
#######################################################
#                                                     #
#                        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        0.65     0.65
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.65     0.65
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.65     0.65
  LCS_AVERAGE:    100.00

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     39   39   39      6   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     2_A     K     2_A     39   39   39     16   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     3_A     L     3_A     39   39   39     16   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     W     4_A     W     4_A     39   39   39     16   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     5_A     I     5_A     39   39   39     13   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     6_A     L     6_A     39   39   39     16   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q     7_A     Q     7_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     8_A     K     8_A     39   39   39     19   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     9_A     I     9_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    10_A     Y    10_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    11_A     E    11_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    12_A     I    12_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    13_A     M    13_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    14_A     V    14_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    15_A     R    15_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    16_A     L    16_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    17_A     D    17_A     39   39   39     16   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    18_A     E    18_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    19_A     E    19_A     39   39   39     20   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    20_A     G    20_A     39   39   39      8   30   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     H    21_A     H    21_A     39   39   39     20   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    22_A     G    22_A     39   39   39     15   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    23_A     E    23_A     39   39   39     15   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    24_A     A    24_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    25_A     S    25_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    26_A     L    26_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    27_A     M    27_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    28_A     V    28_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    29_A     S    29_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    30_A     D    30_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    31_A     L    31_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    32_A     I    32_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    33_A     Y    33_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    34_A     E    34_A     39   39   39     23   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F    35_A     F    35_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    36_A     M    36_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    37_A     K    37_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    38_A     R    38_A     39   39   39     24   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    39_A     D    39_A     39   39   39      4   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     24     38     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  61.54  97.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.62   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65
GDT RMS_ALL_AT   0.74   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65   0.65

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    11_A      E    11_A
#   possible swapping detected:  Y    33_A      Y    33_A
#   possible swapping detected:  F    35_A      F    35_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     1.075     0    0.447   1.168     6.791   79.524   55.536
LGA    K     2_A      K     2_A     0.932     0    0.064   0.284     2.241   90.476   86.614
LGA    L     3_A      L     3_A     0.743     0    0.076   1.411     3.584   90.476   76.310
LGA    W     4_A      W     4_A     0.742     0    0.022   0.054     1.569   90.476   85.340
LGA    I     5_A      I     5_A     1.073     0    0.080   1.350     4.917   90.595   74.524
LGA    L     6_A      L     6_A     0.614     0    0.038   1.392     3.180   95.238   81.429
LGA    Q     7_A      Q     7_A     0.148     0    0.026   1.419     5.240  100.000   74.603
LGA    K     8_A      K     8_A     0.392     0    0.073   1.031     7.619  100.000   68.148
LGA    I     9_A      I     9_A     0.219     0    0.017   0.101     1.135  100.000   96.488
LGA    Y    10_A      Y    10_A     0.426     0    0.027   0.065     1.299   97.619   92.143
LGA    E    11_A      E    11_A     0.493     0    0.039   0.836     3.156  100.000   79.101
LGA    I    12_A      I    12_A     0.287     0    0.055   0.794     1.908   97.619   88.631
LGA    M    13_A      M    13_A     0.514     0    0.009   0.117     1.018   92.857   90.536
LGA    V    14_A      V    14_A     0.667     0    0.022   0.027     0.916   90.476   90.476
LGA    R    15_A      R    15_A     0.493     0    0.011   1.203     5.465   97.619   72.554
LGA    L    16_A      L    16_A     0.406     0    0.007   0.057     0.617   95.238   97.619
LGA    D    17_A      D    17_A     0.749     0    0.016   0.899     2.892   90.476   78.810
LGA    E    18_A      E    18_A     0.536     0    0.033   0.162     2.504   97.619   83.228
LGA    E    19_A      E    19_A     0.660     0    0.097   0.157     2.022   90.595   81.746
LGA    G    20_A      G    20_A     1.239     0    0.054   0.054     1.782   81.548   81.548
LGA    H    21_A      H    21_A     0.500     0    0.025   0.204     0.728   92.857   92.381
LGA    G    22_A      G    22_A     0.941     0    0.081   0.081     0.941   90.476   90.476
LGA    E    23_A      E    23_A     0.857     0    0.016   0.304     3.542   90.476   75.714
LGA    A    24_A      A    24_A     0.345     0    0.034   0.032     0.415  100.000  100.000
LGA    S    25_A      S    25_A     0.133     0    0.020   0.071     0.637  100.000   98.413
LGA    L    26_A      L    26_A     0.497     0    0.026   0.041     0.876   95.238   92.857
LGA    M    27_A      M    27_A     0.586     0    0.027   0.753     2.015   90.476   85.000
LGA    V    28_A      V    28_A     0.394     0    0.039   0.113     0.555  100.000   98.639
LGA    S    29_A      S    29_A     0.432     0    0.022   0.040     0.586   97.619   96.825
LGA    D    30_A      D    30_A     0.527     0    0.024   0.102     0.723   92.857   91.667
LGA    L    31_A      L    31_A     0.637     0    0.014   1.405     3.782   90.476   79.167
LGA    I    32_A      I    32_A     0.589     0    0.034   0.080     0.746   90.476   95.238
LGA    Y    33_A      Y    33_A     0.732     0    0.051   1.425    10.100   90.476   50.873
LGA    E    34_A      E    34_A     0.816     0    0.027   0.552     3.127   90.476   81.058
LGA    F    35_A      F    35_A     0.768     0    0.015   1.043     4.210   90.476   73.766
LGA    M    36_A      M    36_A     0.572     0    0.092   0.150     2.048   95.238   88.512
LGA    K    37_A      K    37_A     0.373     0    0.055   1.029     4.434  100.000   84.180
LGA    R    38_A      R    38_A     0.383     0    0.073   1.292     5.896  100.000   72.294
LGA    D    39_A      D    39_A     0.846     3    0.599   0.572     1.526   83.810   52.083

# 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):     0.649          0.663                  1.897           93.587   82.937

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.65    99.359    99.798     5.209

LGA_LOCAL      RMSD:   0.649  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.649  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.649  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.624376 * X  +  -0.534824 * Y  +  -0.569313 * Z  + -18.005075
  Y_new =  -0.711695 * X  +   0.089115 * Y  +   0.696813 * Z  +   4.251768
  Z_new =  -0.321938 * X  +   0.840251 * Y  +  -0.436273 * Z  + -18.676054 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.290932  0.327776  2.049699   [DEG: -131.2608   18.7802  117.4391 ]
ZXZ: -2.456557  2.022249 -0.365893   [DEG: -140.7504  115.8663  -20.9641 ]
 
# END of job
