
#######################################################
#                                                     #
#                        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        1.78     1.78
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        1.78     1.78
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      25_A - 59_A        0.98     2.19
  LONGEST_CONTINUOUS_SEGMENT:    35      26_A - 60_A        0.67     2.42
  LCS_AVERAGE:     46.64

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     20   60   60      0   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     20   60   60      3   19   33   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     20   60   60     14   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     20   60   60     14   33   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     20   60   60     16   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     20   60   60     23   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     20   60   60     20   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     20   60   60     20   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     20   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     20   60   60     23   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     20   60   60     17   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     20   60   60     23   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     20   60   60     20   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     20   60   60     16   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     20   60   60     16   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     20   60   60     17   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     20   60   60     16   35   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     20   60   60     16   25   46   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     20   60   60     13   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     20   60   60      4   10   30   48   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A      4   60   60      3    4    4    6    8   23   38   54   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A      5   60   60      4    5   18   24   31   43   52   54   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      5   60   60      4   36   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A      5   60   60      4    4    5    7   10   35   42   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A     35   60   60      4   23   37   50   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     35   60   60      3    4   34   43   51   54   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     35   60   60     23   37   42   50   54   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     35   60   60     25   37   45   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     35   60   60     26   37   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     35   60   60     26   37   46   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     35   60   60     26   37   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     35   60   60     26   39   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     35   60   60     26   37   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     35   60   60     26   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     35   60   60     23   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     35   60   60     25   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     35   60   60     23   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     35   60   60     23   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     35   60   60     11   41   48   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     35   60   60      3   17   37   51   55   56   56   57   59   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  82.21  (  46.64  100.00  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     26     41     48     51     55     56     56     57     59     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  43.33  68.33  80.00  85.00  91.67  93.33  93.33  95.00  98.33 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.25   0.63   0.79   0.91   1.14   1.18   1.18   1.28   1.61   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78
GDT RMS_ALL_AT   2.33   1.85   1.83   1.82   1.80   1.81   1.81   1.82   1.79   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    18_A      E    18_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.664     0    0.509   1.247     6.422   62.381   47.679
LGA    D     2_A      D     2_A     2.441     0    0.202   1.110     6.836   66.905   48.214
LGA    K     3_A      K     3_A     0.959     0    0.064   0.581     4.123   88.214   70.529
LGA    A     4_A      A     4_A     1.452     0    0.025   0.032     1.815   83.690   81.524
LGA    A     5_A      A     5_A     0.947     0    0.054   0.058     1.191   88.214   86.857
LGA    C     6_A      C     6_A     0.268     0    0.020   0.028     0.440  100.000  100.000
LGA    A     7_A      A     7_A     0.492     0    0.011   0.019     0.606   95.238   94.286
LGA    D     8_A      D     8_A     0.655     0    0.025   0.068     1.324   92.857   88.274
LGA    G     9_A      G     9_A     0.044     0    0.086   0.086     0.268  100.000  100.000
LGA    I    10_A      I    10_A     0.446     0    0.011   0.044     0.743   95.238   96.429
LGA    A    11_A      A    11_A     0.808     0    0.013   0.017     0.935   90.476   90.476
LGA    A    12_A      A    12_A     0.415     0    0.013   0.018     0.483  100.000  100.000
LGA    V    13_A      V    13_A     0.505     0    0.041   0.048     0.822   92.857   91.837
LGA    K    14_A      K    14_A     1.142     0    0.029   0.639     1.634   83.690   82.540
LGA    A    15_A      A    15_A     1.180     0    0.023   0.032     1.406   81.429   81.429
LGA    R    16_A      R    16_A     0.948     0    0.075   1.115     4.276   81.548   78.571
LGA    V    17_A      V    17_A     1.551     0    0.070   0.169     2.155   72.976   75.374
LGA    E    18_A      E    18_A     2.215     0    0.070   1.028     7.420   68.810   47.989
LGA    K    19_A      K    19_A     1.052     0    0.103   1.003     3.381   81.429   76.085
LGA    L    20_A      L    20_A     3.020     0    0.647   0.536     5.929   43.333   38.274
LGA    A    21_A      A    21_A     6.201     0    0.087   0.091     7.582   36.190   30.381
LGA    P    22_A      P    22_A     6.571     0    0.640   0.642    10.943   23.810   14.014
LGA    E    23_A      E    23_A     1.530     0    0.141   1.098     3.931   63.214   59.524
LGA    A    24_A      A    24_A     4.958     0    0.121   0.125     7.326   33.333   28.667
LGA    V    25_A      V    25_A     3.111     0    0.621   0.673     6.966   57.857   43.197
LGA    P    26_A      P    26_A     3.757     0    0.643   0.655     6.106   55.833   44.558
LGA    Q    27_A      Q    27_A     2.426     0    0.069   1.442     6.366   64.881   49.524
LGA    K    28_A      K    28_A     2.042     0    0.062   0.732     3.800   68.810   63.333
LGA    L    29_A      L    29_A     1.281     0    0.024   0.927     2.996   79.286   76.250
LGA    K    30_A      K    30_A     1.667     0    0.021   0.628     5.921   77.143   60.582
LGA    R    31_A      R    31_A     1.334     0    0.017   0.927     3.708   83.690   67.836
LGA    A    32_A      A    32_A     0.816     0    0.010   0.014     1.007   90.595   90.571
LGA    L    33_A      L    33_A     0.753     0    0.014   1.381     3.022   90.476   81.071
LGA    K    34_A      K    34_A     0.790     0    0.023   1.050     3.559   92.857   75.979
LGA    I    35_A      I    35_A     0.305     0    0.039   0.050     0.448  100.000  100.000
LGA    A    36_A      A    36_A     0.151     0    0.007   0.017     0.260  100.000  100.000
LGA    E    37_A      E    37_A     0.507     0    0.030   0.182     1.670   92.857   87.566
LGA    R    38_A      R    38_A     0.392     0    0.009   1.417     7.102   97.619   68.701
LGA    E    39_A      E    39_A     0.364     0    0.029   0.951     3.851   97.619   83.968
LGA    Q    40_A      Q    40_A     0.620     0    0.016   0.114     0.983   92.857   91.534
LGA    G    41_A      G    41_A     0.981     0    0.015   0.015     1.174   85.952   85.952
LGA    E    42_A      E    42_A     1.086     0    0.026   0.762     2.977   81.429   74.180
LGA    G    43_A      G    43_A     1.070     0    0.055   0.055     1.186   81.429   81.429
LGA    E    44_A      E    44_A     0.823     0    0.026   0.895     4.537   90.476   74.921
LGA    F    45_A      F    45_A     1.174     0    0.060   1.245     8.248   81.429   47.792
LGA    D    46_A      D    46_A     1.335     0    0.010   1.080     4.118   81.429   70.655
LGA    E    47_A      E    47_A     0.870     0    0.022   0.815     4.145   90.476   76.138
LGA    C    48_A      C    48_A     0.264     0    0.059   0.084     0.478  100.000  100.000
LGA    L    49_A      L    49_A     0.478     0    0.018   0.062     1.026   95.238   91.726
LGA    E    50_A      E    50_A     0.642     0    0.021   0.842     4.182   90.476   76.349
LGA    A    51_A      A    51_A     0.424     0    0.024   0.029     0.468  100.000  100.000
LGA    L    52_A      L    52_A     0.243     0    0.031   0.086     0.340  100.000  100.000
LGA    D    53_A      D    53_A     0.246     0    0.020   0.036     0.345  100.000  100.000
LGA    D    54_A      D    54_A     0.352     0    0.040   0.948     4.361  100.000   80.536
LGA    A    55_A      A    55_A     0.467     0    0.029   0.035     0.582   97.619   96.190
LGA    K    56_A      K    56_A     0.405     0    0.012   0.652     1.754  100.000   92.804
LGA    R    57_A      R    57_A     0.343     0    0.064   0.175     0.716   97.619   97.403
LGA    A    58_A      A    58_A     0.428     0    0.125   0.137     1.105   92.976   92.476
LGA    L    59_A      L    59_A     0.788     0    0.038   0.081     1.247   85.952   90.595
LGA    P    60_A      P    60_A     2.016     0    0.032   0.036     2.499   66.786   67.075

# 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):     1.782          1.684                  2.496           83.125   76.497

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     57    1.28    87.083    93.275     4.135

LGA_LOCAL      RMSD:   1.278  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.823  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   1.782  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.281325 * X  +  -0.766647 * Y  +  -0.577156 * Z  +   1.312612
  Y_new =   0.363197 * X  +   0.641770 * Y  +  -0.675440 * Z  +  -6.004264
  Z_new =   0.888225 * X  +  -0.019603 * Y  +   0.458990 * Z  +   7.220697 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.911749 -1.093467 -0.042684   [DEG:   52.2394  -62.6511   -2.4456 ]
ZXZ: -0.707094  1.093939  1.592863   [DEG:  -40.5135   62.6781   91.2643 ]
 
# END of job
