
#######################################################
#                                                     #
#                        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   25 (  204),  selected   25 , name one
# Molecule2: number of CA atoms  198 ( 1543),  selected   25 , 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:    18     159_A - 176_A       4.98    13.17
  LCS_AVERAGE:      8.81

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8     153_A - 160_A       1.93    17.64
  LONGEST_CONTINUOUS_SEGMENT:     8     154_A - 161_A       1.93    15.86
  LONGEST_CONTINUOUS_SEGMENT:     8     165_A - 172_A       1.82    15.15
  LCS_AVERAGE:      3.74

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6     155_A - 160_A       0.68    19.77
  LONGEST_CONTINUOUS_SEGMENT:     6     171_A - 176_A       0.25    20.64
  LCS_AVERAGE:      2.53

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   25
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     T   152_A     T   152_A      4    6   16      0    4    4    4    6    8   11   11   11   12   13   14   15   16   17   17   17   18   18   18 
LCS_GDT     T   153_A     T   153_A      4    8   16      3    4    5    6    7    8   11   11   11   12   13   14   15   16   17   17   17   18   18   18 
LCS_GDT     G   154_A     G   154_A      4    8   16      3    4    4    5    7    8   11   11   11   12   13   14   15   16   17   17   17   18   18   18 
LCS_GDT     T   155_A     T   155_A      6    8   16      3    6    6    6    7    8   11   11   11   12   13   14   15   16   17   17   17   18   18   18 
LCS_GDT     W   156_A     W   156_A      6    8   16      4    6    6    6    7    8   11   11   11   12   13   14   15   16   17   17   17   18   18   18 
LCS_GDT     K   157_A     K   157_A      6    8   16      4    6    6    6    7    8   11   11   11   12   13   14   15   16   17   17   17   18   18   18 
LCS_GDT     P   158_A     P   158_A      6    8   16      4    6    6    6    7    8   11   11   11   12   13   14   15   16   17   17   17   18   18   18 
LCS_GDT     W   159_A     W   159_A      6    8   18      4    6    6    6    7    8   11   11   11   12   13   14   15   16   17   17   17   18   18   18 
LCS_GDT     H   160_A     H   160_A      6    8   18      3    6    6    6    7    8   11   11   12   12   13   14   16   17   17   17   17   18   18   18 
LCS_GDT     N   161_A     N   161_A      3    8   18      3    4    5    5    5    8   11   11   11   12   13   14   15   17   17   17   17   18   18   18 
LCS_GDT     D   162_A     D   162_A      3    5   18      3    3    5    6    7    8   11   11   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     L   163_A     L   163_A      3    4   18      3    3    3    4    4    5    7   10   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     T   164_A     T   164_A      3    6   18      0    3    3    4    4    6    7   10   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     S   165_A     S   165_A      5    8   18      4    5    6    7   10   11   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     K   166_A     K   166_A      5    8   18      4    5    7    7   10   11   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     L   167_A     L   167_A      5    8   18      4    5    7    7   10   11   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     G   168_A     G   168_A      5    8   18      4    5    7    7   10   11   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     S   169_A     S   169_A      5    8   18      3    5    5    5    5    9   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     L   170_A     L   170_A      4    8   18      3    4    7    7   10   11   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     K   171_A     K   171_A      6    8   18      6    6    6    7    8   11   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     S   172_A     S   172_A      6    8   18      6    6    6    7   10   11   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     V   173_A     V   173_A      6    7   18      6    6    6    6   10   11   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     F   174_A     F   174_A      6    7   18      6    6    7    7   10   11   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     F   175_A     F   175_A      6    7   18      6    6    7    7   10   11   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_GDT     E   176_A     E   176_A      6    7   18      6    6    7    7   10   11   11   12   12   13   15   15   16   17   17   17   17   18   18   18 
LCS_AVERAGE  LCS_A:   5.02  (   2.53    3.74    8.81 )

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      6      6      7      7     10     11     11     12     12     13     15     15     16     17     17     17     17     18     18     18 
GDT PERCENT_AT   3.03   3.03   3.54   3.54   5.05   5.56   5.56   6.06   6.06   6.57   7.58   7.58   8.08   8.59   8.59   8.59   8.59   9.09   9.09   9.09
GDT RMS_LOCAL    0.25   0.25   1.20   1.20   1.72   1.86   1.86   2.18   2.18   2.68   3.49   3.49   3.97   4.35   4.35   4.35   4.35   4.98   4.98   4.98
GDT RMS_ALL_AT  20.64  20.64  17.62  17.62  17.05  17.07  17.07  17.00  17.00  16.40  15.55  15.55  14.53  13.91  13.91  13.91  13.91  13.17  13.17  13.17

# Checking swapping
#   possible swapping detected:  F   174_A      F   174_A
#   possible swapping detected:  F   175_A      F   175_A
#   possible swapping detected:  E   176_A      E   176_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T   152_A      T   152_A    37.055     0    0.391   1.065    37.956    0.000    0.000
LGA    T   153_A      T   153_A    35.623     0    0.364   1.222    36.591    0.000    0.000
LGA    G   154_A      G   154_A    35.804     0    0.511   0.511    35.804    0.000    0.000
LGA    T   155_A      T   155_A    29.785     0    0.241   0.993    31.855    0.000    0.000
LGA    W   156_A      W   156_A    27.058     0    0.192   1.103    30.954    0.000    0.000
LGA    K   157_A      K   157_A    21.172     0    0.023   0.661    23.031    0.000    0.000
LGA    P   158_A      P   158_A    22.184     0    0.117   0.125    23.683    0.000    0.000
LGA    W   159_A      W   159_A    15.980     0    0.694   1.070    18.164    0.000    0.000
LGA    H   160_A      H   160_A    10.734     0    0.000   0.322    12.741    0.000   10.857
LGA    N   161_A      N   161_A    10.866     0    0.141   1.225    10.866    0.119    0.060
LGA    D   162_A      D   162_A     6.599     0    0.351   0.890     8.190    8.810   12.321
LGA    L   163_A      L   163_A     8.812     0    0.603   1.371    13.903    5.476    2.798
LGA    T   164_A      T   164_A     8.662     0    0.569   1.347    11.930    8.690    4.966
LGA    S   165_A      S   165_A     2.027     0    0.615   0.547     4.145   61.905   63.175
LGA    K   166_A      K   166_A     1.220     0    0.043   1.380     7.148   83.690   63.757
LGA    L   167_A      L   167_A     0.459     0    0.587   0.625     4.024   77.500   77.440
LGA    G   168_A      G   168_A     1.707     0    0.563   0.563     3.462   69.524   69.524
LGA    S   169_A      S   169_A     3.991     0    0.679   0.816     6.501   55.595   42.143
LGA    L   170_A      L   170_A     1.728     0    0.199   1.399     6.017   67.262   52.440
LGA    K   171_A      K   171_A     3.170     0    0.502   0.845    10.240   63.214   35.397
LGA    S   172_A      S   172_A     2.405     0    0.057   0.675     3.575   73.452   64.524
LGA    V   173_A      V   173_A     2.342     0    0.102   1.178     4.447   66.786   57.823
LGA    F   174_A      F   174_A     1.285     0    0.035   0.289     2.475   75.119   78.442
LGA    F   175_A      F   175_A     2.072     0    0.100   1.337     8.688   65.238   39.307
LGA    E   176_A      E   176_A     1.503     0    0.652   0.831     2.766   71.071   74.127

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       25     100    100  100.00     204    204  100.00               198
SUMMARY(RMSD_GDC):     8.968          8.970                  9.262            4.310    3.783

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   25  198    4.0     12    2.18     5.303     5.185     0.526

LGA_LOCAL      RMSD:   2.183  Number of atoms:   12  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.001  Number of assigned atoms:   25 
Std_ASGN_ATOMS RMSD:   8.968  Standard rmsd on all 25 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.703502 * X  +  -0.287453 * Y  +  -0.649965 * Z  + 250.233810
  Y_new =  -0.596776 * X  +   0.735569 * Y  +   0.320620 * Z  + -44.956985
  Z_new =   0.385931 * X  +   0.613441 * Y  +  -0.689019 * Z  + -78.536568 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.438091 -0.396217  2.414157   [DEG: -139.6923  -22.7016  138.3210 ]
ZXZ: -2.029060  2.330931  0.561561   [DEG: -116.2566  133.5525   32.1750 ]
 
# END of job
