
#######################################################
#                                                     #
#                        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   56 (  424),  selected   56 , name one
# Molecule2: number of CA atoms  124 (  971),  selected   56 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      36_A - 59_A        4.86    17.20
  LONGEST_CONTINUOUS_SEGMENT:    24      37_A - 60_A        4.85    16.29
  LONGEST_CONTINUOUS_SEGMENT:    24      38_A - 61_A        4.94    15.66
  LCS_AVERAGE:     15.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      41_A - 57_A        1.93    16.06
  LCS_AVERAGE:      8.28

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      43_A - 51_A        0.94    15.89
  LCS_AVERAGE:      4.48

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     N    33_F     N    33_A      4    8   14      3    4    6    7    8   10   11   11   11   13   13   13   16   19   20   22   24   26   26   26 
LCS_GDT     C    34_F     C    34_A      4    8   14      3    4    4    4    7    8   11   11   11   13   13   13   16   19   22   24   25   26   26   26 
LCS_GDT     V    35_F     V    35_A      6    8   15      3    5    6    8    8   10   11   11   11   13   13   13   16   17   20   22   25   26   26   26 
LCS_GDT     F    36_F     F    36_A      6    8   24      3    5    6    8    8   10   11   11   11   13   13   15   17   21   23   24   25   26   26   26 
LCS_GDT     T    37_F     T    37_A      6    8   24      3    5    6    8    8   10   11   11   11   13   13   16   20   22   23   24   25   26   26   26 
LCS_GDT     F    38_F     F    38_A      6    8   24      3    5    6    8    8   10   11   11   16   20   20   21   21   22   26   26   26   27   29   30 
LCS_GDT     T    39_F     T    39_A      6    8   24      3    5    6    8    8   10   11   13   18   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     D    40_F     D    40_A      6   16   24      3    5    6    8   12   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     P    41_F     P    41_A      4   17   24      3    4    5    8   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     K    42_F     K    42_A      6   17   24      4    6    6    8   12   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     G    43_F     G    43_A      9   17   24      5    7   10   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     S    44_F     S    44_A      9   17   24      4    6    9   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     L    45_F     L    45_A      9   17   24      5    7   10   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     H    46_F     H    46_A      9   17   24      5    7   10   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     S    47_F     S    47_A      9   17   24      5    7   10   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     I    48_F     I    48_A      9   17   24      4    7    9   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     D    49_F     D    49_A      9   17   24      5    7    9   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     V    50_F     V    50_A      9   17   24      7    9    9   11   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     T    51_F     T    51_A      9   17   24      7    9   10   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     E    52_F     E    52_A      8   17   24      7    9    9   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     V    53_F     V    53_A      8   17   24      7    9   10   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     L    54_F     L    54_A      8   17   24      7    9   10   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     N    55_F     N    55_A      8   17   24      7    9   10   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     N    56_F     N    56_A      8   17   24      7    9   10   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     M    57_F     M    57_A      8   17   24      4    9   10   13   15   17   18   18   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     A    58_F     A    58_A      3    9   24      3    3    4    5    6    7    8   10   14   16   19   21   21   22   24   25   26   27   29   30 
LCS_GDT     K    59_F     K    59_A      4    7   24      3    3    4    5    5    7    8    9   12   16   18   19   23   23   24   25   26   26   29   30 
LCS_GDT     G    60_F     G    60_A      4    7   24      3    3    4    5    6    7    8   11   13   16   18   20   23   23   24   25   26   27   29   30 
LCS_GDT     F    61_F     F    61_A      4    7   24      3    4    4    4    6    7    8    9   10   11   15   16   18   19   20   24   25   25   27   27 
LCS_GDT     R    62_F     R    62_A      4    7   15      3    4    4    5    6    7    8    9   10   11   12   13   14   15   17   19   21   23   23   25 
LCS_GDT     D    63_F     D    63_A      3    5   15      3    4    4    4    5    7    8    9   10   11   12   13   14   15   17   19   21   23   23   25 
LCS_GDT     A    64_F     A    64_A      3    5   15      3    3    4    4    5    6    7    8   10   11   12   13   14   15   17   19   21   23   23   25 
LCS_GDT     Q    65_F     Q    65_A      5    5   15      3    4    5    5    5    6    7    9   10   11   12   13   14   15   17   19   21   23   23   25 
LCS_GDT     N    66_F     N    66_A      5    5   15      3    4    5    5    5    6    7    8    8   10   12   13   14   15   17   19   21   23   23   25 
LCS_GDT     P    67_F     P    67_A      5    5   14      3    4    5    5    5    6    7    8   10   11   12   13   14   15   17   19   21   23   23   25 
LCS_GDT     P    68_F     P    68_A      5    9   15      4    5    6    7    9    9   10   10   10   11   12   13   14   15   17   19   21   23   23   25 
LCS_GDT     S    69_F     S    69_A      5    9   15      4    4    6    7    9    9   10   10   10   12   12   13   14   15   17   18   21   23   23   25 
LCS_GDT     S    70_F     S    70_A      5    9   15      4    5    6    7    9    9   10   10   10   12   12   13   14   15   17   19   21   23   23   25 
LCS_GDT     F    71_F     F    71_A      5    9   15      4    5    5    7    9    9   10   10   10   12   12   13   14   15   17   19   21   23   23   25 
LCS_GDT     T    72_F     T    72_A      5    9   15      4    5    6    7    9    9   10   10   10   12   12   14   15   17   19   20   21   23   24   26 
LCS_GDT     L    73_F     L    73_A      5    9   15      4    5    6    7    9    9   10   13   14   16   18   19   23   23   24   25   26   27   29   30 
LCS_GDT     G    74_F     G    74_A      5    9   15      4    5    6    7    9   13   14   17   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     G    75_F     G    75_A      4    9   15      4    4    4    7    9    9   10   10   19   20   20   21   23   25   26   26   26   27   29   30 
LCS_GDT     H    76_F     H    76_A      4    9   15      4    4    4    5    9    9   10   12   14   16   19   21   23   25   26   26   26   27   29   30 
LCS_GDT     C    77_F     C    77_A      3    6   15      3    3    3    5    7    8   10   11   13   13   13   13   20   23   23   24   26   27   27   29 
LCS_GDT     Q    78_F     Q    78_A      4    7   15      4    4    5    6    7    8    9   11   13   13   19   21   23   25   26   26   26   27   29   30 
LCS_GDT     A    79_F     A    79_A      4    7   15      4    4    5    6    7    8    9   11   13   13   15   21   23   25   26   26   26   27   29   30 
LCS_GDT     P    80_F     P    80_A      4    7   15      4    9    9    9   10   11   11   11   13   14   20   20   23   25   26   26   26   27   29   30 
LCS_GDT     L    81_F     L    81_A      4    7   15      4    4    5    6    7    8    9   11   13   13   14   18   18   19   22   22   23   23   29   30 
LCS_GDT     N    82_F     N    82_A      4    7   15      0    3    5    6    7    8    9   11   13   13   13   18   18   19   22   22   23   25   29   30 
LCS_GDT     A    83_F     A    83_A      3    7   15      0    3    3    3    4    7    9   11   13   13   13   18   18   19   22   22   23   23   24   26 
LCS_GDT     F    84_F     F    84_A      3    7   15      1    3    4    6    7    8    9   11   13   13   14   18   18   19   22   22   23   23   24   26 
LCS_GDT     S    85_F     S    85_A      4    4   15      3    4    4    5    5    8    9   11   13   13   14   18   18   19   22   22   23   23   26   29 
LCS_GDT     F    86_F     F    86_A      4    4   15      3    4    4    5    5    7    9   11   13   13   14   18   18   18   22   22   23   23   23   26 
LCS_GDT     V    87_F     V    87_A      4    4   15      3    4    4    5    5    8    9   11   13   13   13   13   14   15   16   17   23   23   23   24 
LCS_GDT     L    88_F     L    88_A      4    4   15      1    4    4    5    5    6    8   10   13   13   14   18   18   18   22   22   23   23   23   24 
LCS_AVERAGE  LCS_A:   9.39  (   4.48    8.28   15.42 )

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      7      9     10     13     15     17     18     18     19     20     20     21     23     25     26     26     26     27     29     30 
GDT PERCENT_AT   5.65   7.26   8.06  10.48  12.10  13.71  14.52  14.52  15.32  16.13  16.13  16.94  18.55  20.16  20.97  20.97  20.97  21.77  23.39  24.19
GDT RMS_LOCAL    0.18   0.72   1.08   1.37   1.55   1.90   2.05   2.05   2.27   2.50   2.50   2.95   3.74   4.12   4.36   4.36   4.36   4.61   5.25   5.53
GDT RMS_ALL_AT  16.51  17.44  16.12  16.11  16.10  16.11  16.13  16.13  16.02  16.00  16.00  16.10  16.78  16.69  16.71  16.71  16.71  16.91  16.32  16.17

# Checking swapping
#   possible swapping detected:  F    36_F      F    36_A
#   possible swapping detected:  F    38_F      F    38_A
#   possible swapping detected:  D    40_F      D    40_A
#   possible swapping detected:  D    49_F      D    49_A
#   possible swapping detected:  E    52_F      E    52_A
#   possible swapping detected:  D    63_F      D    63_A
#   possible swapping detected:  F    71_F      F    71_A
#   possible swapping detected:  F    84_F      F    84_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    N    33_F      N    33_A    24.814     0    0.566   0.582    31.776    0.000    0.000
LGA    C    34_F      C    34_A    18.716     0    0.033   0.749    20.997    0.000    0.000
LGA    V    35_F      V    35_A    18.038     0    0.668   1.020    20.341    0.000    0.000
LGA    F    36_F      F    36_A    13.244     0    0.107   1.234    14.546    0.000    3.896
LGA    T    37_F      T    37_A    12.876     0    0.031   0.078    16.803    0.000    0.000
LGA    F    38_F      F    38_A     8.543     0    0.070   1.192     9.850    2.738   21.861
LGA    T    39_F      T    39_A     7.628     0    0.182   1.083     9.996   16.667    9.864
LGA    D    40_F      D    40_A     3.342     0    0.195   0.998     8.329   43.690   31.905
LGA    P    41_F      P    41_A     2.616     0    0.663   0.791     5.014   47.619   53.878
LGA    K    42_F      K    42_A     3.374     0    0.636   0.603    13.512   61.190   31.376
LGA    G    43_F      G    43_A     1.789     0    0.000   0.000     3.278   69.286   69.286
LGA    S    44_F      S    44_A     1.570     0    0.000   0.656     5.050   81.667   68.333
LGA    L    45_F      L    45_A     2.023     0    0.086   0.494     5.349   70.833   54.405
LGA    H    46_F      H    46_A     1.289     0    0.088   1.077     6.628   77.143   57.238
LGA    S    47_F      S    47_A     1.118     0    0.045   0.669     2.479   83.690   80.159
LGA    I    48_F      I    48_A     1.916     0    0.064   1.177     5.384   83.810   61.845
LGA    D    49_F      D    49_A     1.572     0    0.250   1.427     5.888   70.833   55.298
LGA    V    50_F      V    50_A     2.603     0    0.350   1.244     5.118   66.905   57.279
LGA    T    51_F      T    51_A     1.626     0    0.007   0.037     2.423   77.381   75.510
LGA    E    52_F      E    52_A     2.207     0    0.105   1.054     6.795   68.810   47.037
LGA    V    53_F      V    53_A     1.790     0    0.041   0.092     2.066   77.143   75.374
LGA    L    54_F      L    54_A     0.601     0    0.051   0.114     1.313   85.952   87.143
LGA    N    55_F      N    55_A     1.257     0    0.117   0.310     2.329   77.381   80.536
LGA    N    56_F      N    56_A     2.335     0    0.155   0.152     3.267   63.095   57.440
LGA    M    57_F      M    57_A     1.522     0    0.251   1.201     8.512   60.238   40.833
LGA    A    58_F      A    58_A     8.337     0    0.039   0.038    10.390    7.262    5.810
LGA    K    59_F      K    59_A     9.944     0    0.664   1.549    14.130    1.667    0.741
LGA    G    60_F      G    60_A     9.327     0    0.024   0.024    12.570    1.071    1.071
LGA    F    61_F      F    61_A    13.593     0    0.672   0.861    16.413    0.000    0.000
LGA    R    62_F      R    62_A    19.575     0    0.596   1.697    25.470    0.000    0.000
LGA    D    63_F      D    63_A    25.710     0    0.671   0.589    27.733    0.000    0.000
LGA    A    64_F      A    64_A    28.286     0    0.054   0.079    30.580    0.000    0.000
LGA    Q    65_F      Q    65_A    33.848     0    0.606   0.735    37.278    0.000    0.000
LGA    N    66_F      N    66_A    35.413     0    0.174   1.182    40.992    0.000    0.000
LGA    P    67_F      P    67_A    32.916     0    0.576   1.033    33.994    0.000    0.000
LGA    P    68_F      P    68_A    33.272     0    0.661   0.651    35.227    0.000    0.000
LGA    S    69_F      S    69_A    34.258     0    0.074   0.143    35.530    0.000    0.000
LGA    S    70_F      S    70_A    28.332     0    0.117   0.307    30.291    0.000    0.000
LGA    F    71_F      F    71_A    22.163     0    0.072   1.325    24.323    0.000    0.000
LGA    T    72_F      T    72_A    15.540     0    0.010   0.085    17.876    0.000    0.000
LGA    L    73_F      L    73_A     9.058     0    0.128   0.196    11.403    3.333    2.679
LGA    G    74_F      G    74_A     4.981     0    0.595   0.595     6.340   22.976   22.976
LGA    G    75_F      G    75_A     5.881     0    0.193   0.193     6.379   24.048   24.048
LGA    H    76_F      H    76_A     9.406     0    0.622   1.012    12.304    1.548    0.619
LGA    C    77_F      C    77_A    12.744     0    0.147   0.730    14.694    0.000    0.000
LGA    Q    78_F      Q    78_A    10.676     0    0.457   0.765    12.317    0.357    0.159
LGA    A    79_F      A    79_A    11.272     0    0.112   0.155    13.566    0.119    0.095
LGA    P    80_F      P    80_A     8.533     0    0.084   0.180    11.272    1.429    4.082
LGA    L    81_F      L    81_A    13.089     0    0.656   1.302    18.010    0.000    0.000
LGA    N    82_F      N    82_A    14.088     0    0.708   1.187    17.072    0.000    0.000
LGA    A    83_F      A    83_A    15.313     0    0.656   0.597    18.287    0.000    0.000
LGA    F    84_F      F    84_A    16.691     0    0.635   1.280    20.731    0.000    0.000
LGA    S    85_F      S    85_A    14.851     0    0.658   0.558    16.845    0.000    0.000
LGA    F    86_F      F    86_A    16.453     0    0.114   1.273    19.118    0.000    0.043
LGA    V    87_F      V    87_A    23.377     0    0.149   0.183    28.379    0.000    0.000
LGA    L    88_F      L    88_A    22.976     0    0.259   1.423    26.168    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       56     224    224  100.00     424    424  100.00               124
SUMMARY(RMSD_GDC):    15.040         15.093                 15.398           10.886    9.539

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56  124    4.0     18    2.05    13.306    12.384     0.838

LGA_LOCAL      RMSD:   2.047  Number of atoms:   18  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  16.134  Number of assigned atoms:   56 
Std_ASGN_ATOMS RMSD:  15.040  Standard rmsd on all 56 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.129750 * X  +   0.085382 * Y  +   0.987864 * Z  + -110.764557
  Y_new =   0.952015 * X  +   0.289238 * Y  +   0.100042 * Z  + -62.881229
  Z_new =  -0.277186 * X  +   0.953442 * Y  +  -0.118814 * Z  + -61.088158 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.706252  0.280864  1.694773   [DEG:   97.7610   16.0923   97.1034 ]
ZXZ:  1.671724  1.689892 -0.282923   [DEG:   95.7827   96.8237  -16.2103 ]
 
# END of job
