
#######################################################
#                                                     #
#                        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   42 (  322),  selected   42 , name one
# Molecule2: number of CA atoms  132 ( 1073),  selected   42 , 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:    22      85_A - 106_A       4.74    20.68
  LONGEST_CONTINUOUS_SEGMENT:    22      86_A - 107_A       4.92    20.89
  LCS_AVERAGE:     14.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      86_A - 95_A        1.88    19.75
  LCS_AVERAGE:      5.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      89_A - 95_A        0.82    21.09
  LONGEST_CONTINUOUS_SEGMENT:     7      99_A - 105_A       0.70    26.71
  LCS_AVERAGE:      3.84

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   42
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     K    70_A     K    70_A      3    5    8      3    3    3    4    4    4    5    6    6    6    6    8    8    9   11   12   12   14   15   15 
LCS_GDT     G    71_A     G    71_A      3    5   11      3    3    3    4    4    4    5    6    6    6    6    6    7    7    8    8   10   10   12   13 
LCS_GDT     A    72_A     A    72_A      4    5   15      3    4    4    4    4    4    5    8    9   10   10   10   11   12   14   14   14   14   15   15 
LCS_GDT     K    73_A     K    73_A      4    5   16      3    4    4    4    4    6    7   10   12   13   13   13   13   13   14   14   16   16   17   17 
LCS_GDT     I    74_A     I    74_A      4    9   16      3    4    4    6    8    9   12   12   12   13   13   13   13   15   15   16   16   16   17   17 
LCS_GDT     N    75_A     N    75_A      6    9   16      5    5    5    8    8    9   12   12   12   13   13   14   14   15   15   16   16   16   17   17 
LCS_GDT     V    76_A     V    76_A      6    9   16      5    5    6    8    8    9   12   12   12   13   13   14   14   15   15   16   16   16   17   17 
LCS_GDT     Y    77_A     Y    77_A      6    9   16      5    5    6    8    8    9   12   12   12   13   13   14   14   15   15   16   16   16   17   17 
LCS_GDT     P    78_A     P    78_A      6    9   16      5    5    6    8    8    9   12   12   12   13   13   14   14   15   15   16   16   16   17   17 
LCS_GDT     S    79_A     S    79_A      6    9   16      5    5    6    8    8    9   12   12   12   13   13   14   14   15   15   16   16   16   17   17 
LCS_GDT     A    80_A     A    80_A      6    9   16      4    5    6    8    8    9   12   12   12   13   13   14   14   15   15   16   16   16   17   17 
LCS_GDT     M    81_A     M    81_A      6    9   16      4    5    6    8    8    9   12   12   12   13   13   14   14   15   15   16   16   16   17   17 
LCS_GDT     S    82_A     S    82_A      6    9   16      4    5    6    8    8    9   12   12   12   13   13   14   14   15   15   16   16   16   17   17 
LCS_GDT     R    83_A     R    83_A      3    9   16      3    3    3    5    7    9   12   12   12   13   13   14   14   15   15   17   19   23   24   26 
LCS_GDT     D    84_A     D    84_A      3    5   20      3    3    3    6    7    9   12   12   12   13   13   15   18   22   23   24   25   26   27   28 
LCS_GDT     M    85_A     M    85_A      3    5   22      3    3    3    4    5    9   12   12   12   14   16   18   22   22   23   24   26   27   27   28 
LCS_GDT     S    86_A     S    86_A      3   10   22      3    3    3    8    9   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     D    87_A     D    87_A      3   10   22      3    3    4    7    9   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     G    88_A     G    88_A      3   10   22      3    3    3    5    9   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     I    89_A     I    89_A      7   10   22      4    6    7    8    9   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     V    90_A     V    90_A      7   10   22      4    6    7    8    9   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     A    91_A     A    91_A      7   10   22      3    6    7    8    9   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     Y    92_A     Y    92_A      7   10   22      4    6    7    8    9   10   11   13   13   16   18   21   22   23   24   25   26   27   27   28 
LCS_GDT     E    93_A     E    93_A      7   10   22      4    6    7    8    9   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     T    94_A     T    94_A      7   10   22      3    5    7    8    9   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     T    95_A     T    95_A      7   10   22      3    6    7    8    9   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     L    96_A     L    96_A      3    8   22      3    3    3    4    6   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     G    97_A     G    97_A      3    8   22      3    3    4    6    8   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     Q    98_A     Q    98_A      3    5   22      3    3    4    5    8   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     P    99_A     P    99_A      7    8   22      6    6    7    7    8   10   11   12   13   14   16   21   22   23   24   25   26   27   27   28 
LCS_GDT     G   100_A     G   100_A      7    8   22      6    6    7    7    8   10   11   12   13   14   17   21   22   23   24   25   26   27   27   28 
LCS_GDT     L   101_A     L   101_A      7    8   22      6    6    7    7    8   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     P   102_A     P   102_A      7    8   22      6    6    7    7    8   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     E   103_A     E   103_A      7    8   22      6    6    7    7    8   10   11   13   15   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     N   104_A     N   104_A      7    8   22      6    6    7    7    8   10   11   12   13   16   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     Q   105_A     Q   105_A      7    8   22      4    5    7    7    8   10   11   12   13   16   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     V   106_A     V   106_A      3    8   22      3    3    4    5    8   10   11   12   13   17   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     H   107_A     H   107_A      4    5   22      4    4    4    5    5    6    9   10   13   13   14   16   18   21   24   25   26   27   27   28 
LCS_GDT     I   108_A     I   108_A      4    5   19      4    4    4    5    5    8   11   11   13   13   14   15   16   18   22   25   26   27   27   28 
LCS_GDT     F   109_A     F   109_A      4    5   19      4    4    4    5    5    5    7   11   13   13   14   15   19   23   24   25   26   27   27   28 
LCS_GDT     D   110_A     D   110_A      4    5   19      4    4    4    5    7   10   11   12   13   16   20   21   22   23   24   25   26   27   27   28 
LCS_GDT     F   111_A     F   111_A      3    5   19      0    3    4    5    7   10   11   12   13   17   20   21   22   23   24   25   26   27   27   28 
LCS_AVERAGE  LCS_A:   8.15  (   3.84    5.95   14.65 )

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      6      7      8      9     10     12     13     15     17     20     21     22     23     24     25     26     27     27     28 
GDT PERCENT_AT   4.55   4.55   5.30   6.06   6.82   7.58   9.09   9.85  11.36  12.88  15.15  15.91  16.67  17.42  18.18  18.94  19.70  20.45  20.45  21.21
GDT RMS_LOCAL    0.34   0.34   0.70   1.38   1.67   1.88   2.49   2.66   3.38   4.01   4.30   4.39   4.56   4.71   4.94   5.17   5.37   5.58   5.58   5.87
GDT RMS_ALL_AT  26.66  26.66  26.71  30.49  20.04  19.75  30.88  20.39  20.19  20.45  20.75  20.68  20.79  20.93  21.12  21.25  21.19  21.40  21.40  21.25

# Checking swapping
#   possible swapping detected:  Y    92_A      Y    92_A
#   possible swapping detected:  E    93_A      E    93_A
#   possible swapping detected:  E   103_A      E   103_A
#   possible swapping detected:  F   109_A      F   109_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    70_A      K    70_A    41.875     0    0.457   0.809    48.082    0.000    0.000
LGA    G    71_A      G    71_A    40.973     0    0.035   0.035    41.177    0.000    0.000
LGA    A    72_A      A    72_A    39.857     0    0.636   0.579    39.934    0.000    0.000
LGA    K    73_A      K    73_A    39.726     0    0.114   0.239    40.009    0.000    0.000
LGA    I    74_A      I    74_A    40.653     0    0.617   1.466    43.374    0.000    0.000
LGA    N    75_A      N    75_A    39.561     0    0.491   1.309    41.176    0.000    0.000
LGA    V    76_A      V    76_A    32.921     0    0.046   0.143    35.049    0.000    0.000
LGA    Y    77_A      Y    77_A    29.966     0    0.055   1.253    35.975    0.000    0.000
LGA    P    78_A      P    78_A    25.034     0    0.031   0.299    28.380    0.000    0.000
LGA    S    79_A      S    79_A    27.658     0    0.092   0.098    27.658    0.000    0.000
LGA    A    80_A      A    80_A    27.318     0    0.111   0.114    29.613    0.000    0.000
LGA    M    81_A      M    81_A    22.209     0    0.165   1.218    24.497    0.000    0.000
LGA    S    82_A      S    82_A    18.357     0    0.580   0.730    20.416    0.000    0.000
LGA    R    83_A      R    83_A    14.853     0    0.625   1.287    20.086    0.000    0.000
LGA    D    84_A      D    84_A    11.335     0    0.550   1.118    16.432    3.214    1.607
LGA    M    85_A      M    85_A     6.758     0    0.651   0.819    13.631   23.095   11.905
LGA    S    86_A      S    86_A     2.281     0    0.278   0.802     6.745   59.405   47.063
LGA    D    87_A      D    87_A     2.378     0    0.224   0.942     4.751   71.310   53.512
LGA    G    88_A      G    88_A     3.864     0    0.231   0.231     3.864   52.143   52.143
LGA    I    89_A      I    89_A     1.554     0    0.276   1.596     6.330   77.262   63.690
LGA    V    90_A      V    90_A     1.672     0    0.043   0.241     5.243   75.476   57.551
LGA    A    91_A      A    91_A     1.320     0    0.132   0.188     3.147   80.000   74.000
LGA    Y    92_A      Y    92_A     2.997     0    0.054   0.164    12.240   71.071   28.333
LGA    E    93_A      E    93_A     2.034     0    0.010   1.005     7.818   61.071   40.529
LGA    T    94_A      T    94_A     1.719     0    0.121   0.182     3.237   83.810   72.449
LGA    T    95_A      T    95_A     1.575     0    0.609   0.517     4.645   71.071   59.388
LGA    L    96_A      L    96_A     4.036     0    0.067   1.441    10.576   59.881   32.440
LGA    G    97_A      G    97_A     3.151     0    0.613   0.613     3.737   59.762   59.762
LGA    Q    98_A      Q    98_A     3.768     0    0.638   0.761    10.756   35.952   19.524
LGA    P    99_A      P    99_A     7.737     0    0.696   0.806     8.868    9.643    9.048
LGA    G   100_A      G   100_A     8.099     0    0.031   0.031     8.099    7.976    7.976
LGA    L   101_A      L   101_A     8.022     0    0.071   0.127    10.422    5.357    3.393
LGA    P   102_A      P   102_A     8.468     0    0.132   0.191     9.168    3.810    2.993
LGA    E   103_A      E   103_A    10.287     0    0.164   1.011    11.647    0.119    0.053
LGA    N   104_A      N   104_A    10.485     0    0.219   1.133    11.860    0.000    0.000
LGA    Q   105_A      Q   105_A     9.603     0    0.587   0.524    11.374    1.071    0.529
LGA    V   106_A      V   106_A    12.062     0    0.574   1.428    13.822    0.000    0.000
LGA    H   107_A      H   107_A    16.984     0    0.647   1.029    23.842    0.000    0.000
LGA    I   108_A      I   108_A    17.568     0    0.120   1.258    21.885    0.000    0.000
LGA    F   109_A      F   109_A    16.825     0    0.242   1.249    17.389    0.000    0.000
LGA    D   110_A      D   110_A    16.834     0    0.697   0.623    18.416    0.000    0.000
LGA    F   111_A      F   111_A    18.335     0    0.054   1.452    20.625    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       42     168    168  100.00     322    322  100.00               132
SUMMARY(RMSD_GDC):    17.114         16.825                 17.385            6.913    5.287

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42  132    4.0     13    2.66     9.848     9.117     0.472

LGA_LOCAL      RMSD:   2.656  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  20.394  Number of assigned atoms:   42 
Std_ASGN_ATOMS RMSD:  17.114  Standard rmsd on all 42 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.897498 * X  +   0.440419 * Y  +   0.022984 * Z  + -141.325287
  Y_new =  -0.273220 * X  +   0.514354 * Y  +   0.812890 * Z  +   5.689170
  Z_new =   0.346190 * X  +  -0.735847 * Y  +   0.581963 * Z  + 130.353363 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.295511 -0.353507 -0.901644   [DEG:  -16.9315  -20.2545  -51.6604 ]
ZXZ:  3.113326  0.949655  2.701851   [DEG:  178.3804   54.4112  154.8047 ]
 
# END of job
