79.881   49.870
LGA    R    29_C      R    29_C     0.577     0    0.059   0.632     3.790   92.857   79.351
LGA    Q    30_C      Q    30_C     0.319     0    0.051   0.912     2.947  100.000   92.116
LGA    C    31_C      C    31_C     0.236     0    0.134   0.303     1.514  100.000   93.889
LGA    L    32_C      L    32_C     0.719     0    0.091   0.226     1.475   90.476   87.083
LGA    V    33_C      V    33_C     0.951     0    0.037   0.510     1.636   90.476   86.667
LGA    C    34_C      C    34_C     0.667     0    0.013   0.133     0.910   90.476   92.063
LGA    N    35_C      N    35_C     1.352     0    0.097   0.089     2.546   77.381   70.119
LGA    E    36_C      E    36_C     1.800     0    0.080   0.872     3.762   77.143   64.550
LGA    R    37_C      R    37_C     1.772     0    0.040   1.515    12.001   66.905   37.403
LGA    F    38_C      F    38_C     2.221     0    0.172   1.174     6.119   75.119   52.554
LGA    T    39_C      T    39_C     0.774     0    0.066   0.949     3.646   81.786   77.619
LGA    T    40_C      T    40_C     2.661     0    0.139   1.349     5.690   55.833   51.565
LGA    F    41_C      F    41_C     5.076     0    0.563   1.408     9.401   18.690   27.403
LGA    E    42_C      E    42_C     9.653     0    0.596   1.442    11.330    2.619    2.540
LGA    V    43_C      V    43_C    13.191     0    0.637   0.800    17.225    0.000    0.000
LGA    A    44_C      A    44_C    17.975     0    0.656   0.609    20.044    0.000    0.000
LGA    E    45_C      E    45_C    21.197     0    0.617   0.815    25.588    0.000    0.000
LGA    L    46_C      L    46_C    25.616     0    0.650   0.506    28.381    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       46     184    184  100.00     368    368  100.00               153
SUMMARY(RMSD_GDC):     6.663          6.682                  7.438           14.009   12.256

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   46  153    4.0     27    1.92    16.993    15.158     1.337

LGA_LOCAL      RMSD:   1.919  Number of atoms:   27  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  12.446  Number of assigned atoms:   46 
Std_ASGN_ATOMS RMSD:   6.663  Standard rmsd on all 46 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.867002 * X  +  -0.043177 * Y  +   0.496430 * Z  +  -7.080974
  Y_new =  -0.498244 * X  +  -0.090633 * Y  +   0.862287 * Z  +  -2.887540
  Z_new =   0.007762 * X  +  -0.994948 * Y  +  -0.100092 * Z  + -15.221064 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.521589 -0.007762 -1.671059   [DEG:  -29.8849   -0.4448  -95.7446 ]
ZXZ:  2.619223  1.671056  3.133791   [DEG:  150.0704   95.7445  179.5530 ]
 
# END of job
