
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , 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:    60       1_A - 60_A        2.23     2.23
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40       1_A - 40_A        2.00     2.66
  LCS_AVERAGE:     64.44

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28      26_A - 53_A        0.89     3.84
  LCS_AVERAGE:     39.36

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     D     1_A     D     1_A     22   40   60      4    8   17   34   42   48   53   56   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     22   40   60     12   22   32   39   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     22   40   60     16   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     22   40   60     12   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     22   40   60     12   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     22   40   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     22   40   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     22   40   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     22   40   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     22   40   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     22   40   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     22   40   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     22   40   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     22   40   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     22   40   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     22   40   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     22   40   60     12   27   32   39   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     22   40   60      6   20   32   39   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     22   40   60     15   27   32   39   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     22   40   60      4   19   31   38   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     22   40   60      2    3   17   38   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     22   40   60      4   16   21   34   42   48   53   56   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      4   40   60      4    4    8   37   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A      4   40   60      4    4    5    7    8   10   29   50   56   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A      4   40   60      4   19   32   39   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     28   40   60      7   21   28   33   38   49   52   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     28   40   60     13   21   28   35   44   49   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     28   40   60     13   21   28   35   45   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     28   40   60     13   21   28   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     28   40   60     13   21   28   39   47   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     28   40   60     13   21   28   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     28   40   60     13   21   28   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     28   40   60     13   21   28   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     28   40   60     13   21   28   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     28   40   60     13   21   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     28   40   60     13   21   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     28   40   60     13   21   29   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     28   40   60     13   21   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     28   40   60     13   25   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     28   40   60     13   19   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     28   36   60     13   21   28   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     28   36   60      6   21   28   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     28   36   60      7    7   28   35   42   49   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     28   36   60      7   17   28   35   44   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     28   36   60      8   21   28   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     28   36   60      7   21   28   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     28   36   60      9   21   29   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     28   36   60     10   21   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     28   36   60     10   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     28   36   60     10   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     28   36   60     10   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     28   36   60     10   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     28   36   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     20   36   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     20   36   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     20   36   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     20   36   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     20   36   60     17   27   32   39   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     20   36   60     17   27   32   41   48   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     17   36   60      3    3    3   34   43   49   53   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  67.94  (  39.36   64.44  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     17     27     32     41     48     53     55     57     58     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  28.33  45.00  53.33  68.33  80.00  88.33  91.67  95.00  96.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   0.58   0.85   1.39   1.48   1.72   1.85   1.98   2.04   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23
GDT RMS_ALL_AT   2.41   2.45   2.36   2.32   2.26   2.23   2.25   2.25   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  D     8_A      D     8_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  F    45_A      F    45_A
#   possible swapping detected:  D    46_A      D    46_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  D    54_A      D    54_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     4.384     0    0.009   1.176     4.918   42.143   40.476
LGA    D     2_A      D     2_A     2.243     0    0.079   0.197     3.726   69.048   61.429
LGA    K     3_A      K     3_A     1.817     0    0.071   1.085     4.194   72.857   63.810
LGA    A     4_A      A     4_A     2.081     0    0.019   0.021     2.346   68.810   68.000
LGA    A     5_A      A     5_A     1.631     0    0.055   0.064     1.803   77.143   76.286
LGA    C     6_A      C     6_A     1.023     0    0.047   0.817     2.586   83.690   78.889
LGA    A     7_A      A     7_A     1.089     0    0.031   0.028     1.286   81.429   81.429
LGA    D     8_A      D     8_A     1.085     0    0.029   0.157     1.781   85.952   82.619
LGA    G     9_A      G     9_A     0.724     0    0.034   0.034     0.855   90.476   90.476
LGA    I    10_A      I    10_A     0.682     0    0.032   0.077     0.878   90.476   90.476
LGA    A    11_A      A    11_A     1.018     0    0.043   0.051     1.138   83.690   83.238
LGA    A    12_A      A    12_A     0.887     0    0.041   0.038     1.000   88.214   88.667
LGA    V    13_A      V    13_A     0.509     0    0.057   0.072     0.803   90.476   94.558
LGA    K    14_A      K    14_A     0.928     0    0.027   0.668     4.648   85.952   67.566
LGA    A    15_A      A    15_A     1.305     0    0.060   0.070     1.389   81.429   81.429
LGA    R    16_A      R    16_A     0.908     0    0.030   0.856     2.697   83.690   80.909
LGA    V    17_A      V    17_A     1.826     0    0.046   0.107     2.925   69.048   67.279
LGA    E    18_A      E    18_A     2.664     0    0.110   0.923     5.170   59.167   47.937
LGA    K    19_A      K    19_A     1.487     0    0.123   1.011     2.673   77.143   76.878
LGA    L    20_A      L    20_A     2.834     0    0.699   0.586     5.960   46.667   46.726
LGA    A    21_A      A    21_A     2.792     0    0.536   0.598     2.889   61.071   61.810
LGA    P    22_A      P    22_A     5.114     0    0.627   0.827     9.542   36.429   22.585
LGA    E    23_A      E    23_A     2.593     0    0.148   1.341     6.946   46.905   35.926
LGA    A    24_A      A    24_A     5.871     0    0.232   0.261     7.803   26.429   22.571
LGA    V    25_A      V    25_A     2.641     0    0.623   0.658     6.274   57.500   45.918
LGA    P    26_A      P    26_A     4.489     0    0.622   0.996     6.743   45.595   35.714
LGA    Q    27_A      Q    27_A     3.666     0    0.045   1.187     6.519   46.667   38.254
LGA    K    28_A      K    28_A     3.079     0    0.053   0.863     4.247   53.571   48.677
LGA    L    29_A      L    29_A     2.429     0    0.054   1.094     2.870   60.952   66.310
LGA    K    30_A      K    30_A     2.765     0    0.014   0.028     4.315   59.048   50.423
LGA    R    31_A      R    31_A     2.304     0    0.018   1.578     6.657   66.905   50.216
LGA    A    32_A      A    32_A     1.841     0    0.029   0.028     1.998   72.857   72.857
LGA    L    33_A      L    33_A     2.008     0    0.027   1.395     2.623   70.833   71.250
LGA    K    34_A      K    34_A     1.883     0    0.049   1.028     3.164   72.857   65.132
LGA    I    35_A      I    35_A     1.336     0    0.037   0.088     1.565   81.548   81.488
LGA    A    36_A      A    36_A     1.444     0    0.025   0.023     1.697   79.286   78.000
LGA    E    37_A      E    37_A     1.620     0    0.080   0.252     3.012   77.143   68.677
LGA    R    38_A      R    38_A     1.196     0    0.027   0.904     2.817   83.690   81.991
LGA    E    39_A      E    39_A     0.584     0    0.035   1.064     3.956   88.214   81.534
LGA    Q    40_A      Q    40_A     1.437     0    0.054   1.150     4.608   77.143   63.651
LGA    G    41_A      G    41_A     2.270     0    0.085   0.085     2.559   64.881   64.881
LGA    E    42_A      E    42_A     2.003     0    0.662   0.986     2.402   70.833   72.063
LGA    G    43_A      G    43_A     3.891     0    0.081   0.081     3.891   45.000   45.000
LGA    E    44_A      E    44_A     3.122     0    0.051   0.838     3.838   55.476   55.026
LGA    F    45_A      F    45_A     2.064     0    0.038   0.437     2.681   68.810   66.320
LGA    D    46_A      D    46_A     1.847     0    0.017   1.138     4.536   72.857   60.952
LGA    E    47_A      E    47_A     1.832     0    0.059   0.679     3.501   72.857   61.958
LGA    C    48_A      C    48_A     1.412     0    0.077   0.132     1.730   81.548   78.651
LGA    L    49_A      L    49_A     0.589     0    0.037   0.112     0.907   92.857   92.857
LGA    E    50_A      E    50_A     1.118     0    0.028   0.788     4.377   83.690   67.831
LGA    A    51_A      A    51_A     1.206     0    0.042   0.040     1.328   81.429   81.429
LGA    L    52_A      L    52_A     0.644     0    0.038   0.115     1.563   95.238   88.393
LGA    D    53_A      D    53_A     0.783     0    0.023   0.786     2.586   88.214   82.917
LGA    D    54_A      D    54_A     1.336     0    0.029   0.176     2.303   81.429   75.119
LGA    A    55_A      A    55_A     1.169     0    0.052   0.057     1.169   85.952   85.048
LGA    K    56_A      K    56_A     0.552     0    0.056   0.653     2.307   90.476   87.937
LGA    R    57_A      R    57_A     1.348     0    0.095   1.107     3.964   79.286   74.069
LGA    A    58_A      A    58_A     1.327     0    0.172   0.192     2.059   77.262   78.095
LGA    L    59_A      L    59_A     0.744     0    0.585   0.580     1.509   83.810   88.333
LGA    P    60_A      P    60_A     3.856     0    0.624   0.929     7.944   48.452   33.061

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     2.225          2.161                  2.680           71.875   67.533

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     57    1.98    77.083    78.136     2.736

LGA_LOCAL      RMSD:   1.983  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.251  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   2.225  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.249155 * X  +   0.201732 * Y  +  -0.947220 * Z  +  28.707794
  Y_new =   0.948344 * X  +   0.147505 * Y  +   0.280865 * Z  +  23.873968
  Z_new =   0.196379 * X  +  -0.968270 * Y  +  -0.154560 * Z  +  15.089470 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.313876 -0.197664 -1.729085   [DEG:   75.2795  -11.3253  -99.0693 ]
ZXZ: -1.859053  1.725978  2.941493   [DEG: -106.5159   98.8913  168.5351 ]
 
# END of job
