
#######################################################
#                                                     #
#                        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   39 (  329),  selected   39 , name one
# Molecule2: number of CA atoms   39 (  326),  selected   39 , 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:    39       1_A - 39_A        1.47     1.47
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        1.47     1.47
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       6_A - 34_A        0.98     1.74
  LCS_AVERAGE:     69.43

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   39
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     21   39   39      3   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     2_A     K     2_A     21   39   39      4   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     3_A     L     3_A     21   39   39     11   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     W     4_A     W     4_A     21   39   39     11   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     5_A     I     5_A     21   39   39      7   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     6_A     L     6_A     29   39   39     11   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q     7_A     Q     7_A     29   39   39     11   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     8_A     K     8_A     29   39   39     11   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     9_A     I     9_A     29   39   39     11   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    10_A     Y    10_A     29   39   39     11   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    11_A     E    11_A     29   39   39     11   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    12_A     I    12_A     29   39   39     11   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    13_A     M    13_A     29   39   39     11   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    14_A     V    14_A     29   39   39     11   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    15_A     R    15_A     29   39   39      9   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    16_A     L    16_A     29   39   39     10   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    17_A     D    17_A     29   39   39      8   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    18_A     E    18_A     29   39   39      9   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    19_A     E    19_A     29   39   39      4   20   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    20_A     G    20_A     29   39   39      4   10   24   34   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     H    21_A     H    21_A     29   39   39      9   21   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    22_A     G    22_A     29   39   39      9   17   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    23_A     E    23_A     29   39   39     10   17   27   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    24_A     A    24_A     29   39   39     10   20   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    25_A     S    25_A     29   39   39     10   20   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    26_A     L    26_A     29   39   39     10   20   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    27_A     M    27_A     29   39   39     10   20   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    28_A     V    28_A     29   39   39     10   20   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    29_A     S    29_A     29   39   39      9   20   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    30_A     D    30_A     29   39   39     10   20   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    31_A     L    31_A     29   39   39      9   20   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    32_A     I    32_A     29   39   39      9   20   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    33_A     Y    33_A     29   39   39      8   20   29   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    34_A     E    34_A     29   39   39     10   20   28   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F    35_A     F    35_A     27   39   39     10   17   28   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    36_A     M    36_A     22   39   39      7   21   28   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    37_A     K    37_A     22   39   39      7   21   26   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    38_A     R    38_A     20   39   39      4   17   26   37   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    39_A     D    39_A     19   39   39      3    3    3    3   16   34   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_AVERAGE  LCS_A:  89.81  (  69.43  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     11     21     29     37     38     38     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  28.21  53.85  74.36  94.87  97.44  97.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.74   1.01   1.29   1.34   1.34   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47
GDT RMS_ALL_AT   2.35   2.00   1.67   1.48   1.48   1.48   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47   1.47

# Checking swapping
#   possible swapping detected:  Y    10_A      Y    10_A
#   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     1.433     0    0.079   0.203     3.646   79.286   67.440
LGA    K     2_A      K     2_A     1.990     0    0.057   1.230     5.666   72.857   54.233
LGA    L     3_A      L     3_A     1.769     0    0.068   0.086     1.923   72.857   72.857
LGA    W     4_A      W     4_A     1.847     0    0.047   0.154     3.018   72.857   62.755
LGA    I     5_A      I     5_A     1.809     0    0.073   1.305     4.529   79.405   66.071
LGA    L     6_A      L     6_A     0.903     0    0.033   1.395     3.809   90.595   78.095
LGA    Q     7_A      Q     7_A     0.542     0    0.030   1.439     5.637   90.476   67.937
LGA    K     8_A      K     8_A     0.797     0    0.110   0.787     5.788   95.238   72.963
LGA    I     9_A      I     9_A     0.466     0    0.072   1.188     2.883   95.238   82.321
LGA    Y    10_A      Y    10_A     0.728     0    0.050   0.191     0.990   90.476   90.476
LGA    E    11_A      E    11_A     0.951     0    0.069   0.840     1.918   90.476   86.614
LGA    I    12_A      I    12_A     0.359     0    0.025   0.974     2.676   92.857   85.357
LGA    M    13_A      M    13_A     0.839     0    0.018   0.905     2.385   88.214   83.869
LGA    V    14_A      V    14_A     1.034     0    0.034   1.192     3.740   88.214   77.483
LGA    R    15_A      R    15_A     0.292     0    0.043   1.000     3.850   95.238   77.965
LGA    L    16_A      L    16_A     1.178     0    0.045   1.127     3.261   81.548   75.476
LGA    D    17_A      D    17_A     1.725     0    0.038   0.924     3.908   75.000   65.417
LGA    E    18_A      E    18_A     1.032     0    0.067   0.922     4.777   79.286   67.884
LGA    E    19_A      E    19_A     1.546     0    0.291   0.628     3.644   67.262   62.804
LGA    G    20_A      G    20_A     2.590     0    0.062   0.062     2.590   60.952   60.952
LGA    H    21_A      H    21_A     0.928     0    0.151   0.598     2.271   88.214   82.619
LGA    G    22_A      G    22_A     1.618     0    0.040   0.040     1.760   75.000   75.000
LGA    E    23_A      E    23_A     2.044     0    0.049   0.929     4.155   70.833   61.058
LGA    A    24_A      A    24_A     1.283     0    0.051   0.050     1.536   85.952   83.333
LGA    S    25_A      S    25_A     0.462     0    0.032   0.072     1.637   95.238   89.206
LGA    L    26_A      L    26_A     1.645     0    0.037   0.936     4.535   75.000   65.774
LGA    M    27_A      M    27_A     1.794     0    0.032   0.869     2.992   75.000   68.988
LGA    V    28_A      V    28_A     0.804     0    0.058   0.078     1.223   88.214   87.891
LGA    S    29_A      S    29_A     0.852     0    0.055   0.545     2.965   88.214   81.905
LGA    D    30_A      D    30_A     1.430     0    0.042   1.144     6.441   81.429   61.250
LGA    L    31_A      L    31_A     1.192     0    0.041   0.120     1.650   85.952   81.548
LGA    I    32_A      I    32_A     0.616     0    0.025   0.155     0.775   90.476   94.048
LGA    Y    33_A      Y    33_A     0.786     0    0.056   0.160     1.104   90.476   89.722
LGA    E    34_A      E    34_A     1.307     0    0.071   0.836     2.820   81.429   74.974
LGA    F    35_A      F    35_A     1.467     0    0.029   0.545     4.173   79.286   64.286
LGA    M    36_A      M    36_A     1.561     0    0.156   0.630     4.984   75.000   60.595
LGA    K    37_A      K    37_A     1.623     0    0.179   1.309     7.727   72.976   58.836
LGA    R    38_A      R    38_A     1.856     0    0.222   1.640     4.964   70.833   53.766
LGA    D    39_A      D    39_A     3.910     3    0.564   0.524     6.138   52.024   28.155

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       39     156    156  100.00     326    326  100.00                39
SUMMARY(RMSD_GDC):     1.474          1.403                  2.179           81.535   72.357

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    1.47    87.179    93.758     2.478

LGA_LOCAL      RMSD:   1.474  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.474  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   1.474  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.572538 * X  +   0.317233 * Y  +  -0.756018 * Z  + 151.135513
  Y_new =   0.302837 * X  +   0.938728 * Y  +   0.164560 * Z  + -174.692200
  Z_new =   0.761899 * X  +  -0.134733 * Y  +  -0.633528 * Z  + -25.010508 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.655064 -0.866240 -2.932043   [DEG:  152.1240  -49.6319 -167.9937 ]
ZXZ: -1.785120  2.256900  1.745825   [DEG: -102.2798  129.3109  100.0284 ]
 
# END of job
