
#######################################################
#                                                     #
#                        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        1.97     1.97
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        1.97     1.97
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      26_A - 60_A        0.87     2.74
  LCS_AVERAGE:     45.81

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      9   21   31   43   50   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     20   60   60     11   23   39   46   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     20   60   60     14   33   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     20   60   60     14   24   40   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     20   60   60     14   33   41   47   51   54   57   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   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     20   60   60     19   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     20   60   60     19   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     20   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     20   60   60     19   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     20   60   60     14   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     20   60   60     19   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     20   60   60     19   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     20   60   60     14   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     20   60   60     14   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     20   60   60     14   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     20   60   60     11   32   40   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     20   60   60     14   23   39   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     20   60   60     13   34   41   47   51   54   57   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   10   25   42   51   54   57   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    7    8   19   38   52   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A      5   60   60      4   10   16   25   30   43   51   54   57   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      5   60   60      4   33   40   47   51   54   57   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      5   60   60      4    4   31   45   51   54   57   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   11   35   41   49   53   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     35   60   60     20   31   39   46   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     35   60   60     20   32   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     35   60   60     20   32   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     35   60   60     20   32   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     35   60   60     20   32   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     35   60   60      6    7   20   32   47   53   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     35   60   60      8   30   39   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     35   60   60      8   29   36   45   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     35   60   60     19   32   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     35   60   60     19   32   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     35   60   60     20   32   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     35   60   60     20   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     35   60   60     19   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     35   60   60     19   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     35   60   60     19   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     35   60   60     19   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     35   60   60     19   34   41   47   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     35   60   60     13   34   41   47   51   54   57   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   17   37   46   51   54   57   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  81.94  (  45.81  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     20     34     41     47     51     54     57     57     58     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  33.33  56.67  68.33  78.33  85.00  90.00  95.00  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    0.23   0.59   0.80   1.00   1.15   1.32   1.53   1.53   1.64   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97
GDT RMS_ALL_AT   2.50   2.01   2.05   2.04   2.02   1.99   2.00   2.00   2.00   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97

# Checking swapping
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    23_A      E    23_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     3.277     0    0.028   0.218     3.440   55.476   53.631
LGA    D     2_A      D     2_A     2.167     0    0.030   0.138     3.672   69.048   60.536
LGA    K     3_A      K     3_A     1.325     0    0.028   1.092     4.361   79.286   65.979
LGA    A     4_A      A     4_A     1.799     0    0.017   0.018     2.202   77.143   74.667
LGA    A     5_A      A     5_A     1.178     0    0.061   0.068     1.499   85.952   85.048
LGA    C     6_A      C     6_A     0.247     0    0.021   0.041     0.568   97.619   98.413
LGA    A     7_A      A     7_A     0.692     0    0.015   0.021     0.880   90.476   90.476
LGA    D     8_A      D     8_A     0.663     0    0.027   0.068     1.357   95.238   89.464
LGA    G     9_A      G     9_A     0.108     0    0.086   0.086     0.244  100.000  100.000
LGA    I    10_A      I    10_A     0.507     0    0.013   0.040     0.827   92.857   94.048
LGA    A    11_A      A    11_A     0.837     0    0.012   0.017     0.947   90.476   90.476
LGA    A    12_A      A    12_A     0.335     0    0.008   0.015     0.448  100.000  100.000
LGA    V    13_A      V    13_A     0.612     0    0.041   0.045     0.935   92.857   91.837
LGA    K    14_A      K    14_A     1.186     0    0.031   0.642     1.700   83.690   82.540
LGA    A    15_A      A    15_A     1.146     0    0.025   0.036     1.366   81.429   81.429
LGA    R    16_A      R    16_A     0.946     0    0.070   1.117     4.281   81.548   77.706
LGA    V    17_A      V    17_A     1.588     0    0.064   0.162     2.212   72.976   75.374
LGA    E    18_A      E    18_A     2.256     0    0.063   1.044     7.486   68.810   47.090
LGA    K    19_A      K    19_A     1.047     0    0.103   1.004     3.406   81.429   75.185
LGA    L    20_A      L    20_A     3.157     0    0.649   0.536     6.074   42.262   37.024
LGA    A    21_A      A    21_A     6.249     0    0.079   0.080     7.564   34.286   28.857
LGA    P    22_A      P    22_A     6.710     0    0.643   0.647    11.076   23.810   13.878
LGA    E    23_A      E    23_A     1.581     0    0.118   1.199     3.484   65.119   66.931
LGA    A    24_A      A    24_A     4.795     0    0.129   0.133     7.145   36.190   30.952
LGA    V    25_A      V    25_A     3.105     0    0.622   0.674     7.023   57.857   42.721
LGA    P    26_A      P    26_A     3.732     0    0.642   0.656     6.105   55.833   44.558
LGA    Q    27_A      Q    27_A     2.512     0    0.069   1.445     6.634   60.952   46.720
LGA    K    28_A      K    28_A     2.150     0    0.060   0.732     3.694   68.810   63.333
LGA    L    29_A      L    29_A     1.298     0    0.024   0.929     3.087   79.286   75.357
LGA    K    30_A      K    30_A     1.662     0    0.019   0.584     5.576   77.143   61.323
LGA    R    31_A      R    31_A     1.423     0    0.015   0.928     3.865   81.548   67.056
LGA    A    32_A      A    32_A     0.898     0    0.012   0.015     1.088   88.214   86.857
LGA    L    33_A      L    33_A     0.700     0    0.014   1.380     3.052   90.476   81.071
LGA    K    34_A      K    34_A     0.764     0    0.023   1.048     3.709   92.857   75.979
LGA    I    35_A      I    35_A     0.419     0    0.038   0.051     0.556   97.619   96.429
LGA    A    36_A      A    36_A     0.211     0    0.004   0.013     0.333  100.000  100.000
LGA    E    37_A      E    37_A     0.332     0    0.009   0.181     1.533  100.000   91.799
LGA    R    38_A      R    38_A     0.229     0    0.048   1.412     7.223  100.000   69.048
LGA    E    39_A      E    39_A     0.143     0    0.028   0.947     3.910  100.000   84.233
LGA    Q    40_A      Q    40_A     0.356     0    0.591   1.110     2.395   92.976   89.048
LGA    G    41_A      G    41_A     3.574     0    0.035   0.035     3.574   48.333   48.333
LGA    E    42_A      E    42_A     1.969     0    0.030   0.768     4.429   68.810   62.963
LGA    G    43_A      G    43_A     2.697     0    0.158   0.158     2.697   62.857   62.857
LGA    E    44_A      E    44_A     1.488     0    0.064   0.913     4.623   79.286   67.196
LGA    F    45_A      F    45_A     1.595     0    0.061   1.220     8.439   75.000   43.939
LGA    D    46_A      D    46_A     1.802     0    0.009   1.085     4.346   72.857   63.452
LGA    E    47_A      E    47_A     1.135     0    0.028   0.816     4.149   85.952   73.122
LGA    C    48_A      C    48_A     0.337     0    0.061   0.085     0.609   97.619   98.413
LGA    L    49_A      L    49_A     0.716     0    0.020   0.071     1.464   90.476   88.214
LGA    E    50_A      E    50_A     0.918     0    0.020   0.839     4.225   90.476   74.339
LGA    A    51_A      A    51_A     0.615     0    0.029   0.034     0.679   90.476   92.381
LGA    L    52_A      L    52_A     0.347     0    0.031   0.085     0.472  100.000  100.000
LGA    D    53_A      D    53_A     0.408     0    0.020   0.038     0.565  100.000   96.429
LGA    D    54_A      D    54_A     0.475     0    0.042   0.945     4.499  100.000   77.619
LGA    A    55_A      A    55_A     0.516     0    0.027   0.031     0.566   95.238   94.286
LGA    K    56_A      K    56_A     0.407     0    0.010   0.652     1.589  100.000   91.746
LGA    R    57_A      R    57_A     0.333     0    0.064   0.176     0.578   97.619   98.268
LGA    A    58_A      A    58_A     0.406     0    0.125   0.138     1.105   92.976   92.476
LGA    L    59_A      L    59_A     0.765     0    0.039   0.076     1.217   88.333   91.786
LGA    P    60_A      P    60_A     2.066     0    0.032   0.036     2.592   66.786   65.986

# 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):     1.965          1.819                  2.530           80.744   74.515

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     57    1.53    82.500    90.387     3.495

LGA_LOCAL      RMSD:   1.531  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.003  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   1.965  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.158712 * X  +   0.954474 * Y  +   0.252567 * Z  +  -0.423766
  Y_new =   0.129381 * X  +   0.233498 * Y  +  -0.963711 * Z  +  -3.973711
  Z_new =  -0.978811 * X  +   0.185630 * Y  +  -0.086432 * Z  +  10.313801 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.683938  1.364572  2.006560   [DEG:   39.1868   78.1842  114.9674 ]
ZXZ:  0.256313  1.657336 -1.383374   [DEG:   14.6857   94.9584  -79.2615 ]
 
# END of job
