
#######################################################
#                                                     #
#                        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        1.84     1.84
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        1.84     1.84
  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     2.33
  LONGEST_CONTINUOUS_SEGMENT:    35      26_A - 60_A        0.66     2.55
  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      8   18   30   40   51   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     20   60   60      8   23   38   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     20   60   60     13   35   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     20   60   60     12   25   44   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     20   60   60     12   35   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     20   60   60     19   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     20   60   60     18   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     20   60   60     18   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     20   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     20   60   60     22   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     20   60   60     13   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     20   60   60     22   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     20   60   60     20   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     20   60   60     13   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     20   60   60     13   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     20   60   60     13   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     20   60   60     13   32   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     20   60   60     11   25   44   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     20   60   60     12   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     20   60   60      4   11   28   48   54   56   56   57   58   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    4    7   23   36   55   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A      5   60   60      7   11   16   27   36   48   52   55   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      5   60   60      4   34   45   51   54   56   56   57   58   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   17   29   55   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A     35   60   60      4    4   33   49   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     35   60   60      3    4   36   42   49   53   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     35   60   60     27   37   41   49   53   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     35   60   60     27   37   44   50   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     35   60   60     27   37   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     35   60   60     27   37   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     35   60   60     27   37   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     35   60   60     27   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     35   60   60     26   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     35   60   60     26   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     35   60   60     25   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     35   60   60     25   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     35   60   60     22   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     35   60   60     22   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     35   60   60     10   38   45   51   54   56   56   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     35   60   60      3   22   43   51   54   56   56   57   58   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     27     38     45     51     54     56     56     57     58     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  45.00  63.33  75.00  85.00  90.00  93.33  93.33  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    0.24   0.59   0.77   0.98   1.16   1.29   1.29   1.38   1.51   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84
GDT RMS_ALL_AT   2.61   2.02   1.95   1.88   1.86   1.86   1.86   1.88   1.88   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84

# Checking swapping
#   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     3.508     0    0.563   1.346     4.200   48.690   47.798
LGA    D     2_A      D     2_A     2.061     0    0.074   1.059     6.298   71.190   53.036
LGA    K     3_A      K     3_A     0.985     0    0.067   0.589     4.219   85.952   69.524
LGA    A     4_A      A     4_A     1.546     0    0.023   0.024     1.984   81.548   79.810
LGA    A     5_A      A     5_A     1.029     0    0.064   0.070     1.360   85.952   85.048
LGA    C     6_A      C     6_A     0.278     0    0.019   0.027     0.520  100.000   98.413
LGA    A     7_A      A     7_A     0.512     0    0.014   0.025     0.660   92.857   92.381
LGA    D     8_A      D     8_A     0.531     0    0.027   0.068     1.163   95.238   90.595
LGA    G     9_A      G     9_A     0.198     0    0.081   0.081     0.346  100.000  100.000
LGA    I    10_A      I    10_A     0.533     0    0.014   0.046     0.807   92.857   94.048
LGA    A    11_A      A    11_A     0.762     0    0.013   0.017     0.844   90.476   90.476
LGA    A    12_A      A    12_A     0.394     0    0.012   0.017     0.479  100.000  100.000
LGA    V    13_A      V    13_A     0.568     0    0.041   0.048     0.827   92.857   91.837
LGA    K    14_A      K    14_A     1.012     0    0.015   0.152     1.256   83.690   86.455
LGA    A    15_A      A    15_A     1.007     0    0.035   0.046     1.254   83.690   83.238
LGA    R    16_A      R    16_A     0.962     0    0.073   1.120     4.547   83.810   78.009
LGA    V    17_A      V    17_A     1.495     0    0.069   0.170     2.108   75.119   76.599
LGA    E    18_A      E    18_A     2.129     0    0.063   1.051     7.408   68.810   47.090
LGA    K    19_A      K    19_A     0.973     0    0.101   0.998     3.530   83.690   74.550
LGA    L    20_A      L    20_A     3.059     0    0.647   0.538     5.905   43.333   38.274
LGA    A    21_A      A    21_A     6.151     0    0.087   0.089     7.568   36.190   30.381
LGA    P    22_A      P    22_A     6.387     0    0.640   0.643    10.773   27.143   15.918
LGA    E    23_A      E    23_A     1.362     0    0.140   1.098     3.637   65.357   62.011
LGA    A    24_A      A    24_A     4.948     0    0.127   0.132     7.284   33.333   28.667
LGA    V    25_A      V    25_A     2.982     0    0.620   0.675     6.840   59.643   44.218
LGA    P    26_A      P    26_A     3.909     0    0.643   0.656     6.257   54.048   43.537
LGA    Q    27_A      Q    27_A     2.625     0    0.068   1.443     6.401   60.952   47.778
LGA    K    28_A      K    28_A     2.201     0    0.062   0.733     3.739   68.810   63.333
LGA    L    29_A      L    29_A     1.368     0    0.017   0.937     2.920   79.286   77.321
LGA    K    30_A      K    30_A     1.793     0    0.017   0.073     4.375   75.000   61.376
LGA    R    31_A      R    31_A     1.452     0    0.015   0.927     4.022   81.548   66.494
LGA    A    32_A      A    32_A     0.829     0    0.008   0.013     1.060   90.595   90.571
LGA    L    33_A      L    33_A     0.770     0    0.015   1.377     3.042   90.476   81.071
LGA    K    34_A      K    34_A     0.904     0    0.026   1.046     3.378   90.476   75.661
LGA    I    35_A      I    35_A     0.352     0    0.041   0.055     0.535   97.619   96.429
LGA    A    36_A      A    36_A     0.121     0    0.007   0.019     0.353  100.000  100.000
LGA    E    37_A      E    37_A     0.626     0    0.026   0.143     1.836   92.857   85.661
LGA    R    38_A      R    38_A     0.679     0    0.029   1.052     4.427   90.476   84.069
LGA    E    39_A      E    39_A     0.626     0    0.022   0.954     3.677   90.476   80.423
LGA    Q    40_A      Q    40_A     0.824     0    0.029   0.118     1.224   85.952   88.466
LGA    G    41_A      G    41_A     1.138     0    0.070   0.070     1.540   79.286   79.286
LGA    E    42_A      E    42_A     1.137     0    0.034   0.058     1.237   81.429   85.450
LGA    G    43_A      G    43_A     1.312     0    0.065   0.065     1.396   81.429   81.429
LGA    E    44_A      E    44_A     1.152     0    0.034   0.892     4.867   81.429   68.148
LGA    F    45_A      F    45_A     1.437     0    0.053   1.263     8.684   81.429   46.320
LGA    D    46_A      D    46_A     1.564     0    0.033   1.076     4.245   77.143   67.560
LGA    E    47_A      E    47_A     0.965     0    0.021   0.802     4.263   88.214   75.132
LGA    C    48_A      C    48_A     0.395     0    0.063   0.087     0.677   97.619   95.238
LGA    L    49_A      L    49_A     0.688     0    0.023   0.074     1.506   90.476   86.012
LGA    E    50_A      E    50_A     0.814     0    0.021   0.843     4.313   90.476   75.344
LGA    A    51_A      A    51_A     0.459     0    0.026   0.030     0.542   97.619   98.095
LGA    L    52_A      L    52_A     0.298     0    0.031   0.082     0.425  100.000  100.000
LGA    D    53_A      D    53_A     0.389     0    0.019   0.032     0.555  100.000   96.429
LGA    D    54_A      D    54_A     0.440     0    0.045   0.942     4.431  100.000   79.345
LGA    A    55_A      A    55_A     0.453     0    0.029   0.035     0.517   97.619   98.095
LGA    K    56_A      K    56_A     0.348     0    0.015   0.649     1.575  100.000   92.804
LGA    R    57_A      R    57_A     0.382     0    0.051   0.170     0.819   97.619   96.537
LGA    A    58_A      A    58_A     0.384     0    0.126   0.136     0.909   95.238   94.286
LGA    L    59_A      L    59_A     0.611     0    0.017   0.066     0.951   92.857   94.048
LGA    P    60_A      P    60_A     1.633     0    0.034   0.048     2.247   75.000   71.769

# 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):     1.843          1.712                  2.446           82.248   76.365

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     57    1.38    85.833    92.317     3.847

LGA_LOCAL      RMSD:   1.382  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.879  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   1.843  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.899590 * X  +   0.378130 * Y  +   0.218528 * Z  +  -3.268175
  Y_new =  -0.350487 * X  +   0.326526 * Y  +   0.877804 * Z  +  -4.005976
  Z_new =   0.260569 * X  +  -0.866255 * Y  +   0.426270 * Z  +  18.947475 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.371515 -0.263611 -1.113502   [DEG:  -21.2862  -15.1038  -63.7990 ]
ZXZ:  2.897603  1.130431  2.849403   [DEG:  166.0204   64.7689  163.2588 ]
 
# END of job
