
#######################################################
#                                                     #
#                        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        1.69     1.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        1.69     1.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      26_A - 60_A        0.89     2.43
  LCS_AVERAGE:     47.75

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   60   60      8   24   36   44   52   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     22   60   60      5   31   44   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     22   60   60      5   24   44   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     22   60   60     12   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     22   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     22   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     22   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     22   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     22   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     22   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     22   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     22   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     22   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     22   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     22   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     22   60   60     13   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     22   60   60     12   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     22   60   60     12   31   43   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     22   60   60     12   31   44   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     22   60   60      6   26   44   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     22   60   60      6   26   43   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     22   60   60     12   28   43   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      4   60   60      3    3    5    9   29   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A      3   60   60      3    3    5    6    8   16   51   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A      3   60   60      3    3    5   18   43   51   54   57   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     35   60   60      3   17   34   48   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     35   60   60     16   29   34   40   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     35   60   60     10   26   37   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     35   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     35   60   60     20   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     35   60   60     20   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     35   60   60     20   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     35   60   60     20   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     35   60   60     20   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     35   60   60     20   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     35   60   60     20   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     35   60   60     20   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     35   60   60     20   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     35   60   60     20   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     35   60   60     20   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     35   60   60     20   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     35   60   60     20   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     35   60   60     20   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     35   60   60     10   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     35   60   60     20   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     35   60   60     20   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     35   60   60     20   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     35   60   60     19   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     35   60   60      8   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     35   60   60     18   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     35   60   60     20   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     35   60   60      9   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     35   60   60     12   28   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     35   60   60     12   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     35   60   60     20   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     35   60   60     20   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     35   60   60     12   29   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     35   60   60     12   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     35   60   60     15   31   45   53   55   56   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     35   60   60      3    3   13   29   38   51   58   59   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  82.58  (  47.75  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     31     45     53     55     56     58     59     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  33.33  51.67  75.00  88.33  91.67  93.33  96.67  98.33 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.69   1.03   1.19   1.25   1.32   1.45   1.57   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69
GDT RMS_ALL_AT   2.50   1.83   1.77   1.71   1.73   1.71   1.71   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69   1.69

# Checking swapping
#   possible swapping detected:  E    37_A      E    37_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  E    44_A      E    44_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     3.071     0    0.335   1.299     4.140   56.190   60.536
LGA    D     2_A      D     2_A     1.336     0    0.072   0.230     3.749   83.810   69.821
LGA    K     3_A      K     3_A     1.513     0    0.076   1.167     3.018   77.143   67.831
LGA    A     4_A      A     4_A     1.188     0    0.047   0.051     1.274   83.690   83.238
LGA    A     5_A      A     5_A     0.599     0    0.080   0.079     0.859   90.476   92.381
LGA    C     6_A      C     6_A     1.111     0    0.038   0.819     2.588   83.690   78.889
LGA    A     7_A      A     7_A     1.147     0    0.036   0.040     1.212   81.429   81.429
LGA    D     8_A      D     8_A     1.167     0    0.059   0.955     4.892   81.429   66.488
LGA    G     9_A      G     9_A     1.124     0    0.040   0.040     1.172   85.952   85.952
LGA    I    10_A      I    10_A     0.757     0    0.018   0.095     0.893   90.476   90.476
LGA    A    11_A      A    11_A     0.935     0    0.030   0.041     1.094   88.214   86.857
LGA    A    12_A      A    12_A     1.043     0    0.033   0.042     1.137   81.429   81.429
LGA    V    13_A      V    13_A     0.966     0    0.029   0.972     3.134   85.952   78.299
LGA    K    14_A      K    14_A     1.143     0    0.045   1.025     4.456   81.429   69.577
LGA    A    15_A      A    15_A     1.001     0    0.059   0.058     1.051   85.952   85.048
LGA    R    16_A      R    16_A     0.847     0    0.039   0.980     2.745   90.476   75.801
LGA    V    17_A      V    17_A     1.063     0    0.055   0.122     1.524   83.690   82.789
LGA    E    18_A      E    18_A     1.505     0    0.131   0.920     4.943   77.143   64.180
LGA    K    19_A      K    19_A     1.159     0    0.117   0.867     4.075   81.429   72.804
LGA    L    20_A      L    20_A     1.563     0    0.077   0.977     3.535   75.000   68.274
LGA    A    21_A      A    21_A     1.922     0    0.161   0.211     2.230   75.000   72.952
LGA    P    22_A      P    22_A     1.976     0    0.602   0.565     3.542   66.905   59.728
LGA    E    23_A      E    23_A     3.319     0    0.669   1.363     8.669   59.167   32.963
LGA    A    24_A      A    24_A     4.810     0    0.571   0.569     6.031   30.833   28.952
LGA    V    25_A      V    25_A     5.065     0    0.606   1.396     9.188   37.976   25.238
LGA    P    26_A      P    26_A     2.479     0    0.662   0.673     4.320   71.190   64.762
LGA    Q    27_A      Q    27_A     2.591     0    0.082   1.365     5.395   62.857   50.370
LGA    K    28_A      K    28_A     2.142     0    0.046   0.810     3.433   68.810   64.127
LGA    L    29_A      L    29_A     0.702     0    0.041   0.967     3.605   88.214   77.083
LGA    K    30_A      K    30_A     1.550     0    0.035   1.037     6.678   79.286   56.667
LGA    R    31_A      R    31_A     1.392     0    0.028   1.223     6.222   83.690   63.247
LGA    A    32_A      A    32_A     0.781     0    0.029   0.038     0.899   90.476   90.476
LGA    L    33_A      L    33_A     0.531     0    0.036   1.147     3.172   90.476   82.202
LGA    K    34_A      K    34_A     1.009     0    0.038   1.214     4.006   88.214   72.381
LGA    I    35_A      I    35_A     0.547     0    0.037   0.656     3.167   95.238   87.798
LGA    A    36_A      A    36_A     0.511     0    0.037   0.045     0.906   92.857   92.381
LGA    E    37_A      E    37_A     1.032     0    0.029   0.684     4.203   83.690   65.556
LGA    R    38_A      R    38_A     0.768     0    0.026   1.342     7.986   88.214   63.377
LGA    E    39_A      E    39_A     1.037     0    0.029   0.225     1.569   81.548   86.508
LGA    Q    40_A      Q    40_A     1.630     0    0.042   0.679     1.980   75.000   73.810
LGA    G    41_A      G    41_A     1.823     0    0.099   0.099     2.271   70.833   70.833
LGA    E    42_A      E    42_A     1.854     0    0.211   1.099     4.154   75.000   59.312
LGA    G    43_A      G    43_A     1.702     0    0.102   0.102     1.911   75.000   75.000
LGA    E    44_A      E    44_A     1.600     0    0.165   0.891     4.652   77.143   64.074
LGA    F    45_A      F    45_A     1.655     0    0.052   1.369     8.752   72.857   42.468
LGA    D    46_A      D    46_A     1.765     0    0.071   1.114     4.999   77.143   61.429
LGA    E    47_A      E    47_A     1.282     0    0.042   0.790     4.511   83.690   69.735
LGA    C    48_A      C    48_A     1.131     0    0.041   0.081     1.493   85.952   84.444
LGA    L    49_A      L    49_A     0.805     0    0.042   1.435     3.144   90.476   78.155
LGA    E    50_A      E    50_A     0.374     0    0.040   0.637     3.669   97.619   76.508
LGA    A    51_A      A    51_A     0.400     0    0.048   0.048     0.509   97.619   98.095
LGA    L    52_A      L    52_A     0.960     0    0.046   1.431     3.224   88.214   78.810
LGA    D    53_A      D    53_A     1.218     0    0.039   0.677     3.454   83.690   75.476
LGA    D    54_A      D    54_A     0.760     0    0.035   1.066     3.431   90.476   78.036
LGA    A    55_A      A    55_A     0.100     0    0.038   0.056     0.381  100.000  100.000
LGA    K    56_A      K    56_A     0.725     0    0.049   0.641     2.862   90.476   83.069
LGA    R    57_A      R    57_A     1.100     0    0.126   0.890     3.343   81.548   74.113
LGA    A    58_A      A    58_A     0.805     0    0.181   0.177     1.660   86.071   86.952
LGA    L    59_A      L    59_A     0.446     0    0.565   1.517     4.622   90.833   76.726
LGA    P    60_A      P    60_A     3.512     0    0.662   0.657     7.010   53.690   39.048

# 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):     1.685          1.595                  2.545           80.383   72.083

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     59    1.57    84.583    92.266     3.528

LGA_LOCAL      RMSD:   1.572  Number of atoms:   59  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.691  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   1.685  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.291631 * X  +  -0.773217 * Y  +  -0.563104 * Z  +  33.615471
  Y_new =   0.802800 * X  +  -0.517924 * Y  +   0.295410 * Z  +   7.840695
  Z_new =  -0.520061 * X  +  -0.365910 * Y  +   0.771781 * Z  +  14.358909 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.919241  0.546922 -0.442722   [DEG:  109.9644   31.3363  -25.3661 ]
ZXZ: -2.053937  0.689158 -2.183928   [DEG: -117.6819   39.4859 -125.1298 ]
 
# END of job
