
#######################################################
#                                                     #
#                        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   30 (  244),  selected   30 , name one
# Molecule2: number of CA atoms   78 (  613),  selected   30 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      59_A - 72_A        4.89    14.62
  LCS_AVERAGE:     17.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      65_A - 70_A        1.96    20.60
  LCS_AVERAGE:      6.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5      60_A - 64_A        0.36    17.36
  LONGEST_CONTINUOUS_SEGMENT:     5      65_A - 69_A        0.96    20.78
  LCS_AVERAGE:      5.13

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   30
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     T    49_A     T    49_A      3    4   11      3    3    3    4    4    5    5    6    6    7    7   10   11   11   17   17   18   19   19   19 
LCS_GDT     R    50_A     R    50_A      3    4   12      3    3    3    4    4    5    6    8    9    9   10   12   16   16   17   17   18   19   19   19 
LCS_GDT     L    51_A     L    51_A      4    5   12      4    4    4    5    5    5    6    8    9    9   10   12   16   16   17   17   18   19   19   19 
LCS_GDT     N    52_A     N    52_A      4    5   12      4    4    4    5    5    5    6    8    9    9   10   12   16   16   17   17   18   19   19   19 
LCS_GDT     G    53_A     G    53_A      4    5   13      4    4    4    5    5    5    6    8    9    9   10   12   16   16   17   17   18   19   19   19 
LCS_GDT     V    54_A     V    54_A      4    5   13      4    4    4    5    5    5    6    8    9    9   10   12   16   16   17   17   18   19   19   19 
LCS_GDT     R    55_A     R    55_A      3    5   13      3    3    3    5    5    5    6    8    9    9   10   12   16   16   17   17   18   19   19   19 
LCS_GDT     Q    56_A     Q    56_A      3    4   13      3    3    3    4    4    4    6    8    9    9   10   12   16   16   17   17   18   19   19   20 
LCS_GDT     F    57_A     F    57_A      3    4   13      0    3    3    4    4    4    6    8    9    9   10   12   16   16   17   17   18   19   19   20 
LCS_GDT     R    58_A     R    58_A      3    3   13      0    3    3    3    3    3    5    8    9    9   10   12   16   16   17   17   18   19   19   20 
LCS_GDT     L    59_A     L    59_A      3    3   14      3    3    3    5    5    7    8   10   12   13   13   15   16   16   17   17   18   19   19   20 
LCS_GDT     D    60_A     D    60_A      5    5   14      5    5    5    5    5    5    8   10   12   13   13   15   16   16   17   17   18   19   19   20 
LCS_GDT     R    61_A     R    61_A      5    5   14      5    5    5    5    5    5    8   10   12   13   13   15   16   16   17   17   18   19   19   20 
LCS_GDT     I    62_A     I    62_A      5    5   14      5    5    5    5    5    5    6    9   10   11   13   15   16   16   17   17   18   19   19   20 
LCS_GDT     S    63_A     S    63_A      5    5   14      5    5    5    5    5    5    6    8    8    9   10   11   16   16   17   17   18   19   19   19 
LCS_GDT     G    64_A     G    64_A      5    5   14      5    5    5    5    5    5    7    9   10   11   13   15   16   16   17   17   18   19   19   20 
LCS_GDT     E    65_A     E    65_A      5    6   14      3    4    5    5    5    6    8    9   12   13   13   15   16   16   17   17   18   19   19   20 
LCS_GDT     L    66_A     L    66_A      5    6   14      3    4    5    5    5    6    8   10   12   13   13   15   15   16   16   17   18   19   19   20 
LCS_GDT     E    67_A     E    67_A      5    6   14      1    4    5    5    5    6    8   10   12   13   13   15   15   16   16   17   18   19   19   20 
LCS_GDT     V    68_A     V    68_A      5    6   14      1    4    5    5    5    7    8   10   12   13   13   15   15   16   16   17   18   19   19   20 
LCS_GDT     V    69_A     V    69_A      5    6   14      1    4    5    5    5    7    8   10   12   13   13   15   15   16   16   17   18   19   19   20 
LCS_GDT     F    70_A     F    70_A      4    6   14      4    4    4    5    5    7    8   10   12   13   13   15   15   16   16   17   18   19   19   20 
LCS_GDT     D    71_A     D    71_A      4    5   14      4    4    5    5    5    7    8   10   12   13   13   15   15   16   16   17   18   19   19   20 
LCS_GDT     P    72_A     P    72_A      4    5   14      4    4    4    5    5    6    7    8   10   10   11   12   14   14   16   17   18   19   19   20 
LCS_GDT     E    73_A     E    73_A      4    5   13      4    4    4    5    5    6    7    8   10   10   10   11   11   14   15   16   18   19   19   20 
LCS_GDT     V    74_A     V    74_A      4    5   13      4    4    4    5    5    6    7    8   10   10   10   11   11   13   14   16   17   19   19   20 
LCS_GDT     V    75_A     V    75_A      4    5   13      4    4    4    5    5    6    7    8   10   10   10   12   13   14   16   17   18   19   19   20 
LCS_GDT     S    76_A     S    76_A      3    5   13      3    4    5    5    5    7    8   10   12   13   13   15   15   16   16   17   18   19   19   20 
LCS_GDT     S    77_A     S    77_A      3    3   13      3    4    4    4    4    5    8   10   12   13   13   15   15   16   16   17   18   19   19   20 
LCS_GDT     R    78_A     R    78_A      3    3   13      3    4    5    5    5    7    8   10   12   13   13   15   15   16   16   17   18   19   19   20 
LCS_AVERAGE  LCS_A:   9.44  (   5.13    6.15   17.05 )

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      5      5      5      5      7      8     10     12     13     13     15     16     16     17     17     18     19     19     20 
GDT PERCENT_AT   6.41   6.41   6.41   6.41   6.41   8.97  10.26  12.82  15.38  16.67  16.67  19.23  20.51  20.51  21.79  21.79  23.08  24.36  24.36  25.64
GDT RMS_LOCAL    0.36   0.36   0.36   0.36   0.36   2.14   2.52   2.98   3.41   3.57   3.57   4.10   5.38   4.42   5.59   4.93   5.65   5.96   5.58   6.10
GDT RMS_ALL_AT  17.36  17.36  17.36  17.36  17.36  12.86  12.85  13.02  13.88  14.06  14.06  14.52  17.40  14.82  17.54  14.03  12.66  12.52  13.96  13.00

# Checking swapping
#   possible swapping detected:  D    60_A      D    60_A
#   possible swapping detected:  E    65_A      E    65_A
#   possible swapping detected:  E    67_A      E    67_A
#   possible swapping detected:  E    73_A      E    73_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T    49_A      T    49_A    20.526     0    0.627   1.383    21.147    0.000    0.000
LGA    R    50_A      R    50_A    23.102     0    0.217   1.152    29.799    0.000    0.000
LGA    L    51_A      L    51_A    25.791     0    0.567   1.382    30.094    0.000    0.000
LGA    N    52_A      N    52_A    26.081     0    0.231   0.900    31.232    0.000    0.000
LGA    G    53_A      G    53_A    24.235     0    0.250   0.250    24.371    0.000    0.000
LGA    V    54_A      V    54_A    21.837     0    0.582   1.024    22.870    0.000    0.000
LGA    R    55_A      R    55_A    21.052     0    0.048   1.564    26.566    0.000    0.000
LGA    Q    56_A      Q    56_A    14.833     0    0.594   1.323    17.330    0.000    0.000
LGA    F    57_A      F    57_A    12.196     0    0.617   1.431    13.209    0.000    0.087
LGA    R    58_A      R    58_A    10.026     0    0.605   1.273    22.898    5.833    2.121
LGA    L    59_A      L    59_A     3.415     0    0.600   1.455     7.821   48.333   35.893
LGA    D    60_A      D    60_A     6.659     0    0.592   1.240    11.491   18.810    9.464
LGA    R    61_A      R    61_A     5.986     0    0.105   1.247    12.050   15.833   11.688
LGA    I    62_A      I    62_A     7.679     0    0.029   1.092     9.701    5.952    4.762
LGA    S    63_A      S    63_A     9.959     0    0.102   0.094    10.847    0.952    0.635
LGA    G    64_A      G    64_A     8.760     0    0.227   0.227     8.844    5.000    5.000
LGA    E    65_A      E    65_A     6.609     0    0.567   1.279    12.184   12.143    7.672
LGA    L    66_A      L    66_A     4.152     0    0.602   1.006     7.595   40.238   30.893
LGA    E    67_A      E    67_A     3.742     0    0.395   1.172    11.028   45.476   22.698
LGA    V    68_A      V    68_A     2.864     0    0.088   0.144     7.349   61.667   42.857
LGA    V    69_A      V    69_A     1.131     0    0.227   0.955     3.653   71.071   64.354
LGA    F    70_A      F    70_A     3.041     0    0.090   1.192    11.605   57.500   24.026
LGA    D    71_A      D    71_A     2.263     0    0.254   0.314     5.383   56.667   48.274
LGA    P    72_A      P    72_A     7.057     0    0.663   0.670     8.026   12.738   14.694
LGA    E    73_A      E    73_A    10.641     0    0.209   1.170    15.674    0.119    0.053
LGA    V    74_A      V    74_A    11.622     0    0.060   0.068    14.439    0.000    0.000
LGA    V    75_A      V    75_A     8.173     0    0.597   0.916     8.956   10.476    8.095
LGA    S    76_A      S    76_A     2.439     0    0.664   0.903     5.148   62.619   53.333
LGA    S    77_A      S    77_A     3.523     0    0.048   0.611     6.819   52.143   41.349
LGA    R    78_A      R    78_A     1.868     0    0.551   0.864    13.279   57.262   27.489

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       30     120    120  100.00     244    244  100.00                78
SUMMARY(RMSD_GDC):    10.489         10.422                 11.400            8.216    5.839

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   30   78    4.0     10    2.98    11.859    10.665     0.325

LGA_LOCAL      RMSD:   2.977  Number of atoms:   10  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.025  Number of assigned atoms:   30 
Std_ASGN_ATOMS RMSD:  10.489  Standard rmsd on all 30 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.678410 * X  +   0.719180 * Y  +  -0.150133 * Z  + -12.615512
  Y_new =  -0.685931 * X  +   0.546826 * Y  +  -0.480084 * Z  +  22.628656
  Z_new =  -0.263170 * X  +   0.428675 * Y  +   0.864280 * Z  + -10.534379 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.790910  0.266307  0.460435   [DEG:  -45.3158   15.2583   26.3810 ]
ZXZ: -0.303087  0.527080 -0.550589   [DEG:  -17.3656   30.1994  -31.5464 ]
 
# END of job
