
#######################################################
#                                                     #
#                        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   57 (  458),  selected   57 , name one
# Molecule2: number of CA atoms  116 (  942),  selected   57 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      88_B - 104_B       4.52    30.05
  LCS_AVERAGE:     13.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      72_B - 80_B        1.95    20.41
  LONGEST_CONTINUOUS_SEGMENT:     9      92_B - 100_B       1.89    29.64
  LCS_AVERAGE:      5.34

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      92_B - 98_B        0.95    23.76
  LCS_AVERAGE:      3.64

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   57
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    48_C     E    48_B      4    5   15      3    4    4    4    4    6    6    6    6    8    9    9   11   13   14   15   17   19   20   22 
LCS_GDT     R    49_C     R    49_B      4    5   15      3    4    4    4    5    6    6    7    8   12   13   13   14   16   18   18   18   19   19   20 
LCS_GDT     S    50_C     S    50_B      5    5   15      3    4    4    5    5    6    6    7    8   12   13   13   14   16   18   18   18   19   22   24 
LCS_GDT     G    51_C     G    51_B      5    5   15      3    4    4    5    5    6    6    7    8   12   13   13   14   16   18   19   22   25   26   28 
LCS_GDT     G    52_C     G    52_B      5    5   16      3    4    4    5    5    6    6    7   10   12   13   13   16   19   20   21   23   25   27   28 
LCS_GDT     I    53_C     I    53_B      5    5   16      3    4    4    5    5    6    8    9   10   12   13   14   16   19   20   21   23   25   27   28 
LCS_GDT     P    54_C     P    54_B      5    5   16      3    4    4    5    7    8    8    9   11   12   13   14   16   19   20   21   23   25   27   28 
LCS_GDT     E    55_C     E    55_B      3    4   16      3    3    3    4    5    6    8    9   11   12   13   14   14   16   18   19   22   24   27   28 
LCS_GDT     G    56_C     G    56_B      3    4   16      1    3    3    4    4    6    8    9   11   12   13   14   14   16   18   19   21   23   27   28 
LCS_GDT     D    57_C     D    57_B      4    6   16      3    4    4    5    6    8    8    9   11   12   13   14   14   16   18   21   23   24   27   28 
LCS_GDT     I    58_C     I    58_B      4    6   16      3    4    4    5    6    8    8    9   11   12   13   14   14   19   20   21   23   25   27   28 
LCS_GDT     Y    59_C     Y    59_B      4    6   16      3    4    4    6    7    8    8    9   11   12   13   14   16   19   20   21   23   25   27   28 
LCS_GDT     L    60_C     L    60_B      4    6   16      3    4    4    6    7    8    8    9   11   12   13   14   16   19   20   23   23   25   27   28 
LCS_GDT     E    61_C     E    61_B      3    6   16      0    3    4    6    7    7    8    9   11   12   13   14   17   19   20   23   23   25   27   28 
LCS_GDT     S    62_C     S    62_B      3    6   16      3    3    4    6    7    7    8    9   11   12   13   14   17   19   20   23   23   25   27   28 
LCS_GDT     N    63_C     N    63_B      3    4   16      3    3    3    4    4    5    7    8    9   10   10   13   14   17   19   23   23   25   27   28 
LCS_GDT     L    64_C     L    64_B      3    4   16      3    3    3    4    4    5    6    8    9   10   10   12   16   17   19   21   23   24   26   26 
LCS_GDT     F    65_C     F    65_B      3    4   16      3    3    3    4    4    6    7    9   11   12   13   13   16   17   19   21   23   24   27   28 
LCS_GDT     L    66_C     L    66_B      3    4   16      3    3    4    6    7    7    8    9   11   12   13   14   16   19   20   23   23   25   27   28 
LCS_GDT     D    67_C     D    67_B      3    4   16      2    3    4    6    7    8    8    9   11   12   13   14   16   17   20   23   23   25   27   28 
LCS_GDT     F    68_C     F    68_B      3    4   16      3    3    3    4    4    6    7    9   11   12   13   14   17   19   20   23   23   25   27   28 
LCS_GDT     N    69_C     N    69_B      4    6   16      4    4    4    5    5    5    6   10   10   11   12   14   17   19   20   23   23   25   27   28 
LCS_GDT     P    70_C     P    70_B      4    6   16      4    4    4    5    6    8   10   10   10   11   12   14   17   17   20   23   23   24   26   27 
LCS_GDT     Y    71_C     Y    71_B      4    6   16      4    4    4    5    5    6    7    8   10   11   13   14   16   17   20   23   23   24   26   26 
LCS_GDT     G    72_C     G    72_B      4    9   16      4    4    4    5    8    9   10   10   10   11   13   14   17   17   20   23   23   25   26   28 
LCS_GDT     L    73_C     L    73_B      4    9   16      3    4    4    5    7    9   10   10   10   11   13   14   17   17   20   23   23   25   27   28 
LCS_GDT     S    74_C     S    74_B      4    9   16      3    4    6    6    8    9   10   10   10   11   13   14   17   19   20   23   23   25   27   28 
LCS_GDT     G    75_C     G    75_B      5    9   16      3    5    6    6    8    9   10   10   10   11   13   14   17   19   20   23   23   25   27   28 
LCS_GDT     Y    76_C     Y    76_B      5    9   16      4    5    6    6    8    9   10   10   10   11   13   14   17   19   20   23   23   25   27   28 
LCS_GDT     L    77_C     L    77_B      5    9   16      4    5    6    6    8    9   10   10   10   11   13   14   17   19   20   23   23   25   27   28 
LCS_GDT     L    78_C     L    78_B      5    9   16      4    5    6    6    8    9   10   10   10   11   13   14   17   19   20   23   23   25   27   28 
LCS_GDT     S    79_C     S    79_B      5    9   16      4    5    6    6    8    9   10   10   11   11   13   14   17   19   20   23   23   25   27   28 
LCS_GDT     E    80_C     E    80_B      5    9   16      3    4    4    6    8    9   10   10   11   11   13   14   17   17   20   23   23   25   26   28 
LCS_GDT     P    81_C     P    81_B      4    6   16      3    4    4    4    6    8    9    9   10   11   13   14   17   17   20   23   23   24   26   27 
LCS_GDT     N    82_C     N    82_B      4    4   16      3    4    4    4    6    8    9    9   10   11   13   14   17   19   20   23   23   25   27   28 
LCS_GDT     C    83_C     C    83_B      3    4   16      3    3    4    4    6    8    8    9   10   11   13   14   17   19   20   23   23   25   27   28 
LCS_GDT     V    84_C     V    84_B      3    4   16      1    3    4    4    6    8    8    9   11   11   13   14   14   15   19   23   23   25   27   28 
LCS_GDT     D    85_C     D    85_B      3    3   16      3    3    3    4    4    5    7    8   11   11   11   13   14   15   16   17   21   24   26   28 
LCS_GDT     L    86_C     L    86_B      3    3   16      3    3    3    4    4    5    7   11   12   13   13   14   15   16   16   17   18   20   22   25 
LCS_GDT     L    87_C     L    87_B      3    5   16      3    3    3    4    5    5    8   11   12   13   13   14   15   16   16   17   18   20   20   22 
LCS_GDT     I    88_C     I    88_B      3    5   17      3    3    3    4    5    6    6    7   12   13   13   14   15   16   16   17   18   20   20   22 
LCS_GDT     E    89_C     E    89_B      3    5   17      3    3    4    5    6    8    9   11   12   13   14   15   16   16   16   17   18   20   20   22 
LCS_GDT     P    90_C     P    90_B      3    5   17      3    3    3    4    5    6    6    8   11   11   12   15   16   16   16   17   18   19   20   22 
LCS_GDT     N    91_C     N    91_B      3    5   17      3    3    3    4    5    6    7   10   11   11   13   14   16   16   16   17   18   19   20   22 
LCS_GDT     N    92_C     N    92_B      7    9   17      4    6    6    9    9   10   10   11   12   13   14   15   16   16   16   17   18   20   20   22 
LCS_GDT     Y    93_C     Y    93_B      7    9   17      5    6    6    9    9   10   10   11   12   13   14   15   16   16   16   17   18   20   22   25 
LCS_GDT     V    94_C     V    94_B      7    9   17      5    6    6    9    9   10   10   11   12   13   14   15   16   16   16   17   18   20   20   22 
LCS_GDT     R    95_C     R    95_B      7    9   17      4    5    5    9    9   10   10   11   12   13   14   15   16   16   16   17   18   21   25   27 
LCS_GDT     L    96_C     L    96_B      7    9   17      5    6    6    9    9   10   10   11   12   13   14   15   16   16   16   17   18   20   20   22 
LCS_GDT     R    97_C     R    97_B      7    9   17      5    6    6    8    9   10   10   11   12   13   14   15   16   16   16   17   18   20   25   27 
LCS_GDT     L    98_C     L    98_B      7    9   17      5    6    6    8    8    8    9   11   12   13   14   15   16   16   16   17   18   20   20   26 
LCS_GDT     I    99_C     I    99_B      4    9   17      4    4    6    9    9   10   10   11   12   13   14   15   16   16   16   17   18   20   20   23 
LCS_GDT     E   100_C     E   100_B      4    9   17      4    4    5    9    9   10   10   11   12   13   14   15   16   16   16   17   18   20   20   22 
LCS_GDT     K   101_C     K   101_B      4    6   17      4    4    4    4    5    7   10   11   12   13   14   15   16   16   16   17   18   20   20   21 
LCS_GDT     I   102_C     I   102_B      4    5   17      4    4    4    9    9   10   10   11   12   13   14   15   16   16   16   17   18   19   20   21 
LCS_GDT     D   103_C     D   103_B      4    5   17      4    4    4    9    9   10   10   11   12   13   14   15   16   16   16   17   18   19   20   21 
LCS_GDT     I   104_C     I   104_B      4    5   17      4    4    4    4    4    5    6    7    8   13   14   15   16   16   16   17   18   18   19   19 
LCS_AVERAGE  LCS_A:   7.66  (   3.64    5.34   13.99 )

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      5      6      6      9      9     10     10     11     12     13     14     15     17     19     20     23     23     25     27     28 
GDT PERCENT_AT   4.31   5.17   5.17   7.76   7.76   8.62   8.62   9.48  10.34  11.21  12.07  12.93  14.66  16.38  17.24  19.83  19.83  21.55  23.28  24.14
GDT RMS_LOCAL    0.27   0.58   0.58   1.46   1.46   1.68   1.68   2.02   2.40   3.18   3.37   3.76   4.99   5.71   5.80   6.09   6.18   6.57   6.85   7.02
GDT RMS_ALL_AT  23.91  23.15  23.15  29.89  29.89  29.73  29.73  29.63  29.68  18.38  29.85  30.05  19.35  15.75  15.61  18.80  19.83  15.74  14.93  14.88

# Checking swapping
#   possible swapping detected:  E    48_C      E    48_B
#   possible swapping detected:  E    55_C      E    55_B
#   possible swapping detected:  D    57_C      D    57_B
#   possible swapping detected:  Y    59_C      Y    59_B
#   possible swapping detected:  E    61_C      E    61_B
#   possible swapping detected:  F    65_C      F    65_B
#   possible swapping detected:  F    68_C      F    68_B
#   possible swapping detected:  E    80_C      E    80_B
#   possible swapping detected:  Y    93_C      Y    93_B
#   possible swapping detected:  E   100_C      E   100_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E    48_C      E    48_B    49.759     0    0.624   1.172    50.846    0.000    0.000
LGA    R    49_C      R    49_B    47.778     0    0.089   0.406    48.703    0.000    0.000
LGA    S    50_C      S    50_B    49.852     0    0.369   0.771    53.666    0.000    0.000
LGA    G    51_C      G    51_B    51.033     0    0.063   0.063    51.688    0.000    0.000
LGA    G    52_C      G    52_B    53.495     0    0.085   0.085    53.495    0.000    0.000
LGA    I    53_C      I    53_B    53.287     0    0.428   1.110    56.452    0.000    0.000
LGA    P    54_C      P    54_B    48.672     0    0.266   0.359    49.799    0.000    0.000
LGA    E    55_C      E    55_B    47.930     0    0.637   1.518    54.164    0.000    0.000
LGA    G    56_C      G    56_B    42.461     0    0.564   0.564    44.299    0.000    0.000
LGA    D    57_C      D    57_B    41.466     0    0.612   1.137    44.700    0.000    0.000
LGA    I    58_C      I    58_B    41.105     0    0.115   0.573    41.817    0.000    0.000
LGA    Y    59_C      Y    59_B    38.181     0    0.103   1.173    43.036    0.000    0.000
LGA    L    60_C      L    60_B    36.204     0    0.235   1.403    37.080    0.000    0.000
LGA    E    61_C      E    61_B    40.251     0    0.642   1.133    48.637    0.000    0.000
LGA    S    62_C      S    62_B    40.608     0    0.602   0.573    41.447    0.000    0.000
LGA    N    63_C      N    63_B    39.279     0    0.056   1.325    39.473    0.000    0.000
LGA    L    64_C      L    64_B    37.676     0    0.588   1.448    39.917    0.000    0.000
LGA    F    65_C      F    65_B    40.952     0    0.561   0.926    49.442    0.000    0.000
LGA    L    66_C      L    66_B    36.495     0    0.608   1.438    37.933    0.000    0.000
LGA    D    67_C      D    67_B    33.346     0    0.613   1.360    34.065    0.000    0.000
LGA    F    68_C      F    68_B    33.174     0    0.589   0.835    38.304    0.000    0.000
LGA    N    69_C      N    69_B    37.061     0    0.594   0.710    40.171    0.000    0.000
LGA    P    70_C      P    70_B    37.087     0    0.118   0.277    40.549    0.000    0.000
LGA    Y    71_C      Y    71_B    32.222     0    0.268   0.266    38.861    0.000    0.000
LGA    G    72_C      G    72_B    28.953     0    0.111   0.111    30.430    0.000    0.000
LGA    L    73_C      L    73_B    24.771     0    0.099   0.868    26.687    0.000    0.000
LGA    S    74_C      S    74_B    22.894     0    0.059   0.088    23.859    0.000    0.000
LGA    G    75_C      G    75_B    22.870     0    0.122   0.122    22.870    0.000    0.000
LGA    Y    76_C      Y    76_B    21.723     0    0.129   0.919    25.805    0.000    0.000
LGA    L    77_C      L    77_B    16.388     0    0.047   1.380    17.985    0.000    0.000
LGA    L    78_C      L    78_B    18.761     0    0.183   0.241    24.753    0.000    0.000
LGA    S    79_C      S    79_B    13.458     0    0.616   0.559    15.585    0.000    0.000
LGA    E    80_C      E    80_B    16.915     0    0.626   1.332    23.416    0.000    0.000
LGA    P    81_C      P    81_B    20.529     0    0.595   0.860    22.138    0.000    0.000
LGA    N    82_C      N    82_B    19.203     0    0.379   1.145    20.336    0.000    0.000
LGA    C    83_C      C    83_B    16.405     0    0.601   1.019    17.977    0.000    0.000
LGA    V    84_C      V    84_B    19.518     0    0.602   0.533    23.874    0.000    0.000
LGA    D    85_C      D    85_B    13.934     0    0.593   1.169    15.910    0.000    0.000
LGA    L    86_C      L    86_B    12.026     0    0.600   1.143    13.514    0.000    0.000
LGA    L    87_C      L    87_B    14.409     0    0.606   1.450    19.675    0.000    0.000
LGA    I    88_C      I    88_B    12.507     0    0.593   1.527    14.194    0.000    0.000
LGA    E    89_C      E    89_B     9.278     0    0.173   1.298    10.844    2.738    1.746
LGA    P    90_C      P    90_B    10.284     0    0.268   0.544    12.449    3.571    2.109
LGA    N    91_C      N    91_B     9.126     0    0.116   1.118    14.044    7.500    3.750
LGA    N    92_C      N    92_B     1.699     0    0.561   1.201     4.279   70.476   63.393
LGA    Y    93_C      Y    93_B     0.890     0    0.092   0.316     2.863   83.810   77.381
LGA    V    94_C      V    94_B     1.930     0    0.584   1.273     5.203   77.381   57.891
LGA    R    95_C      R    95_B     0.695     0    0.102   1.530     9.860   81.667   53.203
LGA    L    96_C      L    96_B     1.784     0    0.164   1.216     7.447   63.452   42.619
LGA    R    97_C      R    97_B     2.908     0    0.222   1.141     7.973   67.143   40.216
LGA    L    98_C      L    98_B     5.184     0    0.080   0.194    11.979   31.786   17.143
LGA    I    99_C      I    99_B     1.466     0    0.067   1.266     3.286   70.952   67.262
LGA    E   100_C      E   100_B     1.363     0    0.684   0.546     5.054   67.738   54.815
LGA    K   101_C      K   101_B     3.838     0    0.644   0.797    13.141   57.500   27.989
LGA    I   102_C      I   102_B     1.723     0    0.102   1.094     6.732   65.119   51.548
LGA    D   103_C      D   103_B     1.956     0    0.169   0.426     4.258   56.548   66.845
LGA    I   104_C      I   104_B     6.666     0    0.114   0.243    11.306   14.881    8.690

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       57     228    228  100.00     458    458  100.00               116
SUMMARY(RMSD_GDC):    13.331         13.333                 14.088            7.088    5.488

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   57  116    4.0     11    2.02    10.560     8.783     0.518

LGA_LOCAL      RMSD:   2.024  Number of atoms:   11  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  29.626  Number of assigned atoms:   57 
Std_ASGN_ATOMS RMSD:  13.331  Standard rmsd on all 57 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.631539 * X  +   0.003429 * Y  +  -0.775337 * Z  + -11.513879
  Y_new =   0.721585 * X  +  -0.363272 * Y  +  -0.589363 * Z  +  -9.921452
  Z_new =  -0.283679 * X  +  -0.931677 * Y  +   0.226946 * Z  + -18.584709 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.289745  0.287629 -1.331861   [DEG:  131.1927   16.4799  -76.3100 ]
ZXZ: -0.920839  1.341855 -2.846029   [DEG:  -52.7602   76.8827 -163.0654 ]
 
# END of job
