
#######################################################
#                                                     #
#                        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   50 (  433),  selected   48 , name one
# Molecule2: number of CA atoms  127 ( 1099),  selected   48 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34      83_C - 116_C       4.74    23.44
  LONGEST_CONTINUOUS_SEGMENT:    34      84_C - 119_C       4.54    22.45
  LCS_AVERAGE:     22.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29      85_C - 113_C       1.52    24.44
  LONGEST_CONTINUOUS_SEGMENT:    29      86_C - 114_C       1.77    24.53
  LCS_AVERAGE:     15.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27      86_C - 112_C       0.96    24.59
  LONGEST_CONTINUOUS_SEGMENT:    27      87_C - 113_C       0.90    24.70
  LCS_AVERAGE:     13.44

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   48
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    70_B     E    70_C      3    4   13      0    3    3    4    4    5    6    7    7   10   11   12   17   20   21   22   22   22   23   24 
LCS_GDT     E    71_B     E    71_C      3    5   13      3    3    4    5    5    5    6    8    9   10   11   13   18   20   21   22   22   22   23   24 
LCS_GDT     G    72_B     G    72_C      3    5   13      3    3    4    5    5    5    6    8    9   10   11   12   15   19   21   22   22   22   23   24 
LCS_GDT     R    73_B     R    73_C      3    5   13      3    3    4    5    5    5    6    8    9   10   11   12   15   16   18   22   22   22   23   24 
LCS_GDT     V    74_B     V    74_C      3    5   13      0    3    4    5    5    5    6    8    9   10   11   13   18   20   21   22   22   22   23   24 
LCS_GDT     W    75_B     W    75_C      3    5   13      3    3    3    4    4    5    6    8    9   10   13   13   18   20   21   22   22   22   23   24 
LCS_GDT     F    76_B     F    76_C      3    3   13      3    3    3    3    3    4    6    7    8   10   13   13   18   20   21   22   22   22   23   24 
LCS_GDT     I    77_B     I    77_C      3    3   13      3    3    3    3    4    5    6    8    9   10   13   13   18   20   21   22   22   22   23   24 
LCS_GDT     V    78_B     V    78_C      3    4   13      3    3    3    3    4    4    6    9    9   10   13   14   18   20   21   22   22   22   23   24 
LCS_GDT     K    79_B     K    79_C      3    4   13      3    3    3    3    4    4    5    7    8    9   11   12   16   20   21   22   22   22   23   24 
LCS_GDT     E    80_B     E    80_C      3    4   13      3    3    3    3    4    5    7    9    9   10   13   14   18   20   21   22   22   22   23   24 
LCS_GDT     M    81_B     M    81_C      3    4   13      3    3    3    3    4    5    7    9    9   10   13   14   18   20   21   22   22   27   30   32 
LCS_GDT     L    82_B     L    82_C      3    4   33      3    3    3    5    5    6    6    9    9   10   13   14   18   20   26   29   30   34   35   36 
LCS_GDT     H    83_B     H    83_C      3    4   34      3    3    3    5    5    6    7    9    9   10   13   18   22   25   28   31   34   35   35   36 
LCS_GDT     A    84_B     A    84_C      4    6   34      4    4    4    5    5    7    8   12   14   19   23   27   30   30   32   34   34   35   35   36 
LCS_GDT     T    85_B     T    85_C      5   29   34      4    4    5    7   12   22   27   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     T    86_B     T    86_C     27   29   34      5    6   11   25   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     E    87_B     E    87_C     27   29   34      5   17   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     E    88_B     E    88_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     E    89_B     E    89_C     27   29   34      5    9   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     A    90_B     A    90_C     27   29   34      5   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     L    91_B     L    91_C     27   29   34      5   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     E    92_B     E    92_C     27   29   34      5   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     N    93_B     N    93_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     M    94_B     M    94_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     D    95_B     D    95_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     K    96_B     K    96_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     F    97_B     F    97_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     L    98_B     L    98_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     E    99_B     E    99_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     S   100_B     S   100_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     W   101_B     W   101_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     E   102_B     E   102_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     K   103_B     K   103_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     V   104_B     V   104_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     F   105_B     F   105_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     K   106_B     K   106_C     27   29   34     15   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     E   107_B     E   107_C     27   29   34     10   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     L   108_B     L   108_C     27   29   34      7   14   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     L   109_B     L   109_C     27   29   34     10   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     E   110_B     E   110_C     27   29   34      9   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     Y   111_B     Y   111_C     27   29   34      9   21   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     H   112_B     H   112_C     27   29   34      8   19   26   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     F   113_B     F   113_C     27   29   34      7   14   22   27   28   28   28   29   29   29   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     E   114_B     E   114_C      3   29   34      3    3    4    4    5    7   12   13   19   27   29   30   31   31   32   34   34   35   35   36 
LCS_GDT     H   115_B     H   115_C      3    4   34      3    3    4    4    4    5    6    7    9   13   16   22   29   31   32   34   34   35   35   36 
LCS_GDT     N   116_B     N   116_C      3    4   34      3    3    3    4    4    5    6    7    8   10   16   21   26   28   32   34   34   35   35   36 
LCS_GDT     S   119_B     S   119_C      3    4   34      0    1    3    4    4    5    8   13   18   22   25   29   31   31   32   34   34   35   35   36 
LCS_AVERAGE  LCS_A:  17.20  (  13.44   15.53   22.62 )

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     21     26     27     28     28     28     29     29     29     29     30     31     31     32     34     34     35     35     36 
GDT PERCENT_AT  11.81  16.54  20.47  21.26  22.05  22.05  22.05  22.83  22.83  22.83  22.83  23.62  24.41  24.41  25.20  26.77  26.77  27.56  27.56  28.35
GDT RMS_LOCAL    0.33   0.58   0.83   0.90   1.02   1.02   1.02   1.52   1.52   1.52   1.52   2.09   3.54   3.54   3.91   4.54   4.54   5.04   5.04   5.51
GDT RMS_ALL_AT  24.62  24.72  24.71  24.70  24.58  24.58  24.58  24.44  24.44  24.44  24.44  24.38  23.15  23.15  22.93  22.45  22.45  21.93  21.93  21.35

# Checking swapping
#   possible swapping detected:  E    80_B      E    80_C
#   possible swapping detected:  E    87_B      E    87_C
#   possible swapping detected:  E   102_B      E   102_C
#   possible swapping detected:  E   110_B      E   110_C
#   possible swapping detected:  F   113_B      F   113_C
#   possible swapping detected:  E   114_B      E   114_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E    70_B      E    70_C    67.455     0    0.163   0.661    70.467    0.000    0.000
LGA    E    71_B      E    71_C    66.319     0    0.560   0.614    71.963    0.000    0.000
LGA    G    72_B      G    72_C    61.391     0    0.293   0.293    63.496    0.000    0.000
LGA    R    73_B      R    73_C    55.450     0    0.537   1.053    60.485    0.000    0.000
LGA    V    74_B      V    74_C    49.510     0    0.587   0.886    51.887    0.000    0.000
LGA    W    75_B      W    75_C    46.605     0    0.604   1.332    50.915    0.000    0.000
LGA    F    76_B      F    76_C    42.588     0    0.592   1.335    48.042    0.000    0.000
LGA    I    77_B      I    77_C    38.838     0    0.601   0.766    44.044    0.000    0.000
LGA    V    78_B      V    78_C    33.420     0    0.598   0.656    35.858    0.000    0.000
LGA    K    79_B      K    79_C    30.877     0    0.098   0.574    32.022    0.000    0.000
LGA    E    80_B      E    80_C    26.816     0    0.556   1.550    28.488    0.000    0.000
LGA    M    81_B      M    81_C    21.720     0    0.621   1.243    23.835    0.000    0.000
LGA    L    82_B      L    82_C    17.802     0    0.555   1.354    21.071    0.000    0.000
LGA    H    83_B      H    83_C    15.046     0    0.361   1.237    18.808    0.000    0.000
LGA    A    84_B      A    84_C     9.379     0    0.624   0.564    11.606    3.929    3.143
LGA    T    85_B      T    85_C     5.890     0    0.319   0.316     8.165   31.190   21.837
LGA    T    86_B      T    86_C     2.094     0    0.258   1.064     5.258   71.667   60.136
LGA    E    87_B      E    87_C     1.072     0    0.051   1.064     2.768   85.952   77.884
LGA    E    88_B      E    88_C     0.551     0    0.016   0.921     5.689   88.214   68.148
LGA    E    89_B      E    89_C     1.307     0    0.035   0.943     3.370   81.548   70.635
LGA    A    90_B      A    90_C     1.362     0    0.184   0.191     1.422   81.429   81.429
LGA    L    91_B      L    91_C     1.365     0    0.095   0.813     2.908   79.286   70.179
LGA    E    92_B      E    92_C     1.193     0    0.000   0.388     3.936   81.429   66.667
LGA    N    93_B      N    93_C     0.873     0    0.068   1.052     2.784   90.476   84.107
LGA    M    94_B      M    94_C     0.697     0    0.036   1.032     2.904   90.476   82.143
LGA    D    95_B      D    95_C     0.496     0    0.031   0.036     0.638   97.619   95.238
LGA    K    96_B      K    96_C     0.707     0    0.039   1.194     4.577   90.476   78.201
LGA    F    97_B      F    97_C     0.695     0    0.026   1.124     6.280   90.476   62.641
LGA    L    98_B      L    98_C     0.223     0    0.113   1.364     3.702   95.238   80.774
LGA    E    99_B      E    99_C     0.833     0    0.064   0.220     1.909   90.476   83.598
LGA    S   100_B      S   100_C     0.943     0    0.123   0.708     1.423   90.476   87.460
LGA    W   101_B      W   101_C     0.991     0    0.051   1.130     5.136   88.214   67.857
LGA    E   102_B      E   102_C     0.672     0    0.024   0.898     3.281   90.476   74.074
LGA    K   103_B      K   103_C     0.725     0    0.047   1.131     5.008   90.476   73.122
LGA    V   104_B      V   104_C     0.665     0    0.058   0.148     1.041   90.476   89.184
LGA    F   105_B      F   105_C     0.930     0    0.076   1.225     6.460   90.476   60.043
LGA    K   106_B      K   106_C     0.655     0    0.037   0.603     3.602   95.238   83.386
LGA    E   107_B      E   107_C     0.236     0    0.050   0.505     1.524   97.619   92.751
LGA    L   108_B      L   108_C     1.166     0    0.123   1.372     5.351   88.214   70.833
LGA    L   109_B      L   109_C     0.669     0    0.032   0.323     3.255   95.238   79.286
LGA    E   110_B      E   110_C     0.854     0    0.065   0.916     2.873   88.333   77.143
LGA    Y   111_B      Y   111_C     1.290     0    0.050   0.114     2.615   79.286   72.381
LGA    H   112_B      H   112_C     1.724     0    0.141   1.136     4.575   70.833   62.000
LGA    F   113_B      F   113_C     2.156     0    0.127   0.484     9.144   50.238   34.372
LGA    E   114_B      E   114_C     8.455     0    0.449   1.106    10.689    6.548    3.280
LGA    H   115_B      H   115_C    14.297     0    0.620   1.019    18.995    0.000    0.000
LGA    N   116_B      N   116_C    15.344     0    0.466   0.395    19.538    0.000    0.000
LGA    S   119_B      S   119_C    21.383     0    0.144   0.745    22.452    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       48     192    192  100.00     418    418  100.00               127
SUMMARY(RMSD_GDC):    16.317         16.086                 17.392           19.386   16.645

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   50  127    4.0     29    1.52    21.850    20.433     1.789

LGA_LOCAL      RMSD:   1.521  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  24.438  Number of assigned atoms:   48 
Std_ASGN_ATOMS RMSD:  16.317  Standard rmsd on all 48 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.340380 * X  +   0.854763 * Y  +  -0.391818 * Z  + -160.831879
  Y_new =   0.899376 * X  +  -0.417537 * Y  +  -0.129563 * Z  + -109.493240
  Z_new =  -0.274345 * X  +  -0.308291 * Y  +  -0.910874 * Z  + 359.337555 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.208993  0.277908 -2.815238   [DEG:   69.2702   15.9230 -161.3013 ]
ZXZ: -1.251443  2.716194 -2.414393   [DEG:  -71.7024  155.6264 -138.3345 ]
 
# END of job
