
#######################################################
#                                                     #
#                        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   64 (  525),  selected   56 , name one
# Molecule2: number of CA atoms   72 (  603),  selected   56 , 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:    49      22_A - 78_A        4.12    11.28
  LCS_AVERAGE:     61.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46      33_A - 78_A        0.32    12.16
  LCS_AVERAGE:     54.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46      33_A - 78_A        0.32    12.16
  LCS_AVERAGE:     54.96

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   56
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     Q    15_A     Q    15_A     10   10   11      6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   11   11 
LCS_GDT     Q    16_A     Q    16_A     10   10   11      6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   11   11 
LCS_GDT     R    17_A     R    17_A     10   10   11      6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   11   12 
LCS_GDT     R    18_A     R    18_A     10   10   11      6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   11   12 
LCS_GDT     N    19_A     N    19_A     10   10   11      6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   11   12 
LCS_GDT     E    20_A     E    20_A     10   10   11      6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   12   13   14 
LCS_GDT     E    21_A     E    21_A     10   10   11      6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   11   13   16   17   22 
LCS_GDT     A    22_A     A    22_A     10   10   49      6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   11   13   19   23   30 
LCS_GDT     L    23_A     L    23_A     10   10   49      6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   11   13   19   27   35 
LCS_GDT     R    24_A     R    24_A     10   10   49      6   10   10   10   10   10   10   10   10   11   16   25   35   41   47   47   47   47   47   47 
LCS_GDT     Q    33_A     Q    33_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     L    34_A     L    34_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     L    35_A     L    35_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     S    36_A     S    36_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     G    37_A     G    37_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     I    38_A     I    38_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     V    39_A     V    39_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     Q    40_A     Q    40_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     Q    41_A     Q    41_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     Q    42_A     Q    42_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     N    43_A     N    43_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     N    44_A     N    44_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     L    45_A     L    45_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     L    46_A     L    46_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     R    47_A     R    47_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     A    48_A     A    48_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     I    49_A     I    49_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     E    50_A     E    50_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     A    51_A     A    51_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     Q    52_A     Q    52_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     Q    53_A     Q    53_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     H    54_A     H    54_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     L    55_A     L    55_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     L    56_A     L    56_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     Q    57_A     Q    57_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     L    58_A     L    58_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     T    59_A     T    59_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     V    60_A     V    60_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     W    61_A     W    61_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     G    62_A     G    62_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     I    63_A     I    63_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     K    64_A     K    64_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     Q    65_A     Q    65_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     L    66_A     L    66_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     Q    67_A     Q    67_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     A    68_A     A    68_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     R    69_A     R    69_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     I    70_A     I    70_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     L    71_A     L    71_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     A    72_A     A    72_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     V    73_A     V    73_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     E    74_A     E    74_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     R    75_A     R    75_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     Y    76_A     Y    76_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     L    77_A     L    77_A     46   46   49     45   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_GDT     R    78_A     R    78_A     46   46   49     22   46   46   46   46   46   46   46   46   46   46   46   46   46   47   47   47   47   47   47 
LCS_AVERAGE  LCS_A:  57.13  (  54.96   54.96   61.46 )

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     45     46     46     46     46     46     46     46     46     46     46     46     46     46     47     47     47     47     47     47 
GDT PERCENT_AT  62.50  63.89  63.89  63.89  63.89  63.89  63.89  63.89  63.89  63.89  63.89  63.89  63.89  63.89  65.28  65.28  65.28  65.28  65.28  65.28
GDT RMS_LOCAL    0.31   0.32   0.32   0.32   0.32   0.32   0.32   0.32   0.32   0.32   0.32   0.32   0.32   0.32   2.31   2.31   2.31   2.31   2.31   2.31
GDT RMS_ALL_AT  12.16  12.16  12.16  12.16  12.16  12.16  12.16  12.16  12.16  12.16  12.16  12.16  12.16  12.16  11.66  11.66  11.66  11.66  11.66  11.66

# Checking swapping
#   possible swapping detected:  E    21_A      E    21_A
#   possible swapping detected:  E    74_A      E    74_A
#   possible swapping detected:  Y    76_A      Y    76_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q    15_A      Q    15_A    39.636     0    0.134   1.383    41.786    0.000    0.000
LGA    Q    16_A      Q    16_A    37.124     0    0.023   1.354    39.714    0.000    0.000
LGA    R    17_A      R    17_A    35.244     0    0.101   1.194    45.967    0.000    0.000
LGA    R    18_A      R    18_A    32.048     0    0.042   1.089    41.310    0.000    0.000
LGA    N    19_A      N    19_A    27.887     0    0.052   1.135    31.077    0.000    0.000
LGA    E    20_A      E    20_A    26.006     0    0.022   1.241    30.148    0.000    0.000
LGA    E    21_A      E    21_A    24.985     0    0.025   1.020    28.102    0.000    0.000
LGA    A    22_A      A    22_A    20.098     0    0.082   0.082    22.356    0.000    0.000
LGA    L    23_A      L    23_A    17.223     0    0.137   0.217    19.226    0.000    0.000
LGA    R    24_A      R    24_A    16.870     0    0.252   1.648    25.719    0.000    0.000
LGA    Q    33_A      Q    33_A     0.382     0    0.057   1.004     3.635  100.000   83.651
LGA    L    34_A      L    34_A     0.466     0    0.000   0.029     0.580  100.000   95.238
LGA    L    35_A      L    35_A     0.394     0    0.000   0.960     2.852  100.000   88.929
LGA    S    36_A      S    36_A     0.378     0    0.000   0.637     2.552  100.000   92.857
LGA    G    37_A      G    37_A     0.419     0    0.046   0.046     0.424  100.000  100.000
LGA    I    38_A      I    38_A     0.242     0    0.058   0.103     0.549  100.000   98.810
LGA    V    39_A      V    39_A     0.324     0    0.000   0.035     0.410  100.000  100.000
LGA    Q    40_A      Q    40_A     0.293     0    0.000   0.141     0.651  100.000   98.942
LGA    Q    41_A      Q    41_A     0.116     0    0.033   0.156     0.608  100.000   98.942
LGA    Q    42_A      Q    42_A     0.217     0    0.044   0.278     0.934  100.000   96.825
LGA    N    43_A      N    43_A     0.381     0    0.015   0.106     0.557  100.000   97.619
LGA    N    44_A      N    44_A     0.336     0    0.025   0.120     0.791  100.000   96.429
LGA    L    45_A      L    45_A     0.210     0    0.037   1.282     2.579  100.000   89.048
LGA    L    46_A      L    46_A     0.170     0    0.020   0.090     0.363  100.000  100.000
LGA    R    47_A      R    47_A     0.281     0    0.037   0.995     3.858  100.000   86.537
LGA    A    48_A      A    48_A     0.247     0    0.025   0.029     0.258  100.000  100.000
LGA    I    49_A      I    49_A     0.255     0    0.028   0.141     0.345  100.000  100.000
LGA    E    50_A      E    50_A     0.332     0    0.062   0.659     2.051  100.000   89.947
LGA    A    51_A      A    51_A     0.358     0    0.000   0.000     0.387  100.000  100.000
LGA    Q    52_A      Q    52_A     0.305     0    0.024   0.199     0.499  100.000  100.000
LGA    Q    53_A      Q    53_A     0.286     0    0.037   0.220     1.062  100.000   95.820
LGA    H    54_A      H    54_A     0.309     0    0.013   1.331     5.475  100.000   70.429
LGA    L    55_A      L    55_A     0.436     0    0.043   0.423     1.974  100.000   91.905
LGA    L    56_A      L    56_A     0.425     0    0.017   1.344     2.978  100.000   86.726
LGA    Q    57_A      Q    57_A     0.333     0    0.033   1.199     3.777  100.000   87.566
LGA    L    58_A      L    58_A     0.240     0    0.042   0.132     0.757  100.000   97.619
LGA    T    59_A      T    59_A     0.141     0    0.030   0.068     0.269  100.000  100.000
LGA    V    60_A      V    60_A     0.181     0    0.031   0.047     0.421  100.000  100.000
LGA    W    61_A      W    61_A     0.385     0    0.077   1.311     9.104  100.000   50.850
LGA    G    62_A      G    62_A     0.347     0    0.068   0.068     0.347  100.000  100.000
LGA    I    63_A      I    63_A     0.150     0    0.030   0.110     0.306  100.000  100.000
LGA    K    64_A      K    64_A     0.325     0    0.011   1.287     6.703  100.000   75.397
LGA    Q    65_A      Q    65_A     0.245     0    0.036   1.501     5.595  100.000   77.831
LGA    L    66_A      L    66_A     0.203     0    0.031   0.322     0.797  100.000   97.619
LGA    Q    67_A      Q    67_A     0.324     0    0.000   0.366     1.419  100.000   94.762
LGA    A    68_A      A    68_A     0.290     0    0.015   0.032     0.327  100.000  100.000
LGA    R    69_A      R    69_A     0.256     0    0.008   0.840     2.432  100.000   93.420
LGA    I    70_A      I    70_A     0.110     0    0.063   0.573     1.424  100.000   96.488
LGA    L    71_A      L    71_A     0.123     0    0.024   0.182     0.803  100.000   97.619
LGA    A    72_A      A    72_A     0.377     0    0.000   0.012     0.475  100.000  100.000
LGA    V    73_A      V    73_A     0.116     0    0.032   0.089     0.303  100.000  100.000
LGA    E    74_A      E    74_A     0.325     0    0.084   0.649     1.563  100.000   91.746
LGA    R    75_A      R    75_A     0.363     0    0.021   0.327     2.475  100.000   89.221
LGA    Y    76_A      Y    76_A     0.457     0    0.066   0.058     0.619   97.619   99.206
LGA    L    77_A      L    77_A     0.364     0    0.160   0.379     1.205   92.976   95.298
LGA    R    78_A      R    78_A     0.652     0    0.584   1.200     5.664   92.976   73.550

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       56     224    224  100.00     468    468  100.00                72
SUMMARY(RMSD_GDC):    10.447         10.077                 11.779           63.661   59.401

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64   72    4.0     46    0.32    64.236    61.748    10.952

LGA_LOCAL      RMSD:   0.320  Number of atoms:   46  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  12.165  Number of assigned atoms:   56 
Std_ASGN_ATOMS RMSD:  10.447  Standard rmsd on all 56 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.469577 * X  +  -0.882887 * Y  +  -0.002895 * Z  +  26.217592
  Y_new =  -0.882883 * X  +   0.469584 * Y  +  -0.002861 * Z  +  16.587093
  Z_new =   0.003885 * X  +   0.001213 * Y  +  -0.999992 * Z  + 281.638367 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.059611 -0.003885  3.140380   [DEG: -118.0070   -0.2226  179.9305 ]
ZXZ:  0.000000  0.000000 -2.059611   [DEG:    0.0000    0.0000 -118.0070 ]
 
# END of job
