
#######################################################
#                                                     #
#                        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   33 (  231),  selected   33 , name one
# Molecule2: number of CA atoms   33 (  231),  selected   33 , 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:    22      12_A - 33_A        4.52    16.77
  LCS_AVERAGE:     56.57

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      14_A - 27_A        1.99    17.74
  LCS_AVERAGE:     30.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      18_A - 24_A        0.60    17.06
  LCS_AVERAGE:     16.07

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   33
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     Y     1_A     Y     1_A      5    7   10      4    4    5    5    6    6    7    8    8    9    9    9    9    9    9   11   11   11   11   12 
LCS_GDT     R     2_A     R     2_A      5    7   10      4    4    5    5    6    6    7    8    8    9    9    9    9    9   10   11   11   11   11   12 
LCS_GDT     Q     3_A     Q     3_A      5    7   10      4    4    5    5    6    6    7    8    8    9    9    9    9    9   10   11   11   11   11   12 
LCS_GDT     S     4_A     S     4_A      5    7   10      4    4    5    5    6    6    7    8    8    9    9    9    9    9   10   11   11   11   11   12 
LCS_GDT     S     5_A     S     5_A      5    7   11      3    4    5    5    6    6    7    8    8    9    9   10   10   11   11   11   11   12   13   14 
LCS_GDT     A     6_A     A     6_A      4    7   11      3    4    4    5    6    6    7    8    9    9    9   10   10   11   11   11   13   13   14   15 
LCS_GDT     T     7_A     T     7_A      4    7   11      3    4    4    5    6    6    9    9    9    9    9   11   11   12   12   13   13   14   14   15 
LCS_GDT     S     8_A     S     8_A      4    4   11      3    4    4    4    5    7    9    9    9    9    9   11   11   12   12   13   13   14   14   18 
LCS_GDT     S     9_A     S     9_A      5    7   11      3    5    5    7    7    7    9    9    9    9    9   11   11   12   12   13   13   14   14   15 
LCS_GDT     F    10_A     F    10_A      5    7   17      4    5    5    7    7    7    9    9    9    9    9   11   11   12   12   13   16   17   17   19 
LCS_GDT     G    11_A     G    11_A      5    7   20      4    5    5    7    7    7    9    9    9   11   13   15   16   17   17   19   19   20   21   22 
LCS_GDT     G    12_A     G    12_A      5    7   22      4    5    5    7    7    9   10   14   14   15   16   17   18   19   20   21   22   22   22   22 
LCS_GDT     L    13_A     L    13_A      5    7   22      4    5    5    7    7    9   12   14   14   15   17   18   19   21   21   21   22   22   22   22 
LCS_GDT     G    14_A     G    14_A      5   14   22      4    7   10   12   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     G    15_A     G    15_A      4   14   22      3    7   10   12   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     G    16_A     G    16_A      3   14   22      3    3    4    8   10   12   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     S    17_A     S    17_A      4   14   22      3    4    8   12   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     V    18_A     V    18_A      7   14   22      3    7   10   12   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     R    19_A     R    19_A      7   14   22      4    7   10   12   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     F    20_A     F    20_A      7   14   22      5    7   10   12   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     G    21_A     G    21_A      7   14   22      5    7   10   12   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     P    22_A     P    22_A      7   14   22      5    7   10   12   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     G    23_A     G    23_A      7   14   22      5    7   10   12   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     V    24_A     V    24_A      7   14   22      5    7   10   12   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     A    25_A     A    25_A      4   14   22      4    4    9   12   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     F    26_A     F    26_A      6   14   22      4    6    9   12   13   13   14   15   15   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     R    27_A     R    27_A      6   14   22      4    6   10   10   13   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     A    28_A     A    28_A      6   12   22      4    6    8    9   10   13   14   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     P    29_A     P    29_A      6    9   22      4    6    9   10   11   12   12   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     S    30_A     S    30_A      6    9   22      4    7    9   10   11   12   12   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     I    31_A     I    31_A      6    9   22      4    6    6    7    9   11   12   15   17   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     H    32_A     H    32_A      5    9   22      3    5    6    7    8   12   12   15   16   17   19   19   19   21   21   21   22   22   22   22 
LCS_GDT     G    33_A     G    33_A      3    4   22      3    3    3    4    6    6    7    9    9   11   11   16   19   21   21   21   22   22   22   22 
LCS_AVERAGE  LCS_A:  34.50  (  16.07   30.85   56.57 )

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      5      7     10     12     13     13     14     15     17     17     19     19     19     21     21     21     22     22     22     22 
GDT PERCENT_AT  15.15  21.21  30.30  36.36  39.39  39.39  42.42  45.45  51.52  51.52  57.58  57.58  57.58  63.64  63.64  63.64  66.67  66.67  66.67  66.67
GDT RMS_LOCAL    0.38   0.53   0.89   1.40   1.54   1.54   1.89   2.20   2.86   2.85   3.26   3.26   3.26   3.99   3.99   3.99   4.52   4.52   4.52   4.52
GDT RMS_ALL_AT  16.82  17.06  17.18  17.80  17.60  17.60  17.39  17.55  17.62  17.53  17.65  17.65  17.65  17.26  17.26  17.26  16.77  16.77  16.77  16.77

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_A
#   possible swapping detected:  F    10_A      F    10_A
#   possible swapping detected:  F    20_A      F    20_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    34.820     0    0.049   0.509    35.943    0.000    0.000
LGA    R     2_A      R     2_A    33.683     0    0.144   1.254    33.795    0.000    0.000
LGA    Q     3_A      Q     3_A    33.295     0    0.023   0.419    36.517    0.000    0.000
LGA    S     4_A      S     4_A    31.790     0    0.067   0.723    32.325    0.000    0.000
LGA    S     5_A      S     5_A    31.161     0    0.555   0.631    32.696    0.000    0.000
LGA    A     6_A      A     6_A    30.727     0    0.182   0.213    31.520    0.000    0.000
LGA    T     7_A      T     7_A    27.654     0    0.188   1.158    30.299    0.000    0.000
LGA    S     8_A      S     8_A    26.023     0    0.420   0.760    27.035    0.000    0.000
LGA    S     9_A      S     9_A    24.797     0    0.580   0.705    24.988    0.000    0.000
LGA    F    10_A      F    10_A    20.061     0    0.566   1.600    21.582    0.000    0.000
LGA    G    11_A      G    11_A    16.394     0    0.307   0.307    17.840    0.000    0.000
LGA    G    12_A      G    12_A    10.666     0    0.207   0.207    13.179    0.238    0.238
LGA    L    13_A      L    13_A     8.482     0    0.273   0.256    13.289   11.190    5.655
LGA    G    14_A      G    14_A     2.612     0    0.627   0.627     5.023   59.405   59.405
LGA    G    15_A      G    15_A     1.011     0    0.346   0.346     3.510   67.619   67.619
LGA    G    16_A      G    16_A     4.398     0    0.627   0.627     4.398   52.262   52.262
LGA    S    17_A      S    17_A     2.526     0    0.039   0.721     5.285   63.333   54.921
LGA    V    18_A      V    18_A     1.380     0    0.241   0.807     3.210   86.071   73.742
LGA    R    19_A      R    19_A     0.991     0    0.199   0.701     2.813   88.214   77.229
LGA    F    20_A      F    20_A     1.412     0    0.148   0.273     2.684   77.143   69.437
LGA    G    21_A      G    21_A     0.768     0    0.103   0.103     1.573   86.071   86.071
LGA    P    22_A      P    22_A     0.811     0    0.597   0.768     4.102   72.738   79.048
LGA    G    23_A      G    23_A     1.769     0    0.633   0.633     1.971   79.405   79.405
LGA    V    24_A      V    24_A     0.661     0    0.139   0.931     2.810   83.810   79.388
LGA    A    25_A      A    25_A     2.579     0    0.075   0.106     3.496   61.071   58.857
LGA    F    26_A      F    26_A     2.673     0    0.200   1.266     5.104   65.000   54.935
LGA    R    27_A      R    27_A     1.883     0    0.082   1.169     7.325   67.143   38.658
LGA    A    28_A      A    28_A     3.441     0    0.023   0.024     4.766   46.429   45.810
LGA    P    29_A      P    29_A     8.153     0    0.033   0.362    10.079    8.810    6.259
LGA    S    30_A      S    30_A     8.509     0    0.109   0.758    12.687    1.429    1.190
LGA    I    31_A      I    31_A    11.846     0    0.600   0.545    13.584    0.119    0.060
LGA    H    32_A      H    32_A    14.112     0    0.032   1.395    16.169    0.000    0.000
LGA    G    33_A      G    33_A    17.765     0    0.515   0.515    21.941    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       33     132    132  100.00     231    231  100.00                33
SUMMARY(RMSD_GDC):    13.481         13.404                 13.881           32.652   30.006

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     15    2.20    41.667    40.768     0.653

LGA_LOCAL      RMSD:   2.198  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.548  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  13.481  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.332563 * X  +  -0.343131 * Y  +  -0.878443 * Z  +  -6.550927
  Y_new =  -0.588448 * X  +   0.803394 * Y  +  -0.091040 * Z  +  -0.578693
  Z_new =   0.736974 * X  +   0.486641 * Y  +  -0.469094 * Z  +  -0.776323 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.085199 -0.828583  2.337837   [DEG: -119.4731  -47.4743  133.9482 ]
ZXZ: -1.467527  2.059061  0.987198   [DEG:  -84.0831  117.9755   56.5623 ]
 
# END of job
