
#######################################################
#                                                     #
#                        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 (  265),  selected   33 , name one
# Molecule2: number of CA atoms  353 ( 2869),  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:    33     133_A - 165_A       4.66     4.66
  LCS_AVERAGE:      9.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14     134_A - 147_A       1.99    15.86
  LONGEST_CONTINUOUS_SEGMENT:    14     135_A - 148_A       1.80    16.11
  LONGEST_CONTINUOUS_SEGMENT:    14     152_A - 165_A       1.75    10.46
  LCS_AVERAGE:      3.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13     153_A - 165_A       0.94     8.34
  LCS_AVERAGE:      2.90

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     M   133_A     M   133_A      3   13   33      3    3    3    8   10   14   15   20   20   21   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     L   134_A     L   134_A      3   14   33      3    4    6    6   10   12   14   16   18   21   23   30   30   33   33   33   33   33   33   33 
LCS_GDT     Q   135_A     Q   135_A     11   14   33      4    9   10   12   13   14   16   20   20   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     E   136_A     E   136_A     11   14   33      5    9   10   12   13   14   14   20   20   21   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     Y   137_A     Y   137_A     11   14   33      5    9   10   12   15   16   17   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     A   138_A     A   138_A     11   14   33      5    9   10   12   13   14   16   20   21   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     S   139_A     S   139_A     11   14   33      5    9   10   12   13   14   16   20   20   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     C   140_A     C   140_A     11   14   33      5    9   10   12   13   14   16   20   20   23   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     L   141_A     L   141_A     11   14   33      4    9   11   14   15   16   17   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     L   142_A     L   142_A     11   14   33      5    9   10   12   13   14   16   20   20   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     F   143_A     F   143_A     11   14   33      5    9   10   12   13   14   16   20   20   21   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     M   144_A     M   144_A     11   14   33      4    7   10   12   13   14   18   20   22   24   26   30   30   33   33   33   33   33   33   33 
LCS_GDT     A   145_A     A   145_A     11   14   33      4    6   10   12   13   14   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     E   146_A     E   146_A      6   14   33      4    6   11   14   15   16   17   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     K   147_A     K   147_A      6   14   33      4    6    6    9   13   14   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     T   148_A     T   148_A      6   14   33      4    6    6    7   12   14   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     R   149_A     R   149_A      6    9   33      4    6    7   10   12   14   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     D   150_A     D   150_A      6    9   33      4    6    6    9   12   14   16   20   21   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     H   151_A     H   151_A      6    9   33      3    5    6    9   12   14   16   20   21   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     Q   152_A     Q   152_A      6   14   33      3    4    6    9   12   14   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     S   153_A     S   153_A     13   14   33      4   10   12   14   15   16   17   20   22   24   26   28   30   33   33   33   33   33   33   33 
LCS_GDT     D   154_A     D   154_A     13   14   33      4   10   12   14   15   16   18   20   22   24   25   28   30   33   33   33   33   33   33   33 
LCS_GDT     L   155_A     L   155_A     13   14   33      4   10   12   14   15   16   18   20   22   24   26   29   30   33   33   33   33   33   33   33 
LCS_GDT     C   156_A     C   156_A     13   14   33      4   10   12   14   15   16   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     K   157_A     K   157_A     13   14   33      7   10   12   14   15   16   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     K   158_A     K   158_A     13   14   33      7   10   12   14   15   16   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     Y   159_A     Y   159_A     13   14   33      7   10   12   14   15   16   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     I   160_A     I   160_A     13   14   33      7   10   12   14   15   16   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     E   161_A     E   161_A     13   14   33      7   10   12   14   15   16   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     A   162_A     A   162_A     13   14   33      7   10   12   14   15   16   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     I   163_A     I   163_A     13   14   33      7   10   12   14   15   16   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     A   164_A     A   164_A     13   14   33      4    9   12   14   15   16   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_GDT     S   165_A     S   165_A     13   14   33      4    5   10   13   13   16   18   20   22   24   28   30   30   33   33   33   33   33   33   33 
LCS_AVERAGE  LCS_A:   5.36  (   2.90    3.83    9.35 )

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      7     10     12     14     15     16     18     20     22     24     28     30     30     33     33     33     33     33     33     33 
GDT PERCENT_AT   1.98   2.83   3.40   3.97   4.25   4.53   5.10   5.67   6.23   6.80   7.93   8.50   8.50   9.35   9.35   9.35   9.35   9.35   9.35   9.35
GDT RMS_LOCAL    0.25   0.58   0.73   1.15   1.41   1.55   2.35   2.76   3.03   3.34   4.14   4.28   4.28   4.66   4.66   4.66   4.66   4.66   4.66   4.66
GDT RMS_ALL_AT   8.70   8.36   8.32   7.61   6.92   6.80   9.76   8.23   7.08   6.75   4.72   4.78   4.78   4.66   4.66   4.66   4.66   4.66   4.66   4.66

# Checking swapping
#   possible swapping detected:  E   136_A      E   136_A
#   possible swapping detected:  Y   137_A      Y   137_A
#   possible swapping detected:  F   143_A      F   143_A
#   possible swapping detected:  E   146_A      E   146_A
#   possible swapping detected:  Y   159_A      Y   159_A
#   possible swapping detected:  E   161_A      E   161_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M   133_A      M   133_A    20.542     0    0.587   1.231    23.289    0.000    0.000
LGA    L   134_A      L   134_A    21.248     0    0.467   0.395    27.769    0.000    0.000
LGA    Q   135_A      Q   135_A    17.926     0    0.487   0.365    22.305    0.000    0.000
LGA    E   136_A      E   136_A    13.856     0    0.063   1.192    16.981    0.000    0.000
LGA    Y   137_A      Y   137_A     7.832     0    0.064   1.318     9.980    5.952   15.556
LGA    A   138_A      A   138_A    12.291     0    0.012   0.012    15.244    0.000    0.000
LGA    S   139_A      S   139_A    13.204     0    0.047   0.058    17.552    0.000    0.000
LGA    C   140_A      C   140_A     7.222     0    0.212   0.796     9.195   20.000   18.413
LGA    L   141_A      L   141_A     4.807     0    0.180   0.815    10.028   24.048   17.083
LGA    L   142_A      L   142_A     9.250     0    0.032   0.098    16.131    5.119    2.560
LGA    F   143_A      F   143_A     8.461     0    0.310   1.225    17.267   14.286    5.195
LGA    M   144_A      M   144_A     3.744     0    0.461   0.826    10.301   44.167   29.286
LGA    A   145_A      A   145_A     2.557     0    0.098   0.110     4.722   64.405   57.810
LGA    E   146_A      E   146_A     3.639     0    0.023   0.814    11.518   55.714   28.307
LGA    K   147_A      K   147_A     3.285     0    0.166   0.816     9.526   50.476   29.471
LGA    T   148_A      T   148_A     3.729     0    0.033   0.146     5.484   40.952   43.946
LGA    R   149_A      R   149_A     4.153     0    0.041   1.388    11.220   37.500   26.061
LGA    D   150_A      D   150_A     6.673     0    0.070   0.766     7.324   14.524   16.964
LGA    H   151_A      H   151_A     6.950     0    0.575   0.592    13.209   21.071    8.714
LGA    Q   152_A      Q   152_A     3.910     0    0.650   0.920     9.544   40.952   24.233
LGA    S   153_A      S   153_A     2.907     0    0.624   0.977     6.184   69.286   54.286
LGA    D   154_A      D   154_A     2.276     0    0.068   1.300     4.674   64.762   59.643
LGA    L   155_A      L   155_A     2.594     0    0.178   0.315     3.285   60.952   59.107
LGA    C   156_A      C   156_A     2.828     0    0.053   0.101     3.634   57.143   53.651
LGA    K   157_A      K   157_A     2.020     0    0.103   1.083     3.762   68.810   61.799
LGA    K   158_A      K   158_A     0.877     0    0.064   0.918     2.845   88.214   80.053
LGA    Y   159_A      Y   159_A     0.829     0    0.024   0.171     1.011   90.476   89.722
LGA    I   160_A      I   160_A     1.041     0    0.058   1.118     3.997   83.690   71.786
LGA    E   161_A      E   161_A     1.149     0    0.069   0.913     4.355   81.429   63.810
LGA    A   162_A      A   162_A     1.155     0    0.029   0.027     1.562   79.286   79.714
LGA    I   163_A      I   163_A     1.359     0    0.082   1.284     2.898   81.429   73.274
LGA    A   164_A      A   164_A     1.220     0    0.090   0.104     1.939   79.286   78.000
LGA    S   165_A      S   165_A     2.342     0    0.616   0.854     4.927   56.905   62.302

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       33     132    132  100.00     265    265  100.00               353
SUMMARY(RMSD_GDC):     4.659          4.413                  6.262            3.968    3.430

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33  353    4.0     20    2.76     5.453     5.192     0.700

LGA_LOCAL      RMSD:   2.758  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.232  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   4.659  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.091939 * X  +  -0.974822 * Y  +   0.203148 * Z  + -47.558380
  Y_new =  -0.943408 * X  +  -0.150555 * Y  +  -0.295490 * Z  + -20.840714
  Z_new =   0.318635 * X  +  -0.164485 * Y  +  -0.933497 * Z  +  35.375179 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.473649 -0.324289 -2.967180   [DEG:  -84.4339  -18.5804 -170.0069 ]
ZXZ:  0.602284  2.774840  2.047332   [DEG:   34.5083  158.9866  117.3035 ]
 
# END of job
