
#######################################################
#                                                     #
#                        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   61 (  495),  selected   54 , name one
# Molecule2: number of CA atoms  285 ( 2384),  selected   54 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28      44_B - 71_B        4.61    17.36
  LCS_AVERAGE:      8.52

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      30_B - 39_B        1.89    16.21
  LONGEST_CONTINUOUS_SEGMENT:    10      31_B - 40_B        1.87    15.26
  LONGEST_CONTINUOUS_SEGMENT:    10      52_B - 61_B        1.29    21.56
  LCS_AVERAGE:      2.88

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      52_B - 60_B        0.92    21.32
  LCS_AVERAGE:      2.14

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   54
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    18_B     E    18_B      3    3   17      0    3    3    5    5    6    7    8    8    8    9    9   12   12   18   18   18   23   25   26 
LCS_GDT     N    19_B     N    19_B      4    5   18      2    4    4    5    5    6    7    8    8    8   11   13   13   15   18   18   18   18   24   26 
LCS_GDT     T    20_B     T    20_B      4    7   19      0    4    6    8    8    9   10   11   12   12   12   14   17   19   20   22   24   24   25   26 
LCS_GDT     Y    21_B     Y    21_B      4    7   19      2    4    4    6    9   10   10   12   13   14   16   16   18   19   20   22   24   24   26   28 
LCS_GDT     L    22_B     L    22_B      4    7   19      3    4    4    8    9   10   10   12   13   14   16   16   18   19   20   22   24   24   26   28 
LCS_GDT     S    23_B     S    23_B      4    7   19      4    4    6    8    9   10   10   12   13   14   16   16   18   19   20   22   24   24   26   28 
LCS_GDT     K    24_B     K    24_B      4    7   19      4    4    6    8    8   10   10   11   13   14   16   16   18   19   20   22   24   24   26   28 
LCS_GDT     S    25_B     S    25_B      4    8   19      4    4    6    8    9   10   10   12   13   14   16   16   18   19   20   22   24   24   25   28 
LCS_GDT     Q    26_B     Q    26_B      5    9   21      4    4    6    8    9   10   10   12   13   14   16   18   19   20   23   23   24   24   26   28 
LCS_GDT     Q    27_B     Q    27_B      5    9   21      3    5    6    6    8    9   12   14   16   17   17   18   19   20   23   23   24   25   31   34 
LCS_GDT     D    28_B     D    28_B      5    9   21      3    5    6    8   10   11   14   14   16   17   17   18   19   20   23   23   24   28   32   36 
LCS_GDT     T    29_B     T    29_B      5    9   21      3    5    6    8   10   11   14   14   16   17   17   18   19   20   23   23   24   28   32   36 
LCS_GDT     Q    30_B     Q    30_B      5   10   21      3    5    6    6    9   11   14   14   16   17   17   18   19   20   23   24   29   31   32   36 
LCS_GDT     V    31_B     V    31_B      5   10   21      3    5    6    8   10   11   14   14   16   17   17   18   19   20   23   23   26   29   32   36 
LCS_GDT     N    32_B     N    32_B      7   10   21      3    6    7    8   10   11   14   14   16   17   17   18   19   20   23   23   24   28   32   36 
LCS_GDT     C    33_B     C    33_B      7   10   21      4    6    7    8   10   11   14   14   16   17   17   18   19   20   23   23   24   28   31   36 
LCS_GDT     Q    34_B     Q    34_B      7   10   21      3    6    7    8   10   11   14   14   16   17   17   18   19   20   23   23   24   28   31   36 
LCS_GDT     L    35_B     L    35_B      7   10   21      4    6    7    8   10   11   14   14   16   17   17   18   19   20   23   23   24   27   31   34 
LCS_GDT     K    36_B     K    36_B      7   10   21      4    6    7    8   10   11   14   14   16   17   17   18   19   20   23   23   24   27   31   34 
LCS_GDT     I    37_B     I    37_B      7   10   21      4    6    7    8   10   11   14   14   16   17   17   18   19   20   23   23   24   24   28   32 
LCS_GDT     N    38_B     N    38_B      7   10   21      4    6    7    8   10   11   14   14   16   17   17   18   19   20   23   23   24   24   26   32 
LCS_GDT     S    39_B     S    39_B      5   10   21      3    4    5    8   10   11   14   14   16   17   17   18   19   20   23   23   24   28   32   36 
LCS_GDT     S    40_B     S    40_B      5   10   21      3    4    5    5    7   11   14   14   16   17   17   18   19   20   23   24   29   31   32   36 
LCS_GDT     Q    41_B     Q    41_B      5    8   21      3    4    5    7    8   11   14   14   16   17   17   18   19   20   23   24   29   31   32   36 
LCS_GDT     H    42_B     H    42_B      6    8   21      3    5    6    7    7    8   10   13   16   17   17   18   19   20   24   26   29   31   32   36 
LCS_GDT     L    43_B     L    43_B      6    8   21      3    5    6    7    7    8   10   13   15   17   17   18   19   20   24   26   29   31   32   36 
LCS_GDT     V    44_B     V    44_B      6    8   28      3    5    6    7    7    8    8   12   14   15   16   23   25   27   28   28   29   31   32   36 
LCS_GDT     V    45_B     V    45_B      6    8   28      3    5    6    7    7    8   10   13   14   15   18   25   26   27   28   28   29   31   32   36 
LCS_GDT     N    46_B     N    46_B      6    8   28      3    5    6    8   10   11   11   13   17   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     S    47_B     S    47_B      6    8   28      3    4    6    7    7   11   11   13   14   20   22   26   26   27   28   28   29   31   32   36 
LCS_GDT     Q    48_B     Q    48_B      3    7   28      3    3    5    8   10   11   11   13   17   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     T    49_B     T    49_B      3    4   28      3    3    7    9    9   10   13   16   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     R    50_B     R    50_B      3    4   28      5    6    7    9    9   11   12   16   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     D    51_B     D    51_B      3    3   28      3    3    3    3    3   10   12   16   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     C    52_B     C    52_B      9   10   28      4    8   10   10   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     F    53_B     F    53_B      9   10   28      4    8    8    9   12   15   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     E    54_B     E    54_B      9   10   28      4    8    8    9   12   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     Y    55_B     Y    55_B      9   10   28      4    8    8    9   13   16   17   18   19   21   24   26   26   27   28   28   29   29   32   33 
LCS_GDT     F    56_B     F    56_B      9   10   28      4    8    8    9   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   33 
LCS_GDT     I    57_B     I    57_B      9   10   28      4    8   10   10   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     T    58_B     T    58_B      9   10   28      4    8    8    9   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   34 
LCS_GDT     Q    59_B     Q    59_B      9   10   28      3    4    6    9   10   10   11   14   18   21   22   26   26   27   28   28   28   28   28   30 
LCS_GDT     Y    60_B     Y    60_B      9   10   28      3    8    8    9   10   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     G    61_B     G    61_B      4   10   28      4    5    7    9   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     E    62_B     E    62_B      4    5   28      3    3    4    4    5   13   14   15   18   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     S    63_B     S    63_B      4    4   28      3    3    4    4    6   13   14   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     N    64_B     N    64_B      8    8   28      5    7   10   10   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     L    65_B     L    65_B      8    8   28      5    7   10   10   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     Q    66_B     Q    66_B      8    8   28      5    7   10   10   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     K    67_B     K    67_B      8    8   28      5    7   10   10   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     V    68_B     V    68_B      8    8   28      5    7   10   10   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     K    69_B     K    69_B      8    8   28      4    7   10   10   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     T    70_B     T    70_B      8    8   28      3    7   10   10   13   16   17   18   19   21   24   26   26   27   28   28   29   31   32   36 
LCS_GDT     H    71_B     H    71_B      8    8   28      3    3   10   10   12   16   17   18   18   21   24   26   26   27   28   28   29   31   32   36 
LCS_AVERAGE  LCS_A:   4.52  (   2.14    2.88    8.52 )

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      8     10     10     13     16     17     18     19     21     24     26     26     27     28     28     29     31     32     36 
GDT PERCENT_AT   1.75   2.81   3.51   3.51   4.56   5.61   5.96   6.32   6.67   7.37   8.42   9.12   9.12   9.47   9.82   9.82  10.18  10.88  11.23  12.63
GDT RMS_LOCAL    0.31   0.51   1.14   1.14   1.73   2.01   2.11   2.42   3.17   3.36   3.95   4.20   4.20   4.33   4.61   4.61   5.52   6.63   6.68   7.92
GDT RMS_ALL_AT  17.04  20.68  16.19  16.19  17.70  17.08  17.23  17.72  18.85  19.03  18.20  18.51  18.51  18.12  17.36  17.36  15.56  13.76  13.89  12.13

# Checking swapping
#   possible swapping detected:  D    28_B      D    28_B
#   possible swapping detected:  D    51_B      D    51_B
#   possible swapping detected:  F    53_B      F    53_B
#   possible swapping detected:  F    56_B      F    56_B
#   possible swapping detected:  Y    60_B      Y    60_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E    18_B      E    18_B    31.482     0    0.642   1.043    32.975    0.000    0.000
LGA    N    19_B      N    19_B    32.628     0    0.564   0.684    37.705    0.000    0.000
LGA    T    20_B      T    20_B    27.730     0    0.627   0.962    29.246    0.000    0.000
LGA    Y    21_B      Y    21_B    23.925     0    0.623   0.554    26.699    0.000    0.000
LGA    L    22_B      L    22_B    29.135     0    0.554   1.212    31.499    0.000    0.000
LGA    S    23_B      S    23_B    31.429     0    0.318   0.687    31.818    0.000    0.000
LGA    K    24_B      K    24_B    34.385     0    0.000   0.942    44.680    0.000    0.000
LGA    S    25_B      S    25_B    35.160     0    0.104   0.109    36.936    0.000    0.000
LGA    Q    26_B      Q    26_B    29.523     0    0.487   1.010    31.356    0.000    0.000
LGA    Q    27_B      Q    27_B    27.287     0    0.526   0.695    28.435    0.000    0.000
LGA    D    28_B      D    28_B    25.381     0    0.116   0.961    27.691    0.000    0.000
LGA    T    29_B      T    29_B    23.809     0    0.222   1.053    26.400    0.000    0.000
LGA    Q    30_B      Q    30_B    19.593     0    0.282   0.901    20.873    0.000    0.000
LGA    V    31_B      V    31_B    19.636     0    0.060   0.963    20.559    0.000    0.000
LGA    N    32_B      N    32_B    21.177     0    0.672   1.230    24.815    0.000    0.000
LGA    C    33_B      C    33_B    20.741     0    0.252   0.766    23.656    0.000    0.000
LGA    Q    34_B      Q    34_B    20.721     0    0.260   0.870    20.927    0.000    0.000
LGA    L    35_B      L    35_B    21.002     0    0.130   0.965    24.524    0.000    0.000
LGA    K    36_B      K    36_B    20.899     0    0.043   0.164    20.899    0.000    0.000
LGA    I    37_B      I    37_B    21.082     0    0.078   0.647    22.189    0.000    0.000
LGA    N    38_B      N    38_B    21.012     0    0.182   1.329    21.966    0.000    0.000
LGA    S    39_B      S    39_B    21.581     0    0.214   0.243    22.236    0.000    0.000
LGA    S    40_B      S    40_B    17.463     0    0.643   0.770    19.022    0.000    0.000
LGA    Q    41_B      Q    41_B    17.135     0    0.283   1.374    22.352    0.000    0.000
LGA    H    42_B      H    42_B    13.484     0    0.136   0.586    14.679    0.000    0.238
LGA    L    43_B      L    43_B    13.878     0    0.000   1.141    19.944    0.000    0.000
LGA    V    44_B      V    44_B    11.077     0    0.069   0.143    12.578    0.000    0.272
LGA    V    45_B      V    45_B    12.300     0    0.037   0.077    14.005    0.000    0.000
LGA    N    46_B      N    46_B    12.113     0    0.131   1.284    13.872    0.000    0.000
LGA    S    47_B      S    47_B    13.962     0    0.597   0.782    14.153    0.000    0.000
LGA    Q    48_B      Q    48_B    12.145     0    0.090   0.290    14.912    0.000    0.000
LGA    T    49_B      T    49_B     9.381     0    0.595   0.564    11.171    2.262    1.293
LGA    R    50_B      R    50_B     9.392     0    0.571   1.251    15.554    1.548    0.606
LGA    D    51_B      D    51_B     8.363     0    0.111   0.761    13.685   13.810    6.964
LGA    C    52_B      C    52_B     1.240     0    0.478   0.864     3.820   74.167   68.571
LGA    F    53_B      F    53_B     2.968     0    0.112   0.739     9.597   67.143   31.299
LGA    E    54_B      E    54_B     2.688     0    0.102   1.110     7.740   60.952   38.201
LGA    Y    55_B      Y    55_B     2.676     0    0.139   1.388    14.340   62.976   27.222
LGA    F    56_B      F    56_B     2.524     0    0.024   1.204     6.189   62.976   46.450
LGA    I    57_B      I    57_B     1.594     0    0.073   1.229     4.202   81.548   70.714
LGA    T    58_B      T    58_B     2.232     0    0.628   0.569     4.863   65.119   55.034
LGA    Q    59_B      Q    59_B     6.163     0    0.138   0.797    13.793   26.548   12.381
LGA    Y    60_B      Y    60_B     3.291     0    0.044   1.256    13.953   59.762   26.429
LGA    G    61_B      G    61_B     0.964     0    0.629   0.629     3.984   65.952   65.952
LGA    E    62_B      E    62_B     6.795     0    0.063   0.537    14.352   16.310    7.407
LGA    S    63_B      S    63_B     4.988     0    0.632   0.762     7.205   41.429   32.143
LGA    N    64_B      N    64_B     2.193     0    0.685   1.206     6.828   70.952   47.024
LGA    L    65_B      L    65_B     2.486     0    0.048   1.421     6.706   66.905   52.262
LGA    Q    66_B      Q    66_B     0.875     0    0.172   0.936     6.099   83.810   60.000
LGA    K    67_B      K    67_B     0.817     0    0.020   1.013     3.439   88.333   76.402
LGA    V    68_B      V    68_B     2.033     0    0.056   0.105     3.462   70.952   62.993
LGA    K    69_B      K    69_B     0.872     0    0.285   0.354     4.935   86.071   65.132
LGA    T    70_B      T    70_B     1.783     0    0.301   1.134     3.979   73.214   67.687
LGA    H    71_B      H    71_B     3.106     0    0.510   1.247     8.574   53.571   33.190

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       54     216    216  100.00     443    443  100.00               285
SUMMARY(RMSD_GDC):    11.279         11.176                 11.888            4.548    3.354

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61  285    4.0     18    2.42     5.614     5.261     0.714

LGA_LOCAL      RMSD:   2.420  Number of atoms:   18  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.721  Number of assigned atoms:   54 
Std_ASGN_ATOMS RMSD:  11.279  Standard rmsd on all 54 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.835241 * X  +   0.312660 * Y  +   0.452345 * Z  + -39.664112
  Y_new =   0.491861 * X  +  -0.057005 * Y  +  -0.868806 * Z  + -70.456955
  Z_new =  -0.245855 * X  +   0.948153 * Y  +  -0.201398 * Z  +  31.590965 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.532207  0.248402  1.780097   [DEG:   30.4932   14.2324  101.9920 ]
ZXZ:  0.480032  1.773581 -0.253712   [DEG:   27.5038  101.6187  -14.5366 ]
 
# END of job
