
#######################################################
#                                                     #
#                        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   65 (  516),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51       6_C - 56_C        2.53     2.53
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       8_C - 53_C        1.97     2.65
  LCS_AVERAGE:     84.28

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      10_C - 24_C        0.98     3.16
  LONGEST_CONTINUOUS_SEGMENT:    15      31_C - 45_C        0.94     2.78
  LONGEST_CONTINUOUS_SEGMENT:    15      32_C - 46_C        0.86     2.69
  LCS_AVERAGE:     21.95

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C      3   13   51      3    3    6    9   11   13   16   28   47   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T     7_C     T     7_C      4   44   51      3    4    6   12   16   26   41   46   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     K     8_C     K     8_C      4   46   51      3    4    6   12   28   41   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     I     9_C     I     9_C     14   46   51      9   15   24   31   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     L    10_C     L    10_C     15   46   51      9   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    11_C     P    11_C     15   46   51     12   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    12_C     C    12_C     15   46   51     12   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    13_C     P    13_C     15   46   51     12   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    14_C     R    14_C     15   46   51     12   22   29   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    15_C     C    15_C     15   46   51     12   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    16_C     N    16_C     15   46   51     12   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     S    17_C     S    17_C     15   46   51     12   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     M    18_C     M    18_C     15   46   51     12   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     E    19_C     E    19_C     15   46   51      6   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T    20_C     T    20_C     15   46   51      9   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     K    21_C     K    21_C     15   46   51      8   21   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     F    22_C     F    22_C     15   46   51      7   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    23_C     C    23_C     15   46   51      0    5   27   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    24_C     Y    24_C     15   46   51      3    5   27   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    25_C     Y    25_C      4   46   51      3    7   16   27   35   41   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    26_C     N    26_C      3   46   51      3   11   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    27_C     N    27_C      3   46   51      3    3    4   30   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    28_C     Y    28_C      5   46   51      3    3    6   34   36   41   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    29_C     N    29_C     11   46   51      4   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     V    30_C     V    30_C     11   46   51      4   14   19   32   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    31_C     N    31_C     15   46   51      4    8   21   31   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Q    32_C     Q    32_C     15   46   51      4   15   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    33_C     P    33_C     15   46   51      5   21   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    34_C     R    34_C     15   46   51      8   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     H    35_C     H    35_C     15   46   51     11   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     F    36_C     F    36_C     15   46   51     12   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    37_C     C    37_C     15   46   51     12   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     K    38_C     K    38_C     15   46   51     12   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     A    39_C     A    39_C     15   46   51     12   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    40_C     C    40_C     15   46   51     10   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Q    41_C     Q    41_C     15   46   51      4   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    42_C     R    42_C     15   46   51      7   19   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    43_C     Y    43_C     15   46   51      9   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     W    44_C     W    44_C     15   46   51      9   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T    45_C     T    45_C     15   46   51      9   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     S    46_C     S    46_C     15   46   51      4   14   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     G    47_C     G    47_C      6   46   51      4    4   18   31   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     G    48_C     G    48_C      6   46   51      4    4   21   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T    49_C     T    49_C      6   46   51      5   22   30   34   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     M    50_C     M    50_C      4   46   51      4    4    5    6    6   34   44   46   48   49   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    51_C     R    51_C      4   46   51      3    4   13   30   39   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     S    52_C     S    52_C      4   46   51      3    4    5    7   16   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     V    53_C     V    53_C      4   46   51      3    4    7   28   37   42   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    54_C     P    54_C      4    7   51      3    4    5   21   25   31   41   43   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     I    55_C     I    55_C      3    6   51      3    8   14   21   33   38   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     G    56_C     G    56_C      3    6   51      3    3   14   24   33   39   45   47   48   50   51   51   51   51   51   51   51   51   51   51 
LCS_AVERAGE  LCS_A:  68.74  (  21.95   84.28  100.00 )

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     12     22     30     34     39     42     45     47     48     50     51     51     51     51     51     51     51     51     51     51 
GDT PERCENT_AT  23.53  43.14  58.82  66.67  76.47  82.35  88.24  92.16  94.12  98.04 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.65   0.98   1.12   1.56   1.68   1.86   2.06   2.18   2.45   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53
GDT RMS_ALL_AT   3.52   3.04   2.71   2.79   2.72   2.67   2.64   2.57   2.57   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53

# Checking swapping
#   possible swapping detected:  Y    25_C      Y    25_C
#   possible swapping detected:  Y    28_C      Y    28_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C     6.977     2    0.094   0.135     7.423   17.738   12.585
LGA    T     7_C      T     7_C     5.333     0    0.643   0.983     8.859   40.952   26.122
LGA    K     8_C      K     8_C     3.719     4    0.093   0.145     4.853   42.262   22.275
LGA    I     9_C      I     9_C     2.558     0    0.579   1.477     8.442   62.976   43.571
LGA    L    10_C      L    10_C     1.503     0    0.028   1.254     3.707   77.143   67.381
LGA    P    11_C      P    11_C     1.267     0    0.044   0.153     1.873   81.429   77.755
LGA    C    12_C      C    12_C     1.255     0    0.028   0.183     1.314   81.429   81.429
LGA    P    13_C      P    13_C     1.679     0    0.079   0.124     1.976   72.857   72.857
LGA    R    14_C      R    14_C     1.927     0    0.036   1.525     8.258   72.857   49.654
LGA    C    15_C      C    15_C     1.622     0    0.025   0.179     1.631   77.143   77.143
LGA    N    16_C      N    16_C     1.308     0    0.102   0.277     1.477   81.429   82.560
LGA    S    17_C      S    17_C     1.132     0    0.055   0.576     1.499   83.690   82.937
LGA    M    18_C      M    18_C     0.388     0    0.114   0.874     2.912   92.976   86.429
LGA    E    19_C      E    19_C     1.159     4    0.187   0.200     1.693   88.214   47.302
LGA    T    20_C      T    20_C     0.635     0    0.094   1.014     2.815   88.214   79.660
LGA    K    21_C      K    21_C     1.016     0    0.109   1.024     3.425   90.595   78.360
LGA    F    22_C      F    22_C     0.915     0    0.110   0.933     5.684   85.952   62.035
LGA    C    23_C      C    23_C     2.611     0    0.595   0.912     6.143   58.214   50.000
LGA    Y    24_C      Y    24_C     2.701     0    0.373   1.194    14.231   57.619   23.452
LGA    Y    25_C      Y    25_C     3.162     0    0.623   1.217    12.387   65.238   25.238
LGA    N    26_C      N    26_C     1.474     0    0.169   0.630     3.762   75.119   65.357
LGA    N    27_C      N    27_C     3.423     0    0.410   0.416     8.206   57.381   35.476
LGA    Y    28_C      Y    28_C     3.183     0    0.397   1.395    13.942   61.071   26.310
LGA    N    29_C      N    29_C     1.458     0    0.291   0.838     3.050   77.262   70.298
LGA    V    30_C      V    30_C     2.215     0    0.053   1.002     3.770   67.024   59.796
LGA    N    31_C      N    31_C     2.435     0    0.041   1.174     3.433   64.881   61.131
LGA    Q    32_C      Q    32_C     1.445     0    0.159   0.175     2.604   85.952   73.386
LGA    P    33_C      P    33_C     0.699     0    0.074   0.315     1.583   95.238   88.095
LGA    R    34_C      R    34_C     0.456     0    0.043   0.776     2.729   92.857   82.900
LGA    H    35_C      H    35_C     0.781     0    0.135   0.493     2.637   88.214   79.190
LGA    F    36_C      F    36_C     0.368     0    0.091   1.043     7.065   97.619   61.255
LGA    C    37_C      C    37_C     0.276     0    0.084   0.146     1.149   92.976   92.143
LGA    K    38_C      K    38_C     0.852     0    0.071   0.743     1.873   86.190   84.603
LGA    A    39_C      A    39_C     1.238     0    0.309   0.323     1.529   85.952   83.333
LGA    C    40_C      C    40_C     1.664     0    0.021   0.114     1.818   79.405   78.651
LGA    Q    41_C      Q    41_C     0.890     0    0.064   0.171     2.330   88.214   79.735
LGA    R    42_C      R    42_C     0.995     0    0.059   1.070     5.270   95.238   60.303
LGA    Y    43_C      Y    43_C     0.867     0    0.166   0.710     3.653   90.476   72.579
LGA    W    44_C      W    44_C     1.015     0    0.101   0.989     8.467   88.214   46.599
LGA    T    45_C      T    45_C     1.046     0    0.162   0.350     1.928   83.690   82.789
LGA    S    46_C      S    46_C     1.262     0    0.611   0.729     3.243   79.524   73.492
LGA    G    47_C      G    47_C     2.653     0    0.496   0.496     2.653   73.452   73.452
LGA    G    48_C      G    48_C     2.018     0    0.048   0.048     2.260   70.952   70.952
LGA    T    49_C      T    49_C     1.008     0    0.619   0.898     3.525   67.738   65.510
LGA    M    50_C      M    50_C     5.003     0    0.078   1.351    12.409   33.214   17.679
LGA    R    51_C      R    51_C     3.679     0    0.273   1.121     8.220   45.000   30.216
LGA    S    52_C      S    52_C     3.445     0    0.095   0.724     6.211   55.476   47.063
LGA    V    53_C      V    53_C     2.698     0    0.087   1.178     4.496   48.690   52.925
LGA    P    54_C      P    54_C     5.911     0    0.269   0.441     7.865   27.619   21.973
LGA    I    55_C      I    55_C     4.434     0    0.038   1.276     5.160   32.976   30.952
LGA    G    56_C      G    56_C     4.102     0    0.183   0.183     5.451   34.524   34.524

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     2.527          2.418                  3.959           71.394   59.832

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     47    2.06    75.490    82.085     2.178

LGA_LOCAL      RMSD:   2.058  Number of atoms:   47  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.567  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   2.527  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.614157 * X  +  -0.789033 * Y  +   0.015448 * Z  +  -8.858406
  Y_new =   0.450584 * X  +   0.366655 * Y  +   0.813964 * Z  + -95.289917
  Z_new =  -0.647908 * X  +  -0.492941 * Y  +   0.580709 * Z  + -40.753262 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.632963  0.704835 -0.703832   [DEG:   36.2661   40.3841  -40.3266 ]
ZXZ:  3.122617  0.951196 -2.221186   [DEG:  178.9128   54.4995 -127.2646 ]
 
# END of job
