
#######################################################
#                                                     #
#                        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        1.86     1.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        1.86     1.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      25_A - 59_A        1.00     2.33
  LONGEST_CONTINUOUS_SEGMENT:    35      26_A - 60_A        0.69     2.57
  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      9   23   33   47   55   56   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   38   50   55   56   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     13   34   45   50   55   56   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   26   45   50   55   56   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   34   45   50   55   56   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   36   45   50   55   56   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     16   36   45   50   55   56   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     16   36   45   50   55   56   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     27   36   45   50   55   56   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     20   36   45   50   55   56   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   36   45   50   55   56   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     22   36   45   50   55   56   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     18   36   45   50   55   56   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   36   45   50   55   56   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   36   45   50   55   56   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   36   45   50   55   56   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   30   45   50   55   56   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   42   50   55   56   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   36   45   50   55   56   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   45   55   56   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    6    8   22   39   54   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A      5   60   60      4   13   16   25   29   43   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   33   45   50   55   56   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     35   60   60      4    4   33   47   55   56   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    4   34   42   48   54   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     27   36   42   49   53   56   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     27   36   43   49   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     27   36   45   50   55   56   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     25   36   45   50   55   56   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     25   36   45   50   55   56   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   36   45   50   55   56   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     22   36   45   50   55   56   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     17   36   45   50   55   56   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     17   36   45   50   55   56   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      6   36   45   50   55   56   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   13   33   48   55   56   57   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     36     45     50     55     56     57     57     58     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  45.00  60.00  75.00  83.33  91.67  93.33  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    0.25   0.53   0.80   0.98   1.25   1.29   1.38   1.38   1.51   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86
GDT RMS_ALL_AT   2.59   2.38   2.00   1.90   1.87   1.88   1.90   1.90   1.89   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86

# 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     2.841     0    0.226   1.273     4.020   59.524   55.893
LGA    D     2_A      D     2_A     2.038     0    0.093   1.073     6.240   73.095   54.643
LGA    K     3_A      K     3_A     0.983     0    0.030   0.583     4.093   85.952   69.524
LGA    A     4_A      A     4_A     1.533     0    0.013   0.016     1.937   79.286   78.000
LGA    A     5_A      A     5_A     1.002     0    0.053   0.061     1.305   85.952   85.048
LGA    C     6_A      C     6_A     0.165     0    0.018   0.023     0.473  100.000  100.000
LGA    A     7_A      A     7_A     0.555     0    0.013   0.021     0.705   92.857   92.381
LGA    D     8_A      D     8_A     0.588     0    0.025   0.064     1.323   95.238   89.464
LGA    G     9_A      G     9_A     0.152     0    0.081   0.081     0.305  100.000  100.000
LGA    I    10_A      I    10_A     0.518     0    0.013   0.038     0.787   92.857   94.048
LGA    A    11_A      A    11_A     0.762     0    0.011   0.016     0.852   90.476   90.476
LGA    A    12_A      A    12_A     0.334     0    0.008   0.015     0.431  100.000  100.000
LGA    V    13_A      V    13_A     0.607     0    0.042   0.051     0.921   92.857   91.837
LGA    K    14_A      K    14_A     1.164     0    0.033   0.641     1.576   83.690   82.540
LGA    A    15_A      A    15_A     1.146     0    0.031   0.039     1.419   81.429   81.429
LGA    R    16_A      R    16_A     0.971     0    0.072   1.098     3.757   81.548   79.740
LGA    V    17_A      V    17_A     1.601     0    0.063   0.159     2.210   72.976   75.374
LGA    E    18_A      E    18_A     2.230     0    0.059   1.044     7.429   68.810   47.090
LGA    K    19_A      K    19_A     1.110     0    0.071   1.036     3.392   81.429   74.497
LGA    L    20_A      L    20_A     3.165     0    0.638   0.531     6.024   42.262   38.333
LGA    A    21_A      A    21_A     6.238     0    0.084   0.086     7.585   34.286   28.857
LGA    P    22_A      P    22_A     6.578     0    0.645   0.649    10.973   23.810   14.014
LGA    E    23_A      E    23_A     1.482     0    0.115   1.200     3.338   65.357   67.937
LGA    A    24_A      A    24_A     4.944     0    0.128   0.132     7.281   33.333   28.667
LGA    V    25_A      V    25_A     3.074     0    0.623   0.674     6.948   57.857   43.197
LGA    P    26_A      P    26_A     3.821     0    0.642   0.655     6.182   55.833   44.558
LGA    Q    27_A      Q    27_A     2.561     0    0.070   1.442     6.430   60.952   47.778
LGA    K    28_A      K    28_A     2.165     0    0.063   0.731     3.758   68.810   63.333
LGA    L    29_A      L    29_A     1.330     0    0.026   0.925     2.968   79.286   76.250
LGA    K    30_A      K    30_A     1.740     0    0.020   0.587     5.715   77.143   60.582
LGA    R    31_A      R    31_A     1.449     0    0.016   0.927     3.970   81.548   67.836
LGA    A    32_A      A    32_A     0.880     0    0.011   0.015     1.088   90.595   90.571
LGA    L    33_A      L    33_A     0.773     0    0.015   1.379     3.055   90.476   79.940
LGA    K    34_A      K    34_A     0.870     0    0.023   1.053     3.488   90.476   75.661
LGA    I    35_A      I    35_A     0.375     0    0.041   0.052     0.530   97.619   96.429
LGA    A    36_A      A    36_A     0.115     0    0.008   0.019     0.281  100.000  100.000
LGA    E    37_A      E    37_A     0.546     0    0.035   0.180     1.743   92.857   87.566
LGA    R    38_A      R    38_A     0.501     0    0.009   1.418     7.180   92.857   66.970
LGA    E    39_A      E    39_A     0.356     0    0.023   0.954     3.841   95.238   82.910
LGA    Q    40_A      Q    40_A     0.720     0    0.016   0.979     2.992   88.214   82.804
LGA    G    41_A      G    41_A     1.144     0    0.018   0.018     1.397   81.429   81.429
LGA    E    42_A      E    42_A     1.255     0    0.029   0.762     3.057   81.429   73.386
LGA    G    43_A      G    43_A     1.312     0    0.052   0.052     1.452   81.429   81.429
LGA    E    44_A      E    44_A     1.014     0    0.041   0.894     4.630   81.429   69.153
LGA    F    45_A      F    45_A     1.467     0    0.056   1.239     8.732   81.429   46.320
LGA    D    46_A      D    46_A     1.646     0    0.033   1.078     4.165   77.143   68.512
LGA    E    47_A      E    47_A     1.042     0    0.025   0.804     4.124   85.952   74.127
LGA    C    48_A      C    48_A     0.404     0    0.064   0.086     0.637   95.238   93.651
LGA    L    49_A      L    49_A     0.739     0    0.022   0.075     1.545   90.476   86.012
LGA    E    50_A      E    50_A     0.880     0    0.020   0.842     4.275   90.476   74.339
LGA    A    51_A      A    51_A     0.531     0    0.025   0.030     0.615   95.238   96.190
LGA    L    52_A      L    52_A     0.324     0    0.031   0.081     0.448  100.000  100.000
LGA    D    53_A      D    53_A     0.391     0    0.020   0.032     0.540  100.000   96.429
LGA    D    54_A      D    54_A     0.466     0    0.047   0.939     4.485   97.619   76.429
LGA    A    55_A      A    55_A     0.515     0    0.031   0.036     0.600   95.238   94.286
LGA    K    56_A      K    56_A     0.420     0    0.009   0.646     1.531   97.619   90.688
LGA    R    57_A      R    57_A     0.446     0    0.056   0.183     0.969   95.238   94.805
LGA    A    58_A      A    58_A     0.485     0    0.128   0.141     1.124   92.976   92.476
LGA    L    59_A      L    59_A     0.775     0    0.033   0.094     1.427   85.952   89.405
LGA    P    60_A      P    60_A     2.212     0    0.024   0.024     2.565   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):     1.857          1.728                  2.506           81.831   75.520

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     57    1.38    84.583    92.142     3.844

LGA_LOCAL      RMSD:   1.383  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.896  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   1.857  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.290069 * X  +   0.914817 * Y  +   0.281016 * Z  +  -0.401721
  Y_new =   0.411829 * X  +   0.145739 * Y  +  -0.899532 * Z  +  -5.623127
  Z_new =  -0.863862 * X  +   0.376657 * Y  +  -0.334473 * Z  +   9.674108 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.957161  1.042886  2.296945   [DEG:   54.8413   59.7530  131.6053 ]
ZXZ:  0.302797  1.911843 -1.159633   [DEG:   17.3490  109.5405  -66.4421 ]
 
# END of job
