
#######################################################
#                                                     #
#                        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   48 (  415),  selected   43 , name one
# Molecule2: number of CA atoms   76 (  680),  selected   43 , 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:    31      35_B - 70_B        4.99    11.57
  LCS_AVERAGE:     39.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      41_B - 57_B        1.81    12.94
  LONGEST_CONTINUOUS_SEGMENT:    17      42_B - 58_B        1.45    13.91
  LCS_AVERAGE:     14.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      42_B - 56_B        0.50    13.43
  LCS_AVERAGE:     10.95

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
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     E    28_B     E    28_B      3    3    8      0    3    3    3    3    3    4    5    6    6    7    7   10   11   12   14   15   15   15   15 
LCS_GDT     R    29_B     R    29_B      3    3   30      0    3    3    3    3    4    4    5    7    9   10   10   13   15   15   15   15   17   24   30 
LCS_GDT     L    30_B     L    30_B      3    3   30      0    3    3    3    3    4    4    5    7    9    9    9   13   15   15   15   18   22   24   30 
LCS_GDT     L    31_B     L    31_B      3    3   30      0    3    3    4    4    4    4    5    7    9   16   16   18   26   27   27   29   29   32   36 
LCS_GDT     M    32_B     M    32_B      3    7   30      3    3    4    8   11   14   17   22   23   24   25   25   26   26   27   27   31   33   34   36 
LCS_GDT     V    33_B     V    33_B      4    8   30      3    4    6    6   10   14   18   21   23   24   25   25   26   28   31   32   34   35   36   37 
LCS_GDT     F    34_B     F    34_B      5    8   30      3    4    6    8   12   15   18   22   23   24   25   25   29   31   32   33   35   35   36   37 
LCS_GDT     D    35_B     D    35_B      5    8   31      4    5    6    8   12   15   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     E    36_B     E    36_B      5    8   31      4    5    6    7   10   12   14   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     E    37_B     E    37_B      5    8   31      4    5    6   10   14   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     R    38_B     R    38_B      5    8   31      4    5    6    7    7    8    9   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     V    39_B     V    39_B      5    8   31      4    5    5    7    7   13   18   19   21   24   25   25   29   31   32   33   35   35   36   37 
LCS_GDT     E    40_B     E    40_B      3    8   31      3    3    3    7    7    8    8    9   13   20   24   27   29   31   32   33   35   35   36   37 
LCS_GDT     E    41_B     E    41_B      3   17   31      3    3    3    7   12   15   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     Y    42_B     Y    42_B     15   17   31     11   15   15   15   15   17   18   19   22   24   25   26   29   31   32   33   35   35   36   37 
LCS_GDT     M    43_B     M    43_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     K    44_B     K    44_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     I    45_B     I    45_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   26   29   31   32   33   35   35   36   37 
LCS_GDT     M    46_B     M    46_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     K    47_B     K    47_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     E    48_B     E    48_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     V    49_B     V    49_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     I    50_B     I    50_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     E    51_B     E    51_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     K    52_B     K    52_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     I    53_B     I    53_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     L    54_B     L    54_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     E    55_B     E    55_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     N    56_B     N    56_B     15   17   31     11   15   15   15   15   17   18   22   23   24   25   27   29   31   32   33   35   35   36   37 
LCS_GDT     R    57_B     R    57_B      3   17   31      3    3    3    7   14   17   18   22   23   24   25   26   29   31   32   33   35   35   36   37 
LCS_GDT     K    58_B     K    58_B      3   17   31      3    3    3    7    8   14   17   17   17   19   23   24   26   27   28   31   34   35   36   37 
LCS_GDT     K    64_B     K    64_B      6    6   31      3    4    6    8   10   12   14   17   18   21   24   27   29   31   32   33   35   35   36   37 
LCS_GDT     V    65_B     V    65_B      6    6   31      3    4    6    8   10   12   14   17   18   21   24   27   29   31   32   33   35   35   36   37 
LCS_GDT     E    66_B     E    66_B      6    6   31      3    4    5    8   10   12   14   17   18   21   24   27   29   31   32   33   35   35   36   37 
LCS_GDT     I    67_B     I    67_B      6    6   31      3    4    6    8   10   12   14   17   18   21   24   27   29   31   32   33   35   35   36   37 
LCS_GDT     P    68_B     P    68_B      6    7   31      3    4    6    8   10   12   14   17   18   21   24   27   29   31   32   33   35   35   36   37 
LCS_GDT     P    69_B     P    69_B      6    7   31      3    4    6    8    9   12   14   17   18   21   24   27   29   31   32   33   35   35   36   37 
LCS_GDT     G    70_B     G    70_B      6    7   31      3    4    5    6    7    8    8   11   14   16   21   24   25   27   31   33   35   35   36   37 
LCS_GDT     M    71_B     M    71_B      6    7   28      5    5    5    6    7    8    8   10   14   18   20   23   25   27   28   32   35   35   36   37 
LCS_GDT     E    72_B     E    72_B      6    7   28      5    5    5    6    7    8   10   15   17   20   24   27   29   31   32   33   35   35   36   37 
LCS_GDT     W    73_B     W    73_B      6    7   28      5    5    5    8   10   12   14   17   18   21   24   27   29   31   32   33   35   35   36   37 
LCS_GDT     F    74_B     F    74_B      6    7   27      5    5    5    6    7    8    9   10   15   18   20   21   25   27   28   30   35   35   36   37 
LCS_GDT     Y    75_B     Y    75_B      6    7   24      5    5    5    6    7    8    8    8    8    9   10   12   13   15   16   22   24   29   32   36 
LCS_AVERAGE  LCS_A:  21.53  (  10.95   14.35   39.29 )

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     15     15     15     15     17     18     22     23     24     25     27     29     31     32     33     35     35     36     37 
GDT PERCENT_AT  14.47  19.74  19.74  19.74  19.74  22.37  23.68  28.95  30.26  31.58  32.89  35.53  38.16  40.79  42.11  43.42  46.05  46.05  47.37  48.68
GDT RMS_LOCAL    0.29   0.50   0.50   0.50   0.50   1.69   2.01   2.70   2.75   2.88   3.09   4.17   4.41   4.61   4.80   4.95   5.30   5.30   5.50   5.73
GDT RMS_ALL_AT  13.31  13.43  13.43  13.43  13.43  13.22  13.61  11.95  11.68  11.82  11.87  10.60  10.26  10.42  10.57  10.61  10.41  10.41  10.03  10.18

# Checking swapping
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  E    40_B      E    40_B
#   possible swapping detected:  E    41_B      E    41_B
#   possible swapping detected:  Y    42_B      Y    42_B
#   possible swapping detected:  E    48_B      E    48_B
#   possible swapping detected:  E    55_B      E    55_B
#   possible swapping detected:  Y    75_B      Y    75_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E    28_B      E    28_B    18.755     0    0.555   1.135    21.904    0.000    0.000
LGA    R    29_B      R    29_B    12.491     0    0.643   1.139    14.763    0.000    0.000
LGA    L    30_B      L    30_B    12.334     0    0.653   0.663    16.134    0.000    0.000
LGA    L    31_B      L    31_B     9.677     0    0.639   1.366    10.921    3.095    1.845
LGA    M    32_B      M    32_B     3.923     0    0.608   0.886     8.590   36.548   26.786
LGA    V    33_B      V    33_B     4.315     0    0.640   0.565     8.238   41.905   28.980
LGA    F    34_B      F    34_B     2.988     0    0.138   0.190     4.740   53.571   46.710
LGA    D    35_B      D    35_B     2.786     0    0.171   0.351     3.901   67.143   56.905
LGA    E    36_B      E    36_B     3.920     0    0.082   1.060     8.606   50.119   29.471
LGA    E    37_B      E    37_B     0.977     0    0.132   0.947     6.787   66.548   51.111
LGA    R    38_B      R    38_B     4.115     0    0.182   1.093    11.698   33.452   18.745
LGA    V    39_B      V    39_B     6.255     0    0.582   1.503     8.311   15.833   15.850
LGA    E    40_B      E    40_B     9.441     0    0.257   0.618    15.132    3.095    1.376
LGA    E    41_B      E    41_B     4.189     0    0.553   1.174     5.987   36.429   34.497
LGA    Y    42_B      Y    42_B     4.933     0    0.593   1.466    16.082   37.262   13.095
LGA    M    43_B      M    43_B     3.593     0    0.028   1.150     7.538   46.905   37.857
LGA    K    44_B      K    44_B     2.896     0    0.039   1.046     6.219   55.357   48.095
LGA    I    45_B      I    45_B     3.069     0    0.014   0.676     6.356   55.476   46.964
LGA    M    46_B      M    46_B     2.602     0    0.020   0.955     5.333   62.976   51.250
LGA    K    47_B      K    47_B     1.977     0    0.078   0.817     6.154   72.976   52.857
LGA    E    48_B      E    48_B     1.930     0    0.033   0.917     5.514   75.000   58.042
LGA    V    49_B      V    49_B     1.418     0    0.022   0.091     2.112   81.548   76.667
LGA    I    50_B      I    50_B     1.170     0    0.022   0.056     1.954   83.690   80.417
LGA    E    51_B      E    51_B     0.859     0    0.023   0.120     1.929   88.214   83.492
LGA    K    52_B      K    52_B     1.008     0    0.027   1.080     6.659   83.690   63.545
LGA    I    53_B      I    53_B     1.614     0    0.017   0.044     2.313   72.976   70.893
LGA    L    54_B      L    54_B     1.619     0    0.029   0.066     2.268   72.976   75.119
LGA    E    55_B      E    55_B     2.205     0    0.196   0.773     5.214   66.786   53.598
LGA    N    56_B      N    56_B     2.748     0    0.599   0.756     3.495   55.357   52.679
LGA    R    57_B      R    57_B     3.102     0    0.590   1.379    10.005   40.000   20.130
LGA    K    58_B      K    58_B     7.369     0    0.562   1.019     8.968    9.286   10.476
LGA    K    64_B      K    64_B    16.267     0    0.057   0.656    22.898    0.000    0.000
LGA    V    65_B      V    65_B    13.090     0    0.029   0.076    14.929    0.000    0.476
LGA    E    66_B      E    66_B    17.394     0    0.086   0.143    25.791    0.000    0.000
LGA    I    67_B      I    67_B    15.102     0    0.192   0.802    19.456    0.000    0.000
LGA    P    68_B      P    68_B    18.748     0    0.128   0.433    19.401    0.000    0.000
LGA    P    69_B      P    69_B    22.989     0    0.728   0.863    23.960    0.000    0.000
LGA    G    70_B      G    70_B    22.893     0    0.227   0.227    23.251    0.000    0.000
LGA    M    71_B      M    71_B    21.798     0    0.250   1.100    22.939    0.000    0.000
LGA    E    72_B      E    72_B    23.958     0    0.026   0.812    26.235    0.000    0.000
LGA    W    73_B      W    73_B    23.418     0    0.059   1.288    24.259    0.000    0.000
LGA    F    74_B      F    74_B    21.580     0    0.031   1.446    22.168    0.000    0.000
LGA    Y    75_B      Y    75_B    23.747     0    0.555   0.586    30.513    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     378    378  100.00                76
SUMMARY(RMSD_GDC):     8.734          8.604                 10.389           19.319   15.894

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   48   76    4.0     22    2.70    27.961    24.086     0.786

LGA_LOCAL      RMSD:   2.700  Number of atoms:   22  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.947  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   8.734  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.690489 * X  +   0.401219 * Y  +  -0.601871 * Z  +  21.435331
  Y_new =   0.103944 * X  +   0.878469 * Y  +   0.466356 * Z  + -47.725590
  Z_new =   0.715836 * X  +   0.259453 * Y  +  -0.648277 * Z  + -14.874015 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.992178 -0.797821  2.760897   [DEG:  171.4392  -45.7118  158.1878 ]
ZXZ: -2.230009  2.276116  1.223076   [DEG: -127.7701  130.4118   70.0771 ]
 
# END of job
