
#######################################################
#                                                     #
#                        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   41 (  355),  selected   40 , name one
# Molecule2: number of CA atoms  127 ( 1099),  selected   40 , 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:    33      77_C - 109_C       4.64    10.70
  LCS_AVERAGE:     24.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      82_C - 105_C       1.85    12.53
  LONGEST_CONTINUOUS_SEGMENT:    24      83_C - 106_C       1.92    12.43
  LCS_AVERAGE:     14.90

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      83_C - 102_C       0.99    13.35
  LCS_AVERAGE:     11.28

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   40
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    77_B     I    77_C      3    3   33      0    3    3    3    3    3    5    8   10   12   13   16   25   31   31   31   32   32   33   33 
LCS_GDT     V    78_B     V    78_C      3    4   33      3    3    3    3    4    4   10   12   20   25   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     K    79_B     K    79_C      3    4   33      3    3    3    3    6    8   11   14   23   25   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     E    80_B     E    80_C      3    4   33      3    3    3    3    4    7   17   23   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     M    81_B     M    81_C      3   22   33      3    3    3    3    4    8   17   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     L    82_B     L    82_C      3   24   33      3    3    3    6    7   17   22   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     H    83_B     H    83_C     20   24   33      4    9   14   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     A    84_B     A    84_C     20   24   33      5   11   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     T    85_B     T    85_C     20   24   33      4   11   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     T    86_B     T    86_C     20   24   33      6   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     E    87_B     E    87_C     20   24   33      5   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     E    88_B     E    88_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     E    89_B     E    89_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     A    90_B     A    90_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     L    91_B     L    91_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     E    92_B     E    92_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     N    93_B     N    93_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     M    94_B     M    94_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     D    95_B     D    95_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     K    96_B     K    96_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     F    97_B     F    97_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     L    98_B     L    98_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     E    99_B     E    99_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     S   100_B     S   100_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     W   101_B     W   101_C     20   24   33     14   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     E   102_B     E   102_C     20   24   33      5   16   19   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     K   103_B     K   103_C     18   24   33      5    6    9   17   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     V   104_B     V   104_C      5   24   33      5    6   11   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     F   105_B     F   105_C     11   24   33      5    6   13   20   22   23   23   25   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     K   106_B     K   106_C     11   24   33      3    9   10   12   12   14   22   24   27   27   28   29   31   31   31   31   32   32   33   33 
LCS_GDT     E   107_B     E   107_C     11   12   33      3    9   10   12   12   12   12   13   15   18   27   27   31   31   31   31   32   32   33   33 
LCS_GDT     L   108_B     L   108_C     11   12   33      3    9   10   12   12   12   12   13   16   20   27   28   31   31   31   31   32   32   33   33 
LCS_GDT     L   109_B     L   109_C     11   12   33      3    7   10   12   12   12   12   13   15   15   16   16   17   18   19   24   28   32   33   33 
LCS_GDT     E   110_B     E   110_C     11   12   31      5    9   10   12   12   12   12   13   15   15   16   16   17   18   20   24   26   30   32   33 
LCS_GDT     Y   111_B     Y   111_C     11   12   18      5    9   10   12   12   12   12   13   15   15   16   16   17   18   19   24   25   27   31   32 
LCS_GDT     H   112_B     H   112_C     11   12   18      5    9   10   12   12   12   12   13   15   15   16   16   17   18   19   20   21   23   25   26 
LCS_GDT     F   113_B     F   113_C     11   12   18      5    9   10   12   12   12   12   13   15   15   16   16   17   17   18   19   21   23   24   26 
LCS_GDT     E   114_B     E   114_C     11   12   18      5    9   10   12   12   12   12   13   15   15   16   16   17   17   18   19   21   23   24   26 
LCS_GDT     H   115_B     H   115_C     11   12   18      4    9   10   12   12   12   12   13   15   15   16   16   17   17   19   19   21   23   24   26 
LCS_GDT     N   116_B     N   116_C     11   12   18      4    4    8   12   12   12   12   13   15   15   16   16   17   17   18   19   21   23   24   26 
LCS_AVERAGE  LCS_A:  16.78  (  11.28   14.90   24.17 )

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     14     16     19     20     22     23     23     25     27     27     28     29     31     31     31     31     32     32     33     33 
GDT PERCENT_AT  11.02  12.60  14.96  15.75  17.32  18.11  18.11  19.69  21.26  21.26  22.05  22.83  24.41  24.41  24.41  24.41  25.20  25.20  25.98  25.98
GDT RMS_LOCAL    0.32   0.49   0.80   0.99   1.35   1.46   1.46   2.12   2.58   2.58   2.94   3.18   3.94   3.94   3.94   3.94   4.19   4.19   4.64   4.64
GDT RMS_ALL_AT  13.65  13.71  13.49  13.35  12.81  12.74  12.74  12.43  12.08  12.08  11.91  11.75  10.96  10.96  10.96  10.96  10.95  10.95  10.70  10.70

# Checking swapping
#   possible swapping detected:  E    88_B      E    88_C
#   possible swapping detected:  E    89_B      E    89_C
#   possible swapping detected:  F    97_B      F    97_C
#   possible swapping detected:  E   102_B      E   102_C
#   possible swapping detected:  Y   111_B      Y   111_C
#   possible swapping detected:  F   113_B      F   113_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    I    77_B      I    77_C     9.953     0    0.603   0.699    12.204    0.357    0.238
LGA    V    78_B      V    78_C     8.599     0    0.655   0.942    11.273    1.786    5.850
LGA    K    79_B      K    79_C     8.735     0    0.087   0.914    13.394    4.048    2.169
LGA    E    80_B      E    80_C     5.611     0    0.605   0.533     7.052   18.571   28.254
LGA    M    81_B      M    81_C     5.260     0    0.626   1.077     7.715   25.238   21.012
LGA    L    82_B      L    82_C     5.076     0    0.476   0.433    10.527   33.214   18.869
LGA    H    83_B      H    83_C     2.266     0    0.468   1.054     5.706   64.762   50.619
LGA    A    84_B      A    84_C     1.585     0    0.051   0.058     1.689   77.143   76.286
LGA    T    85_B      T    85_C     1.426     0    0.061   1.190     4.080   81.429   72.653
LGA    T    86_B      T    86_C     0.439     0    0.069   0.965     2.168   95.238   84.558
LGA    E    87_B      E    87_C     1.897     0    0.026   1.179     2.892   72.857   69.418
LGA    E    88_B      E    88_C     1.496     0    0.031   1.059     4.934   83.810   59.947
LGA    E    89_B      E    89_C     0.210     0    0.055   0.160     1.745   92.976   87.672
LGA    A    90_B      A    90_C     1.732     0    0.038   0.054     2.273   75.000   72.952
LGA    L    91_B      L    91_C     1.352     0    0.043   0.840     3.502   85.952   75.714
LGA    E    92_B      E    92_C     0.320     0    0.060   0.246     1.067   92.857   92.646
LGA    N    93_B      N    93_C     1.247     0    0.018   1.046     3.456   83.690   76.488
LGA    M    94_B      M    94_C     1.354     0    0.073   1.213     3.171   83.690   74.405
LGA    D    95_B      D    95_C     0.628     0    0.073   0.069     2.062   92.857   82.917
LGA    K    96_B      K    96_C     0.920     0    0.029   1.071     4.337   85.952   73.862
LGA    F    97_B      F    97_C     1.801     0    0.093   1.146     3.521   75.000   66.623
LGA    L    98_B      L    98_C     1.089     0    0.096   1.380     3.799   85.952   74.940
LGA    E    99_B      E    99_C     1.022     0    0.056   1.338     5.026   81.548   64.339
LGA    S   100_B      S   100_C     1.818     0    0.058   0.113     2.474   68.810   67.460
LGA    W   101_B      W   101_C     2.239     0    0.239   1.056     9.195   77.381   33.878
LGA    E   102_B      E   102_C     0.222     0    0.054   0.984     2.741   84.167   80.000
LGA    K   103_B      K   103_C     3.123     0    0.160   0.976     5.428   57.500   43.122
LGA    V   104_B      V   104_C     2.287     0    0.041   0.058     3.795   66.786   62.857
LGA    F   105_B      F   105_C     2.106     0    0.542   1.253     9.138   50.119   30.260
LGA    K   106_B      K   106_C     6.585     0    0.023   0.107    12.924   11.548    7.460
LGA    E   107_B      E   107_C    12.686     0    0.115   0.566    16.187    0.000    0.000
LGA    L   108_B      L   108_C    11.777     0    0.035   0.142    15.469    0.000    0.655
LGA    L   109_B      L   109_C    14.915     0    0.155   0.301    19.116    0.000    0.000
LGA    E   110_B      E   110_C    18.710     0    0.014   0.118    23.027    0.000    0.000
LGA    Y   111_B      Y   111_C    22.221     0    0.011   1.437    25.592    0.000    0.000
LGA    H   112_B      H   112_C    23.223     0    0.043   0.658    27.393    0.000    0.000
LGA    F   113_B      F   113_C    26.743     0    0.098   0.969    31.093    0.000    0.000
LGA    E   114_B      E   114_C    30.373     0    0.156   0.386    34.233    0.000    0.000
LGA    H   115_B      H   115_C    32.733     0    0.279   1.430    34.952    0.000    0.000
LGA    N   116_B      N   116_C    33.564     0    0.424   0.980    37.150    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       40     160    160  100.00     347    347  100.00               127
SUMMARY(RMSD_GDC):     9.024          9.175                  9.833           15.041   13.056

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   41  127    4.0     25    2.12    18.110    17.912     1.128

LGA_LOCAL      RMSD:   2.117  Number of atoms:   25  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  12.427  Number of assigned atoms:   40 
Std_ASGN_ATOMS RMSD:   9.024  Standard rmsd on all 40 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.799163 * X  +  -0.190079 * Y  +  -0.570270 * Z  +   9.206677
  Y_new =  -0.215088 * X  +  -0.795457 * Y  +   0.566556 * Z  + -32.674683
  Z_new =  -0.561316 * X  +   0.575429 * Y  +   0.594816 * Z  +  17.019413 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.878682  0.595975  0.768832   [DEG: -164.9363   34.1468   44.0508 ]
ZXZ: -2.352927  0.933759 -0.772983   [DEG: -134.8128   53.5005  -44.2887 ]
 
# END of job
