
#######################################################
#                                                     #
#                        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   49 (  407),  selected   49 , name one
# Molecule2: number of CA atoms  226 ( 1803),  selected   49 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41      86_B - 126_B       4.82     8.70
  LONGEST_CONTINUOUS_SEGMENT:    41      87_B - 127_B       4.79     8.62
  LCS_AVERAGE:     17.09

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      92_B - 113_B       1.99    10.36
  LONGEST_CONTINUOUS_SEGMENT:    22      93_B - 114_B       1.84    10.23
  LONGEST_CONTINUOUS_SEGMENT:    22      94_B - 115_B       1.72    10.18
  LCS_AVERAGE:      6.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      94_B - 114_B       0.97    10.51
  LCS_AVERAGE:      5.16

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     I    84_B     I    84_B      3    3   31      0    3    3    3    3    4    4    6    6    7   14   17   20   22   23   28   31   38   40   42 
LCS_GDT     H    85_B     H    85_B      3    3   39      0    3    3    3    3    4    4    6    6    7    8   17   20   22   24   30   32   35   39   42 
LCS_GDT     R    86_B     R    86_B      3    3   41      1    3    3    3    3    4    4    6    6   11   14   17   24   28   33   35   36   40   41   42 
LCS_GDT     I    87_B     I    87_B      3    3   41      3    3    3    3    3    9   15   21   25   29   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     T    88_B     T    88_B      3    3   41      3    3    3    3    5    5    7   11   15   19   24   27   27   33   39   39   40   40   41   42 
LCS_GDT     L    89_B     L    89_B      3    3   41      3    3    3    3    5    6    9   20   25   29   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     E    90_B     E    90_B      3    4   41      3    3    3    3    5   18   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     S    91_B     S    91_B      3    5   41      3    3    4    4    7   20   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     T    92_B     T    92_B      3   22   41      3    3    4    7   11   20   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     R    93_B     R    93_B      3   22   41      3    4    4    4    5    6   12   19   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     S    94_B     S    94_B     21   22   41      3   20   20   20   21   21   21   24   30   33   34   35   36   39   39   39   40   40   41   41 
LCS_GDT     M    95_B     M    95_B     21   22   41      3   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     P    96_B     P    96_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     P    97_B     P    97_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     R    98_B     R    98_B     21   22   41     12   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     A    99_B     A    99_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     A   100_B     A   100_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     L   101_B     L   101_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     D   102_B     D   102_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     D   103_B     D   103_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     A   104_B     A   104_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     L   105_B     L   105_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     R   106_B     R   106_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     L   107_B     L   107_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     G   108_B     G   108_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     R   109_B     R   109_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     E   110_B     E   110_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     F   111_B     F   111_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     V   112_B     V   112_B     21   22   41     15   20   20   20   21   21   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     E   113_B     E   113_B     21   22   41      3   20   20   20   21   21   21   24   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     S   114_B     S   114_B     21   22   41      3    3    5   13   21   21   21   24   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     R   115_B     R   115_B      4   22   41      3    3    4    7    7   15   19   23   27   32   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     Q   116_B     Q   116_B      4    8   41      3    3    4    7    8   11   16   22   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     P   117_B     P   117_B      7   10   41      5    7    7    8   10   10   11   17   26   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     V   118_B     V   118_B      7   10   41      5    7    7    8   10   10   19   25   29   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     F   119_B     F   119_B      7   10   41      5    7    7    8   10   10   18   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     E   120_B     E   120_B      7   10   41      5    7    7    8   10   15   21   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     S   121_B     S   121_B      7   10   41      5    7    7    8   10   12   19   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     F   122_B     F   122_B      7   10   41      4    7    7    8   10   12   20   25   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     R   123_B     R   123_B      7   10   41      4    7    7    8   10   15   19   24   30   33   34   36   38   39   39   39   40   40   41   42 
LCS_GDT     D   124_B     D   124_B      5   10   41      4    5    5    8   10   10   10   11   15   20   30   36   38   39   39   39   40   40   41   42 
LCS_GDT     R   125_B     R   125_B      5   10   41      4    5    5    8   10   10   11   22   26   32   33   36   38   39   39   39   40   40   41   42 
LCS_GDT     T   126_B     T   126_B      5   10   41      3    5    5    8   10   10   12   17   22   26   32   36   38   39   39   39   40   40   41   42 
LCS_GDT     K   127_B     K   127_B      3    6   41      3    3    4    5    8   10   11   12   13   17   18   21   27   31   33   39   40   40   41   41 
LCS_GDT     F   128_B     F   128_B      5    5   39      3    5    5    5    5    5    6    7    8    9   13   13   15   15   16   19   22   23   27   33 
LCS_GDT     T   129_B     T   129_B      5    5   16      3    5    5    5    5    5    6    7    8   10   13   13   15   15   15   16   18   20   21   22 
LCS_GDT     F   130_B     F   130_B      5    5   15      3    5    5    5    5    5    6    6    8   10   13   13   15   15   15   16   18   20   21   22 
LCS_GDT     V   131_B     V   131_B      5    5   15      3    5    5    5    5    5    6    6    6   10   13   13   15   15   15   16   18   20   21   22 
LCS_GDT     T   132_B     T   132_B      5    5   15      3    5    5    5    5    5    6    6    8   10   13   13   15   15   15   16   18   20   20   22 
LCS_AVERAGE  LCS_A:   9.50  (   5.16    6.27   17.09 )

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     15     20     20     20     21     21     21     25     30     33     34     36     38     39     39     39     40     40     41     42 
GDT PERCENT_AT   6.64   8.85   8.85   8.85   9.29   9.29   9.29  11.06  13.27  14.60  15.04  15.93  16.81  17.26  17.26  17.26  17.70  17.70  18.14  18.58
GDT RMS_LOCAL    0.27   0.46   0.46   0.46   0.97   0.97   0.97   2.91   3.21   3.44   3.53   4.00   4.26   4.31   4.31   4.31   4.53   4.53   4.79   5.32
GDT RMS_ALL_AT  10.56  10.63  10.63  10.63  10.51  10.51  10.51   9.17   9.20   9.24   9.21   8.85   8.69   8.75   8.75   8.75   8.73   8.73   8.62   8.74

# Checking swapping
#   possible swapping detected:  E   113_B      E   113_B
#   possible swapping detected:  F   119_B      F   119_B
#   possible swapping detected:  E   120_B      E   120_B
#   possible swapping detected:  F   122_B      F   122_B
#   possible swapping detected:  F   130_B      F   130_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    I    84_B      I    84_B    14.353     0    0.554   0.996    19.611    0.000    0.000
LGA    H    85_B      H    85_B    14.708     0    0.655   1.301    19.213    0.000    0.000
LGA    R    86_B      R    86_B    12.934     0    0.617   1.067    13.580    0.000    0.000
LGA    I    87_B      I    87_B     8.395     0    0.656   1.456    11.014    1.429    5.893
LGA    T    88_B      T    88_B    11.121     0    0.581   0.564    14.861    0.119    0.068
LGA    L    89_B      L    89_B     8.147     0    0.610   0.630     9.470    5.595    6.071
LGA    E    90_B      E    90_B     4.312     0    0.578   0.797     8.068   43.214   29.683
LGA    S    91_B      S    91_B     4.394     0    0.578   0.934     8.404   35.714   26.270
LGA    T    92_B      T    92_B     4.724     0    0.039   0.183     5.756   29.048   30.068
LGA    R    93_B      R    93_B     5.120     0    0.089   1.136    17.564   41.190   16.017
LGA    S    94_B      S    94_B     3.871     0    0.249   0.252     5.331   44.405   40.079
LGA    M    95_B      M    95_B     2.458     0    0.030   0.925     3.066   62.857   66.131
LGA    P    96_B      P    96_B     2.524     0    0.070   0.386     2.665   60.952   61.497
LGA    P    97_B      P    97_B     2.408     0    0.025   0.046     2.751   64.762   61.497
LGA    R    98_B      R    98_B     1.845     0    0.023   1.341     7.242   72.857   53.074
LGA    A    99_B      A    99_B     1.409     0    0.054   0.060     1.513   81.429   79.714
LGA    A   100_B      A   100_B     1.794     0    0.017   0.038     2.083   72.857   71.238
LGA    L   101_B      L   101_B     1.547     0    0.011   0.117     2.148   72.857   71.845
LGA    D   102_B      D   102_B     1.513     0    0.048   0.119     1.868   75.000   75.000
LGA    D   103_B      D   103_B     1.583     0    0.079   0.283     2.201   72.857   72.917
LGA    A   104_B      A   104_B     1.588     0    0.054   0.068     1.629   75.000   74.571
LGA    L   105_B      L   105_B     1.533     0    0.087   0.194     1.850   75.000   73.929
LGA    R   106_B      R   106_B     2.017     0    0.034   1.263     6.588   70.833   53.247
LGA    L   107_B      L   107_B     1.468     0    0.083   1.392     4.791   77.143   66.071
LGA    G   108_B      G   108_B     1.740     0    0.023   0.023     2.101   68.810   68.810
LGA    R   109_B      R   109_B     2.459     0    0.035   0.819     4.649   62.857   53.723
LGA    E   110_B      E   110_B     2.401     0    0.097   0.145     2.783   62.857   61.376
LGA    F   111_B      F   111_B     2.046     0    0.040   0.226     2.489   64.762   70.000
LGA    V   112_B      V   112_B     2.736     0    0.037   0.306     4.208   55.476   52.313
LGA    E   113_B      E   113_B     3.824     0    0.291   0.713    10.763   45.119   23.757
LGA    S   114_B      S   114_B     4.172     0    0.457   0.782     5.893   35.000   39.048
LGA    R   115_B      R   115_B     6.578     0    0.077   1.169    15.876   19.524    7.359
LGA    Q   116_B      Q   116_B     5.482     0    0.409   1.168    13.613   26.548   12.963
LGA    P   117_B      P   117_B     5.318     0    0.545   0.819     6.103   33.095   35.918
LGA    V   118_B      V   118_B     4.880     0    0.024   0.061     6.559   34.286   27.007
LGA    F   119_B      F   119_B     4.620     0    0.000   1.349    11.798   34.286   16.623
LGA    E   120_B      E   120_B     4.718     0    0.131   1.184     6.738   34.286   26.772
LGA    S   121_B      S   121_B     4.243     0    0.087   0.635     5.073   37.143   35.317
LGA    F   122_B      F   122_B     4.307     0    0.270   1.351     9.774   34.286   19.481
LGA    R   123_B      R   123_B     5.732     0    0.171   1.238     7.969   17.500   16.450
LGA    D   124_B      D   124_B     9.733     0    0.063   0.123    12.320    1.429    0.714
LGA    R   125_B      R   125_B     8.696     0    0.046   1.326    13.019    1.786    2.684
LGA    T   126_B      T   126_B     9.847     0    0.566   0.892    10.798    0.833    0.612
LGA    K   127_B      K   127_B    13.776     0    0.601   0.530    21.183    0.000    0.000
LGA    F   128_B      F   128_B    17.375     0    0.427   1.284    19.701    0.000    0.000
LGA    T   129_B      T   129_B    20.202     0    0.072   0.145    22.702    0.000    0.000
LGA    F   130_B      F   130_B    20.784     0    0.644   1.186    22.529    0.000    0.000
LGA    V   131_B      V   131_B    23.172     0    0.434   0.378    23.643    0.000    0.000
LGA    T   132_B      T   132_B    26.357     0    0.137   1.044    29.023    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       49     196    196  100.00     407    407  100.00               226
SUMMARY(RMSD_GDC):     8.246          8.101                  9.307            7.987    7.105

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   49  226    4.0     25    2.91    11.504    10.393     0.830

LGA_LOCAL      RMSD:   2.912  Number of atoms:   25  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.175  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   8.246  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.297677 * X  +  -0.809468 * Y  +   0.506113 * Z  + 222.610535
  Y_new =  -0.240145 * X  +  -0.449607 * Y  +  -0.860339 * Z  + 412.649139
  Z_new =   0.923969 * X  +  -0.377643 * Y  +  -0.060552 * Z  + -127.799530 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.462760 -1.178331 -1.729786   [DEG: -141.1057  -67.5134  -99.1094 ]
ZXZ:  0.531751  1.631386  1.958796   [DEG:   30.4671   93.4715  112.2308 ]
 
# END of job
