
#######################################################
#                                                     #
#                        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   47 (  371),  selected   47 , name one
# Molecule2: number of CA atoms  116 (  942),  selected   47 , 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      29_B - 45_B        4.87    15.56
  LONGEST_CONTINUOUS_SEGMENT:    17      30_B - 46_B        4.93    15.43
  LONGEST_CONTINUOUS_SEGMENT:    17      31_B - 47_B        4.98    15.57
  LCS_AVERAGE:     13.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      33_B - 45_B        1.96    14.97
  LCS_AVERAGE:      7.63

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8      36_B - 43_B        0.92    14.94
  LONGEST_CONTINUOUS_SEGMENT:     8      38_B - 45_B        0.93    16.01
  LCS_AVERAGE:      4.38

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   47
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     A    29_C     A    29_B      4    5   17      3    3    4    6    6   10   12   14   14   15   17   18   22   24   25   27   28   31   31   32 
LCS_GDT     S    30_C     S    30_B      4    6   17      3    3    4    6    6   10   12   14   14   15   16   18   19   22   24   27   28   31   31   32 
LCS_GDT     D    31_C     D    31_B      4    6   17      3    3    4    6    6   10   12   14   14   15   17   18   19   22   24   27   28   31   31   32 
LCS_GDT     S    32_C     S    32_B      4    6   17      2    3    5    9    9   10   12   14   14   16   17   20   22   24   25   27   28   31   31   32 
LCS_GDT     Y    33_C     Y    33_B      5   13   17      6    7    9   11   11   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     E    34_C     E    34_B      5   13   17      4    8    9   10   12   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     V    35_C     V    35_B      5   13   17      4    5    5    8   12   12   13   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     P    36_C     P    36_B      8   13   17      4    8    9   11   12   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     E    37_C     E    37_B      8   13   17      4    5    8   11   12   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     Q    38_C     Q    38_B      8   13   17      3    8    9   11   12   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     Y    39_C     Y    39_B      8   13   17      6    8    9   11   12   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     F    40_C     F    40_B      8   13   17      6    8    9   11   12   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     I    41_C     I    41_B      8   13   17      6    8    9   11   12   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     I    42_C     I    42_B      8   13   17      6    8    9   11   12   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     T    43_C     T    43_B      8   13   17      6    8    9   11   12   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     R    44_C     R    44_B      8   13   17      2    6    9   11   12   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     S    45_C     S    45_B      8   13   17      2    6    9   11   12   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     T    46_C     T    46_B      4    6   17      3    4    5    5    6    7    9   10   13   13   14   14   15   18   21   24   28   31   31   32 
LCS_GDT     T    47_C     T    47_B      4    6   17      3    4    5    5    6    6    7    9    9   10   11   13   14   17   17   17   18   23   27   29 
LCS_GDT     E    48_C     E    48_B      4    6   14      3    4    5    5    6    6    7    9    9   10   11   13   14   17   17   17   18   18   20   21 
LCS_GDT     R    49_C     R    49_B      4    6   14      3    3    5    5    6    6    7    9    9   10   12   13   14   17   17   17   18   18   20   20 
LCS_GDT     S    50_C     S    50_B      4    7   14      3    4    4    6    6    6    8    9    9   11   12   13   14   17   17   17   18   18   20   20 
LCS_GDT     G    51_C     G    51_B      3    7   14      3    4    4    6    6    6    8    9   10   11   12   13   13   13   14   14   14   17   19   19 
LCS_GDT     G    52_C     G    52_B      5    7   14      4    4    5    5    5    6    8    9    9   11   12   13   13   13   14   14   14   15   15   15 
LCS_GDT     I    53_C     I    53_B      5    7   14      4    4    5    6    6    6    8    9   10   11   12   13   13   13   14   14   14   15   15   15 
LCS_GDT     P    54_C     P    54_B      5    8   14      4    4    5    7    8    8    8    9   10   11   12   13   13   13   14   14   14   15   15   16 
LCS_GDT     E    55_C     E    55_B      5    8   14      4    4    5    7    8    8    8    9   10   11   12   13   13   13   14   14   14   15   15   16 
LCS_GDT     G    56_C     G    56_B      6    8   14      3    5    6    7    8    8    8    9   10   11   12   13   13   13   14   14   14   15   15   16 
LCS_GDT     D    57_C     D    57_B      6    8   14      3    5    6    7    8    8    8    9   10   11   12   13   13   13   14   14   14   15   15   16 
LCS_GDT     I    58_C     I    58_B      6    8   14      3    5    6    6    8    8    8    9   10   11   12   13   13   13   14   18   19   19   21   23 
LCS_GDT     Y    59_C     Y    59_B      6    8   14      3    5    6    7    8    8    8    9   10   11   12   13   14   14   16   18   19   19   21   23 
LCS_GDT     L    60_C     L    60_B      6    8   14      3    5    6    7    8    8    8    9   10   11   12   13   14   15   16   18   19   19   24   27 
LCS_GDT     E    61_C     E    61_B      6    8   14      3    5    6    7    8    8    8    9   10   11   12   13   14   15   21   24   28   31   31   32 
LCS_GDT     S    62_C     S    62_B      3    7   14      3    3    4    5    6    7    8    9    9   12   12   13   14   14   20   23   28   31   31   32 
LCS_GDT     N    63_C     N    63_B      3    4   14      3    3    3    4    6    6    7    8    8   15   17   19   22   24   25   27   28   31   31   32 
LCS_GDT     L    64_C     L    64_B      3    5   14      3    3    3    6    6   10   12   14   14   15   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     F    65_C     F    65_B      3    5   14      3    3    3    4    5    7   12   14   14   15   17   20   22   24   25   27   27   31   31   32 
LCS_GDT     L    66_C     L    66_B      3    6   14      3    3    3    6    6   10   13   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     D    67_C     D    67_B      3    9   14      3    3    5    7    8   10   12   14   16   18   18   21   22   24   25   27   27   31   31   32 
LCS_GDT     F    68_C     F    68_B      4    9   14      3    4    4    7   10   12   13   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     N    69_C     N    69_B      4    9   14      3    4    6    9   11   12   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     P    70_C     P    70_B      4    9   14      3    4    5    7    8    8    9   13   13   16   18   21   22   24   25   27   28   31   31   32 
LCS_GDT     Y    71_C     Y    71_B      4    9   14      3    4    5    7    8    8   14   15   17   18   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     G    72_C     G    72_B      4    9   14      3    3    4    4    6    7    9   10   10   14   19   21   22   24   25   27   28   31   31   32 
LCS_GDT     L    73_C     L    73_B      4    9   14      3    3    5    7    8    8    9   10   10   12   13   14   19   19   21   24   27   31   31   32 
LCS_GDT     S    74_C     S    74_B      4    9   14      3    3    4    7    8    8    9   10   10   10   13   13   14   14   17   23   24   27   28   32 
LCS_GDT     G    75_C     G    75_B      3    9   14      3    3    3    6    8    8    9   10   10   10   13   13   14   14   14   18   21   22   26   27 
LCS_AVERAGE  LCS_A:   8.38  (   4.38    7.63   13.11 )

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      6      8      9     11     12     12     14     15     17     18     19     21     22     24     25     27     28     31     31     32 
GDT PERCENT_AT   5.17   6.90   7.76   9.48  10.34  10.34  12.07  12.93  14.66  15.52  16.38  18.10  18.97  20.69  21.55  23.28  24.14  26.72  26.72  27.59
GDT RMS_LOCAL    0.36   0.71   0.90   1.32   1.44   1.44   2.16   2.28   2.78   2.93   3.42   3.69   3.96   4.42   4.65   5.12   5.83   6.15   6.15   6.51
GDT RMS_ALL_AT  15.16  14.85  14.94  15.29  14.86  14.86  15.27  15.42  15.52  15.64  15.57  15.75  15.65  15.74  15.72  15.71  15.04  15.11  15.11  14.95

# Checking swapping
#   possible swapping detected:  D    31_C      D    31_B
#   possible swapping detected:  Y    39_C      Y    39_B
#   possible swapping detected:  E    48_C      E    48_B
#   possible swapping detected:  Y    59_C      Y    59_B
#   possible swapping detected:  D    67_C      D    67_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    29_C      A    29_B    10.184     0    0.628   0.598    12.195    0.000    0.286
LGA    S    30_C      S    30_B    12.727     0    0.044   0.078    13.628    0.000    0.000
LGA    D    31_C      D    31_B    13.292     0    0.694   0.849    14.297    0.000    0.000
LGA    S    32_C      S    32_B     9.555     0    0.557   0.486    10.911    5.119    3.651
LGA    Y    33_C      Y    33_B     3.728     0    0.618   1.104    11.700   47.619   23.968
LGA    E    34_C      E    34_B     2.398     0    0.105   0.976     6.431   59.167   44.392
LGA    V    35_C      V    35_B     3.705     0    0.064   0.105     6.609   57.500   40.952
LGA    P    36_C      P    36_B     1.132     0    0.046   0.312     4.434   77.381   63.878
LGA    E    37_C      E    37_B     1.443     0    0.638   0.509     9.307   79.881   46.032
LGA    Q    38_C      Q    38_B     0.828     0    0.063   0.351     4.807   83.810   64.815
LGA    Y    39_C      Y    39_B     0.711     0    0.072   1.187     8.768   85.952   53.294
LGA    F    40_C      F    40_B     1.056     0    0.023   0.080     1.249   83.690   82.251
LGA    I    41_C      I    41_B     1.411     0    0.014   0.127     2.024   81.429   76.131
LGA    I    42_C      I    42_B     1.047     0    0.114   0.154     1.816   81.429   80.357
LGA    T    43_C      T    43_B     1.796     0    0.198   0.988     3.912   79.286   70.068
LGA    R    44_C      R    44_B     1.596     0    0.627   1.223    11.534   62.143   35.671
LGA    S    45_C      S    45_B     3.262     0    0.616   0.576     5.962   39.405   47.937
LGA    T    46_C      T    46_B    10.647     0    0.668   0.584    13.576    1.190    0.680
LGA    T    47_C      T    47_B    14.984     0    0.374   0.381    19.291    0.000    0.000
LGA    E    48_C      E    48_B    19.693     0    0.036   0.763    24.421    0.000    0.000
LGA    R    49_C      R    49_B    21.066     0    0.629   1.013    28.731    0.000    0.000
LGA    S    50_C      S    50_B    21.845     0    0.508   0.466    22.487    0.000    0.000
LGA    G    51_C      G    51_B    25.008     0    0.319   0.319    25.875    0.000    0.000
LGA    G    52_C      G    52_B    27.925     0    0.306   0.306    28.472    0.000    0.000
LGA    I    53_C      I    53_B    30.711     0    0.105   1.100    36.160    0.000    0.000
LGA    P    54_C      P    54_B    30.302     0    0.644   0.565    33.617    0.000    0.000
LGA    E    55_C      E    55_B    32.254     0    0.064   1.161    36.452    0.000    0.000
LGA    G    56_C      G    56_B    32.492     0    0.628   0.628    32.908    0.000    0.000
LGA    D    57_C      D    57_B    28.631     0    0.112   1.163    29.583    0.000    0.000
LGA    I    58_C      I    58_B    24.778     0    0.071   1.017    29.233    0.000    0.000
LGA    Y    59_C      Y    59_B    17.422     0    0.111   1.261    20.043    0.000    0.000
LGA    L    60_C      L    60_B    16.157     0    0.127   1.436    20.832    0.000    0.000
LGA    E    61_C      E    61_B    12.334     0    0.634   0.721    15.390    0.000    0.000
LGA    S    62_C      S    62_B    12.835     0    0.644   0.792    14.677    0.357    0.238
LGA    N    63_C      N    63_B     8.939     0    0.195   1.184    12.493    5.000    2.679
LGA    L    64_C      L    64_B     9.146     0    0.586   1.388    13.893    3.571    1.786
LGA    F    65_C      F    65_B    10.704     0    0.477   1.328    17.461    0.119    0.043
LGA    L    66_C      L    66_B     6.735     0    0.673   0.967     9.025   25.476   17.083
LGA    D    67_C      D    67_B     5.342     0    0.418   1.194    11.114   32.024   16.667
LGA    F    68_C      F    68_B     3.500     0    0.144   1.191     7.354   38.810   35.238
LGA    N    69_C      N    69_B     2.663     0    0.072   0.268     3.963   55.357   56.429
LGA    P    70_C      P    70_B     6.272     0    0.213   0.202     8.184   20.000   15.238
LGA    Y    71_C      Y    71_B     4.396     0    0.598   1.293    10.207   34.286   23.373
LGA    G    72_C      G    72_B     7.274     0    0.605   0.605     9.900    6.667    6.667
LGA    L    73_C      L    73_B    12.390     0    0.021   1.324    16.291    0.000    0.000
LGA    S    74_C      S    74_B    16.343     0    0.268   0.590    18.396    0.000    0.000
LGA    G    75_C      G    75_B    18.729     0    0.702   0.702    18.729    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       47     188    188  100.00     371    371  100.00               116
SUMMARY(RMSD_GDC):    13.177         13.078                 13.403            9.885    7.843

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   47  116    4.0     15    2.28    13.147    11.727     0.631

LGA_LOCAL      RMSD:   2.279  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.417  Number of assigned atoms:   47 
Std_ASGN_ATOMS RMSD:  13.177  Standard rmsd on all 47 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.613953 * X  +   0.710911 * Y  +  -0.343027 * Z  + -51.370979
  Y_new =   0.355085 * X  +  -0.636862 * Y  +  -0.684340 * Z  +   6.944082
  Z_new =  -0.704966 * X  +   0.298349 * Y  +  -0.643437 * Z  +  -8.743459 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.524355  0.782375  2.707420   [DEG:   30.0433   44.8268  155.1238 ]
ZXZ: -0.464648  2.269776 -1.170442   [DEG:  -26.6224  130.0486  -67.0614 ]
 
# END of job
