
#######################################################
#                                                     #
#                        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 (  442),  selected   56 , name one
# Molecule2: number of CA atoms  270 ( 2127),  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      32_A - 80_A        4.82     6.32
  LCS_AVERAGE:     17.40

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      56_A - 79_A        1.41    13.31
  LONGEST_CONTINUOUS_SEGMENT:    24      57_A - 80_A        1.90    12.92
  LCS_AVERAGE:      7.40

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      57_A - 79_A        0.66    13.09
  LCS_AVERAGE:      6.57

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     S    32_A     S    32_A     20   21   49     14   20   20   20   20   20   20   22   29   36   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     W    33_A     W    33_A     20   21   49     12   20   20   20   20   20   20   20   20   23   28   31   42   47   48   49   53   55   55   56 
LCS_GDT     A    34_A     A    34_A     20   21   49     16   20   20   20   20   20   20   20   20   24   34   44   47   47   48   49   53   55   55   56 
LCS_GDT     D    35_A     D    35_A     20   21   49     16   20   20   20   20   20   20   22   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     L    36_A     L    36_A     20   21   49     16   20   20   20   20   20   20   22   27   35   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     R    37_A     R    37_A     20   21   49     16   20   20   20   20   20   20   20   20   24   32   44   47   47   48   49   53   55   55   56 
LCS_GDT     D    38_A     D    38_A     20   21   49     16   20   20   20   20   20   20   20   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     V    39_A     V    39_A     20   21   49     16   20   20   20   20   20   20   22   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     L    40_A     L    40_A     20   21   49     16   20   20   20   20   20   20   22   27   35   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     F    41_A     F    41_A     20   21   49     16   20   20   20   20   20   20   20   29   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     N    42_A     N    42_A     20   21   49     16   20   20   20   20   20   20   20   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     L    43_A     L    43_A     20   21   49     16   20   20   20   20   20   20   22   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     C    44_A     C    44_A     20   21   49     16   20   20   20   20   20   20   22   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     E    45_A     E    45_A     20   21   49     16   20   20   20   20   20   20   20   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     N    46_A     N    46_A     20   21   49     16   20   20   20   20   20   20   20   25   34   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     L    47_A     L    47_A     20   21   49     16   20   20   20   20   20   20   22   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     V    48_A     V    48_A     20   21   49     16   20   20   20   20   20   20   21   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     K    49_A     K    49_A     20   21   49     16   20   20   20   20   20   20   20   20   29   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     S    50_A     S    50_A     20   21   49     16   20   20   20   20   20   20   20   20   21   22   26   38   47   48   49   50   54   55   56 
LCS_GDT     S    51_A     S    51_A     20   21   49     16   20   20   20   20   20   20   22   32   37   41   44   47   47   48   49   51   55   55   56 
LCS_GDT     E    52_A     E    52_A      4   21   49      3    3    5    5    8   10   19   22   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     A    53_A     A    53_A      4    5   49      3    4    5    5    5    7   12   18   29   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     N    54_A     N    54_A      4    5   49      3    4    6    7    9   11   16   22   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     S    55_A     S    55_A      4    5   49      3    4    5    5    7   10   14   19   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     P    56_A     P    56_A      4   24   49      3    4    5    5    7   10   14   18   25   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     A    57_A     A    57_A     23   24   49      3    9   23   23   23   23   23   23   30   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     H    58_A     H    58_A     23   24   49     18   21   23   23   23   23   23   23   23   36   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     E    59_A     E    59_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     E    60_A     E    60_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     F    61_A     F    61_A     23   24   49     18   21   23   23   23   23   23   23   30   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     K    62_A     K    62_A     23   24   49     18   21   23   23   23   23   23   23   28   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     T    63_A     T    63_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     M    64_A     M    64_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     L    65_A     L    65_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     L    66_A     L    66_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     I    67_A     I    67_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     A    68_A     A    68_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     H    69_A     H    69_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     Y    70_A     Y    70_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     Y    71_A     Y    71_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     A    72_A     A    72_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     T    73_A     T    73_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     R    74_A     R    74_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     S    75_A     S    75_A     23   24   49     18   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     A    76_A     A    76_A     23   24   49     15   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     A    77_A     A    77_A     23   24   49     10   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     Q    78_A     Q    78_A     23   24   49     17   21   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     S    79_A     S    79_A     23   24   49      5   17   23   23   23   23   23   23   32   37   41   44   47   47   48   49   53   55   55   56 
LCS_GDT     V    80_A     V    80_A      6   24   49      4    5    6    8    8    9   10   18   20   24   34   39   47   47   48   49   53   55   55   56 
LCS_GDT     K    81_A     K    81_A      6    9   48      4    5    6    8    8    9   10   12   15   19   23   29   32   39   45   48   53   55   55   56 
LCS_GDT     Q    82_A     Q    82_A      6    9   34      4    5    6    8    8    9   10   12   15   19   23   29   32   38   44   48   53   55   55   56 
LCS_GDT     L    83_A     L    83_A      6    9   32      5    5    6    8    8    9   10   12   15   19   24   29   32   39   44   48   53   55   55   56 
LCS_GDT     E    84_A     E    84_A      6    9   29      5    5    6    8    8    9   10   12   15   19   22   29   32   38   44   48   53   55   55   56 
LCS_GDT     T    85_A     T    85_A      5    9   29      5    5    5    8    8    9   10   12   15   20   25   29   32   39   45   48   53   55   55   56 
LCS_GDT     V    86_A     V    86_A      5    9   29      5    5    5    8    8    8   10   12   15   20   24   29   32   39   45   48   53   55   55   56 
LCS_GDT     A    87_A     A    87_A      5    9   29      5    5    5    8    8    8   10   12   15   19   22   28   32   35   37   48   52   55   55   56 
LCS_AVERAGE  LCS_A:  10.46  (   6.57    7.40   17.40 )

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     18     21     23     23     23     23     23     23     32     37     41     44     47     47     48     49     53     55     55     56 
GDT PERCENT_AT   6.67   7.78   8.52   8.52   8.52   8.52   8.52   8.52  11.85  13.70  15.19  16.30  17.41  17.41  17.78  18.15  19.63  20.37  20.37  20.74
GDT RMS_LOCAL    0.25   0.42   0.66   0.66   0.66   0.66   0.66   0.66   3.93   4.10   4.29   4.43   4.66   4.63   4.73   4.82   5.65   5.80   5.75   5.86
GDT RMS_ALL_AT  13.28  13.11  13.09  13.09  13.09  13.09  13.09  13.09   6.59   6.46   6.45   6.44   6.29   6.43   6.32   6.32   5.87   5.87   5.87   5.86

# Checking swapping
#   possible swapping detected:  D    35_A      D    35_A
#   possible swapping detected:  D    38_A      D    38_A
#   possible swapping detected:  E    52_A      E    52_A
#   possible swapping detected:  E    59_A      E    59_A
#   possible swapping detected:  F    61_A      F    61_A
#   possible swapping detected:  Y    70_A      Y    70_A
#   possible swapping detected:  Y    71_A      Y    71_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S    32_A      S    32_A    16.155     0    0.068   0.063    17.317    0.000    0.000
LGA    W    33_A      W    33_A    12.978     0    0.064   0.240    14.694    0.000    0.306
LGA    A    34_A      A    34_A    18.495     0    0.038   0.035    20.602    0.000    0.000
LGA    D    35_A      D    35_A    19.212     0    0.060   1.109    23.388    0.000    0.000
LGA    L    36_A      L    36_A    13.802     0    0.059   1.388    15.377    0.000    0.000
LGA    R    37_A      R    37_A    15.893     0    0.063   0.688    23.118    0.000    0.000
LGA    D    38_A      D    38_A    20.501     0    0.026   1.099    24.292    0.000    0.000
LGA    V    39_A      V    39_A    17.462     0    0.034   1.263    18.183    0.000    0.000
LGA    L    40_A      L    40_A    14.496     0    0.027   0.065    16.136    0.000    0.000
LGA    F    41_A      F    41_A    19.775     0    0.029   1.435    28.312    0.000    0.000
LGA    N    42_A      N    42_A    20.596     0    0.032   1.398    25.254    0.000    0.000
LGA    L    43_A      L    43_A    15.433     0    0.047   1.396    16.887    0.000    0.000
LGA    C    44_A      C    44_A    17.871     0    0.039   0.046    19.845    0.000    0.000
LGA    E    45_A      E    45_A    22.307     0    0.087   0.571    28.370    0.000    0.000
LGA    N    46_A      N    46_A    19.064     0    0.041   0.076    21.706    0.000    0.000
LGA    L    47_A      L    47_A    16.140     0    0.072   1.443    18.035    0.000    0.000
LGA    V    48_A      V    48_A    21.971     0    0.039   1.223    25.040    0.000    0.000
LGA    K    49_A      K    49_A    23.021     0    0.072   0.138    30.178    0.000    0.000
LGA    S    50_A      S    50_A    17.612     0    0.152   0.630    19.209    0.000    0.000
LGA    S    51_A      S    51_A    18.485     0    0.147   0.686    22.953    0.000    0.000
LGA    E    52_A      E    52_A    15.244     0    0.613   1.553    17.618    0.000    0.000
LGA    A    53_A      A    53_A    14.388     0    0.670   0.609    16.565    0.000    0.000
LGA    N    54_A      N    54_A    10.981     0    0.015   0.782    15.502    0.476    0.238
LGA    S    55_A      S    55_A     8.741     0    0.633   0.956     9.539    5.833    4.603
LGA    P    56_A      P    56_A     6.663     0    0.249   0.573     7.894   19.881   15.306
LGA    A    57_A      A    57_A     1.531     0    0.547   0.507     2.690   75.119   71.524
LGA    H    58_A      H    58_A     0.364     0    0.178   0.938     3.809  100.000   78.048
LGA    E    59_A      E    59_A     0.371     0    0.050   0.333     1.406  100.000   93.704
LGA    E    60_A      E    60_A     0.628     0    0.046   1.095     3.537   92.857   76.984
LGA    F    61_A      F    61_A     0.469     0    0.099   1.161     6.516  100.000   66.234
LGA    K    62_A      K    62_A     0.179     0    0.024   0.689     2.586  100.000   91.323
LGA    T    63_A      T    63_A     0.311     0    0.033   0.046     0.560  100.000   98.639
LGA    M    64_A      M    64_A     0.352     0    0.039   0.972     3.901  100.000   90.536
LGA    L    65_A      L    65_A     0.265     0    0.017   1.418     3.241  100.000   83.095
LGA    L    66_A      L    66_A     0.200     0    0.025   1.396     3.429  100.000   83.988
LGA    I    67_A      I    67_A     0.217     0    0.021   0.203     0.600  100.000   98.810
LGA    A    68_A      A    68_A     0.313     0    0.041   0.049     0.381  100.000  100.000
LGA    H    69_A      H    69_A     0.227     0    0.031   0.409     1.891   97.619   88.952
LGA    Y    70_A      Y    70_A     0.266     0    0.031   1.257     8.644  100.000   60.159
LGA    Y    71_A      Y    71_A     0.223     0    0.063   1.335     8.362   97.619   60.317
LGA    A    72_A      A    72_A     0.788     0    0.084   0.104     1.000   90.476   90.476
LGA    T    73_A      T    73_A     0.955     0    0.046   0.143     1.521   90.476   85.374
LGA    R    74_A      R    74_A     0.699     0    0.060   1.287     9.233   90.476   55.628
LGA    S    75_A      S    75_A     0.527     0    0.140   0.577     1.215   92.857   90.556
LGA    A    76_A      A    76_A     0.388     0    0.068   0.074     0.742   95.238   94.286
LGA    A    77_A      A    77_A     0.790     0    0.037   0.039     0.914   90.476   90.476
LGA    Q    78_A      Q    78_A     0.493     0    0.198   0.898     4.835   88.452   70.952
LGA    S    79_A      S    79_A     1.679     0    0.457   0.662     5.796   54.048   50.794
LGA    V    80_A      V    80_A     9.362     0    0.429   1.037    12.294    3.690    2.109
LGA    K    81_A      K    81_A    13.959     0    0.041   1.216    17.283    0.000    0.000
LGA    Q    82_A      Q    82_A    19.421     0    0.222   1.026    21.352    0.000    0.000
LGA    L    83_A      L    83_A    16.381     0    0.255   0.229    19.040    0.000    0.000
LGA    E    84_A      E    84_A    15.335     0    0.045   1.145    18.584    0.000    0.000
LGA    T    85_A      T    85_A    21.147     0    0.047   0.089    25.511    0.000    0.000
LGA    V    86_A      V    86_A    19.852     0    0.124   0.152    21.701    0.000    0.000
LGA    A    87_A      A    87_A    15.127     0    0.531   0.551    16.657    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     442    442  100.00               270
SUMMARY(RMSD_GDC):     5.862          5.615                  7.399            8.095    7.013

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56  270    4.0     23    0.66    10.741    10.286     3.023

LGA_LOCAL      RMSD:   0.661  Number of atoms:   23  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.094  Number of assigned atoms:   56 
Std_ASGN_ATOMS RMSD:   5.862  Standard rmsd on all 56 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.695336 * X  +  -0.007168 * Y  +   0.718649 * Z  + -43.061085
  Y_new =   0.237684 * X  +  -0.941388 * Y  +  -0.239363 * Z  +   4.933837
  Z_new =   0.678244 * X  +   0.337250 * Y  +  -0.652877 * Z  +  77.439743 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.329375 -0.745370  2.664786   [DEG:   18.8718  -42.7065  152.6810 ]
ZXZ:  1.249279  2.282173  1.109360   [DEG:   71.5784  130.7589   63.5616 ]
 
# END of job
