
#######################################################
#                                                     #
#                        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        1.35     1.35
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        1.35     1.35
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        1.00     1.43
  LONGEST_CONTINUOUS_SEGMENT:    33       6_A - 38_A        0.95     1.44
  LCS_AVERAGE:     79.55

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      5   14   20   21   35   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     12   16   23   37   37   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     12   25   33   37   37   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     12   16   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     5_A     I     5_A     33   39   39     12   16   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     6_A     L     6_A     33   39   39     12   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q     7_A     Q     7_A     33   39   39     12   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     8_A     K     8_A     33   39   39     12   23   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     9_A     I     9_A     33   39   39     12   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    10_A     Y    10_A     33   39   39     12   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    11_A     E    11_A     33   39   39     12   20   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    12_A     I    12_A     33   39   39     12   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    13_A     M    13_A     33   39   39     12   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    14_A     V    14_A     33   39   39     12   16   32   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    15_A     R    15_A     33   39   39      5   24   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    16_A     L    16_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    17_A     D    17_A     33   39   39      5   17   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    18_A     E    18_A     33   39   39     12   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    19_A     E    19_A     33   39   39     14   24   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    20_A     G    20_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     H    21_A     H    21_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    22_A     G    22_A     33   39   39      5   21   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    23_A     E    23_A     33   39   39     14   20   32   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    24_A     A    24_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    25_A     S    25_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    26_A     L    26_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    27_A     M    27_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    28_A     V    28_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    29_A     S    29_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    30_A     D    30_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    31_A     L    31_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    32_A     I    32_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    33_A     Y    33_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    34_A     E    34_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F    35_A     F    35_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    36_A     M    36_A     33   39   39     14   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    37_A     K    37_A     33   39   39     12   25   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    38_A     R    38_A     33   39   39      4   20   33   37   37   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    39_A     D    39_A      4   39   39      3    4    5   12   26   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_AVERAGE  LCS_A:  93.18  (  79.55  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     14     25     33     37     37     38     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  35.90  64.10  84.62  94.87  94.87  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    0.30   0.73   0.94   1.11   1.11   1.24   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35
GDT RMS_ALL_AT   2.25   1.47   1.39   1.37   1.37   1.36   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  D    17_A      D    17_A
#   possible swapping detected:  E    19_A      E    19_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     3.590     0    0.286   1.165     6.666   41.190   37.083
LGA    K     2_A      K     2_A     2.453     0    0.080   1.008     4.970   66.905   57.937
LGA    L     3_A      L     3_A     0.321     0    0.098   0.946     4.476   92.976   75.833
LGA    W     4_A      W     4_A     1.443     0    0.042   1.138     6.391   81.429   50.544
LGA    I     5_A      I     5_A     1.845     0    0.053   1.394     5.575   79.405   62.917
LGA    L     6_A      L     6_A     0.953     0    0.020   0.981     2.372   90.595   86.190
LGA    Q     7_A      Q     7_A     0.586     0    0.053   0.835     3.819   92.857   78.571
LGA    K     8_A      K     8_A     0.794     0    0.070   0.722     6.394   95.238   66.878
LGA    I     9_A      I     9_A     0.553     0    0.043   1.261     4.386   92.857   76.845
LGA    Y    10_A      Y    10_A     1.195     0    0.035   0.130     3.741   83.690   67.460
LGA    E    11_A      E    11_A     1.216     0    0.041   0.713     5.067   83.690   64.339
LGA    I    12_A      I    12_A     0.260     0    0.043   0.881     2.621   95.238   84.286
LGA    M    13_A      M    13_A     1.120     0    0.000   1.067     2.777   83.690   75.298
LGA    V    14_A      V    14_A     1.625     0    0.029   1.231     4.838   79.286   69.456
LGA    R    15_A      R    15_A     1.029     0    0.046   0.940     4.408   85.952   68.701
LGA    L    16_A      L    16_A     1.000     0    0.014   1.170     3.147   85.952   77.679
LGA    D    17_A      D    17_A     1.475     0    0.017   0.992     5.677   81.429   63.333
LGA    E    18_A      E    18_A     0.618     0    0.085   0.271     2.681   90.476   79.206
LGA    E    19_A      E    19_A     1.347     0    0.703   1.113     5.338   68.452   53.175
LGA    G    20_A      G    20_A     1.231     0    0.235   0.235     2.885   75.476   75.476
LGA    H    21_A      H    21_A     0.894     0    0.135   0.729     4.683   92.857   71.619
LGA    G    22_A      G    22_A     1.473     0    0.045   0.045     1.495   81.429   81.429
LGA    E    23_A      E    23_A     1.719     0    0.045   0.853     4.154   77.143   63.069
LGA    A    24_A      A    24_A     1.155     0    0.046   0.044     1.315   85.952   85.048
LGA    S    25_A      S    25_A     0.397     0    0.037   0.068     1.258   97.619   93.730
LGA    L    26_A      L    26_A     1.113     0    0.044   1.439     5.266   83.690   63.512
LGA    M    27_A      M    27_A     1.318     0    0.048   1.083     3.446   81.429   70.417
LGA    V    28_A      V    28_A     0.789     0    0.042   0.061     1.069   90.476   87.891
LGA    S    29_A      S    29_A     0.373     0    0.052   0.712     2.177  100.000   94.127
LGA    D    30_A      D    30_A     0.770     0    0.050   0.051     1.323   90.476   85.952
LGA    L    31_A      L    31_A     0.976     0    0.041   0.232     1.922   90.476   83.810
LGA    I    32_A      I    32_A     0.697     0    0.031   1.009     2.936   90.476   80.893
LGA    Y    33_A      Y    33_A     0.761     0    0.049   1.468     9.121   90.476   54.802
LGA    E    34_A      E    34_A     1.069     0    0.053   1.042     3.177   83.690   75.185
LGA    F    35_A      F    35_A     1.246     0    0.035   1.186     4.295   81.429   71.299
LGA    M    36_A      M    36_A     0.813     0    0.152   0.949     2.626   95.238   87.679
LGA    K    37_A      K    37_A     0.452     0    0.186   1.135     7.356   92.857   68.254
LGA    R    38_A      R    38_A     0.939     0    0.122   0.759     2.705   81.667   74.675
LGA    D    39_A      D    39_A     3.407     3    0.402   0.511     4.519   45.833   27.560

# 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):     1.352          1.402                  2.496           84.103   71.594

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    1.35    89.744    95.164     2.685

LGA_LOCAL      RMSD:   1.352  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.352  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   1.352  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.544508 * X  +   0.226896 * Y  +  -0.807483 * Z  + 164.380447
  Y_new =   0.222112 * X  +   0.967353 * Y  +   0.122042 * Z  + -157.423157
  Z_new =   0.808812 * X  +  -0.112899 * Y  +  -0.577128 * Z  + -44.501698 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.754284 -0.942130 -2.948411   [DEG:  157.8089  -53.9800 -168.9315 ]
ZXZ: -1.720800  2.186004  1.709486   [DEG:  -98.5946  125.2488   97.9463 ]
 
# END of job
