
#######################################################
#                                                     #
#                        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:    21      12_A - 32_A        4.94    18.49
  LONGEST_CONTINUOUS_SEGMENT:    21      13_A - 33_A        4.48    19.27
  LCS_AVERAGE:     53.81

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      15_A - 27_A        1.94    20.09
  LCS_AVERAGE:     29.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      18_A - 26_A        0.84    19.67
  LCS_AVERAGE:     17.91

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   11      3    4    5    6    6    7    8    9    9    9    9    9    9   11   11   11   11   11   11   12 
LCS_GDT     R     2_A     R     2_A      5    7   11      3    4    5    6    6    7    8    9    9    9    9    9    9   11   11   11   11   11   11   12 
LCS_GDT     Q     3_A     Q     3_A      5    7   11      3    4    5    6    6    7    8    9    9    9    9    9    9   11   11   11   11   11   11   12 
LCS_GDT     S     4_A     S     4_A      5    7   11      3    4    5    6    6    7    8    9    9    9    9    9    9   11   11   11   11   11   11   12 
LCS_GDT     S     5_A     S     5_A      5    7   11      3    4    5    6    6    7    8    9    9    9    9    9    9   11   11   11   11   11   12   13 
LCS_GDT     A     6_A     A     6_A      4    7   11      3    4    5    6    6    7    8    9    9    9    9   11   12   13   13   13   14   14   14   15 
LCS_GDT     T     7_A     T     7_A      4    7   11      3    4    4    6    6    7    8    9    9   11   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     S     8_A     S     8_A      4    4   11      3    4    4    4    4    6    8    9   10   11   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     S     9_A     S     9_A      5    7   11      4    5    5    6    6    7    8    9   10   11   11   11   12   13   13   13   14   14   14   15 
LCS_GDT     F    10_A     F    10_A      5    7   11      4    5    5    6    6    7    8    9   10   11   11   11   12   13   13   13   14   14   14   16 
LCS_GDT     G    11_A     G    11_A      5    7   14      4    5    5    6    6    7    8    9   10   11   11   11   12   13   14   14   16   18   18   19 
LCS_GDT     G    12_A     G    12_A      5    7   21      4    5    5    6    6    7    8    9   10   11   12   13   15   16   18   19   19   20   22   22 
LCS_GDT     L    13_A     L    13_A      5    7   21      3    5    5    6    6    7    9   10   12   13   16   17   18   18   20   20   21   21   22   22 
LCS_GDT     G    14_A     G    14_A      4    7   21      3    4    6   11   11   12   12   13   15   16   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     G    15_A     G    15_A      4   13   21      5    8   10   11   11   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     G    16_A     G    16_A      4   13   21      3    4    4    8    9   11   13   14   14   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     S    17_A     S    17_A      4   13   21      3    4    7   10   11   12   13   14   14   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     V    18_A     V    18_A      9   13   21      3    8   10   11   11   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     R    19_A     R    19_A      9   13   21      4    8   10   11   11   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     F    20_A     F    20_A      9   13   21      5    8   10   11   11   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     G    21_A     G    21_A      9   13   21      5    8   10   11   11   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     P    22_A     P    22_A      9   13   21      5    8   10   11   11   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     G    23_A     G    23_A      9   13   21      5    8   10   11   11   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     V    24_A     V    24_A      9   13   21      5    8   10   11   11   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     A    25_A     A    25_A      9   13   21      4    4   10   11   11   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     F    26_A     F    26_A      9   13   21      4    8   10   11   11   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     R    27_A     R    27_A      6   13   21      4    5    9   11   11   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     A    28_A     A    28_A      6   12   21      4    5    6    9    9   12   13   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     P    29_A     P    29_A      6   10   21      4    5    7   10   10   11   12   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     S    30_A     S    30_A      6   10   21      3    5    6   10   10   11   12   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     I    31_A     I    31_A      6   10   21      3    4    6    7    8   10   12   14   16   17   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     H    32_A     H    32_A      3   10   21      3    4    6    7    8   10   12   14   16   16   19   19   19   19   20   20   21   21   22   22 
LCS_GDT     G    33_A     G    33_A      3   10   21      3    3    3    5    7   10   10   10   11   12   13   13   14   16   17   18   21   21   22   22 
LCS_AVERAGE  LCS_A:  33.88  (  17.91   29.94   53.81 )

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      5      8     10     11     11     12     13     14     16     17     19     19     19     19     20     20     21     21     22     22 
GDT PERCENT_AT  15.15  24.24  30.30  33.33  33.33  36.36  39.39  42.42  48.48  51.52  57.58  57.58  57.58  57.58  60.61  60.61  63.64  63.64  66.67  66.67
GDT RMS_LOCAL    0.30   0.52   0.89   1.04   1.04   1.50   1.87   2.18   3.00   3.20   3.56   3.56   3.56   3.56   4.07   4.07   4.48   4.48   5.24   5.24
GDT RMS_ALL_AT  19.55  19.58  19.77  19.76  19.76  19.94  19.90  20.02  20.09  20.24  19.69  19.69  19.69  19.69  19.19  19.19  19.27  19.27  18.59  18.59

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_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    36.326     0    0.097   0.387    36.861    0.000    0.000
LGA    R     2_A      R     2_A    35.868     0    0.131   1.168    37.086    0.000    0.000
LGA    Q     3_A      Q     3_A    36.080     0    0.098   0.147    38.305    0.000    0.000
LGA    S     4_A      S     4_A    35.525     0    0.103   0.712    37.125    0.000    0.000
LGA    S     5_A      S     5_A    35.312     0    0.545   0.559    36.401    0.000    0.000
LGA    A     6_A      A     6_A    35.547     0    0.224   0.257    36.182    0.000    0.000
LGA    T     7_A      T     7_A    33.527     0    0.212   1.004    36.981    0.000    0.000
LGA    S     8_A      S     8_A    31.615     0    0.333   0.304    32.389    0.000    0.000
LGA    S     9_A      S     9_A    30.402     0    0.504   0.439    32.961    0.000    0.000
LGA    F    10_A      F    10_A    24.529     0    0.514   1.209    26.531    0.000    0.000
LGA    G    11_A      G    11_A    22.458     0    0.268   0.268    23.349    0.000    0.000
LGA    G    12_A      G    12_A    16.893     0    0.272   0.272    19.226    0.000    0.000
LGA    L    13_A      L    13_A    11.113     0    0.316   0.299    14.737    1.071    0.536
LGA    G    14_A      G    14_A     6.729     0    0.477   0.477     8.344   26.310   26.310
LGA    G    15_A      G    15_A     1.826     0    0.183   0.183     3.716   65.595   65.595
LGA    G    16_A      G    16_A     4.192     0    0.579   0.579     4.192   52.262   52.262
LGA    S    17_A      S    17_A     2.982     0    0.114   0.169     5.637   61.190   50.556
LGA    V    18_A      V    18_A     1.104     0    0.252   1.070     3.784   88.214   72.925
LGA    R    19_A      R    19_A     0.439     0    0.255   0.991     6.113   95.238   72.294
LGA    F    20_A      F    20_A     1.065     0    0.128   0.231     2.204   83.690   77.662
LGA    G    21_A      G    21_A     0.910     0    0.105   0.105     1.643   83.810   83.810
LGA    P    22_A      P    22_A     0.969     0    0.574   0.744     3.754   74.286   77.347
LGA    G    23_A      G    23_A     1.305     0    0.625   0.625     2.054   81.786   81.786
LGA    V    24_A      V    24_A     0.452     0    0.158   0.486     1.841   90.595   85.442
LGA    A    25_A      A    25_A     2.592     0    0.043   0.047     3.544   59.286   56.095
LGA    F    26_A      F    26_A     2.049     0    0.213   1.209     5.614   68.810   57.922
LGA    R    27_A      R    27_A     2.782     0    0.010   1.081    13.474   55.595   23.939
LGA    A    28_A      A    28_A     3.402     0    0.039   0.046     4.915   46.429   45.810
LGA    P    29_A      P    29_A     8.650     0    0.087   0.383    10.885    7.024    4.694
LGA    S    30_A      S    30_A     8.185     0    0.140   0.673    12.754    1.905    2.540
LGA    I    31_A      I    31_A    12.303     0    0.595   0.548    14.971    0.000    0.000
LGA    H    32_A      H    32_A    13.644     0    0.121   0.417    17.491    0.000    3.238
LGA    G    33_A      G    33_A    19.959     0    0.571   0.571    21.138    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):    14.806         14.682                 15.482           31.609   28.508

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     14    2.18    40.152    39.156     0.615

LGA_LOCAL      RMSD:   2.175  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  20.025  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  14.806  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.961758 * X  +   0.162329 * Y  +   0.220613 * Z  +  -1.851744
  Y_new =  -0.002524 * X  +  -0.800166 * Y  +   0.599773 * Z  +  -0.714810
  Z_new =   0.273887 * X  +  -0.577394 * Y  +  -0.769157 * Z  +  -3.710101 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.002625 -0.277432 -2.497654   [DEG:   -0.1504  -15.8957 -143.1050 ]
ZXZ:  2.789126  2.448317  2.698674   [DEG:  159.8051  140.2782  154.6227 ]
 
# END of job
