
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   18 (   72),  selected   18 , name T0358AL381_1
# Molecule2: number of CA atoms   66 ( 1047),  selected   18 , name T0358.pdb
# PARAMETERS: T0358AL381_1.T0358.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        40 - 57          4.68     5.32
  LCS_AVERAGE:     25.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        45 - 53          1.88     6.81
  LCS_AVERAGE:     11.03

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        49 - 54          0.62    10.14
  LCS_AVERAGE:      6.73

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   66
LCS_GDT     V      40     V      40      3    3   17     3    4    4    4    4    4    6    7    8   10   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     V      41     V      41      3    5   17     3    4    4    4    4    5    6    7    8   10   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     R      42     R      42      3    5   17     3    4    4    4    4    5    6    7    8   10   13   13   16   16   16   17   17   18   18   18 
LCS_GDT     D      43     D      43      3    5   17     1    3    3    7    9   10   11   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     E      45     E      45      4    9   17     3    4    6    7    9   10   11   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     G      46     G      46      4    9   17     3    4    6    7    9   10   11   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     R      47     R      47      4    9   17     3    4    6    7    9   10   11   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     M      48     M      48      4    9   17     3    4    6    7    9   10   11   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     V      49     V      49      6    9   17     3    6    6    7    9    9   10   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     W      50     W      50      6    9   17     3    6    6    7    9   10   11   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     R      51     R      51      6    9   17     4    6    6    7    9   10   11   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     A      52     A      52      6    9   17     4    6    6    7    9   10   11   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     W      53     W      53      6    9   17     4    6    6    7    9   10   11   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     N      54     N      54      6    8   17     4    6    6    7    9   10   11   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     F      55     F      55      5    8   17     4    4    6    7    9    9   11   12   12   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     E      56     E      56      5    8   17     4    4    6    7    9    9    9   10   10   13   13   14   16   16   16   17   17   18   18   18 
LCS_GDT     P      57     P      57      3    5   17     3    3    3    3    4    5    6    7    7    8   10   10   11   13   16   17   17   18   18   18 
LCS_GDT     D      58     D      58      3    3   16     3    3    3    7    9    9    9   10   10   10   12   12   12   13   16   16   17   18   18   18 
LCS_AVERAGE  LCS_A:  14.48  (   6.73   11.03   25.67 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
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_CA      4      6      6      7      9     10     11     12     12     13     13     14     16     16     16     17     17     18     18     18 
GDT PERCENT_CA   6.06   9.09   9.09  10.61  13.64  15.15  16.67  18.18  18.18  19.70  19.70  21.21  24.24  24.24  24.24  25.76  25.76  27.27  27.27  27.27
GDT RMS_LOCAL    0.25   0.62   0.62   1.10   1.59   1.81   2.18   2.47   2.47   3.07   3.07   3.50   4.08   4.08   4.08   4.68   4.68   5.19   5.19   5.19
GDT RMS_ALL_CA  15.62  10.14  10.14   6.36   6.29   6.23   5.92   6.04   6.04   5.70   5.70   5.59   5.56   5.56   5.56   5.32   5.32   5.19   5.19   5.19

#      Molecule1      Molecule2       DISTANCE
LGA    V      40      V      40          7.515
LGA    V      41      V      41          7.664
LGA    R      42      R      42          8.465
LGA    D      43      D      43          3.734
LGA    E      45      E      45          2.153
LGA    G      46      G      46          1.110
LGA    R      47      R      47          0.507
LGA    M      48      M      48          1.592
LGA    V      49      V      49          3.877
LGA    W      50      W      50          2.022
LGA    R      51      R      51          2.517
LGA    A      52      A      52          0.629
LGA    W      53      W      53          3.642
LGA    N      54      N      54          3.932
LGA    F      55      F      55          2.425
LGA    E      56      E      56          6.516
LGA    P      57      P      57         11.222
LGA    D      58      D      58         13.030

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18   66    4.0     12    2.47    15.909    14.958     0.467

LGA_LOCAL      RMSD =  2.467  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.812  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  5.192  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.881752 * X  +   0.124684 * Y  +   0.454936 * Z  +  55.105446
  Y_new =  -0.471690 * X  +  -0.242666 * Y  +  -0.847716 * Z  +  14.280729
  Z_new =   0.004701 * X  +  -0.962064 * Y  +   0.272783 * Z  +  37.113800 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.294509    1.847084  [ DEG:   -74.1699    105.8301 ]
  Theta =  -0.004701   -3.136892  [ DEG:    -0.2694   -179.7307 ]
  Phi   =  -2.650381    0.491212  [ DEG:  -151.8556     28.1444 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0358AL381_1                                  
REMARK     2: T0358.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0358AL381_1.T0358.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18   66   4.0   12   2.47  14.958     5.19
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL381_1
REMARK Aligment from pdb entry: 1zorA
ATOM      1  N   VAL    40      -2.354  -6.837   1.730  1.00  0.00              
ATOM      2  CA  VAL    40      -3.391  -6.152   0.938  1.00  0.00              
ATOM      3  C   VAL    40      -3.682  -6.943  -0.324  1.00  0.00              
ATOM      4  O   VAL    40      -4.823  -7.333  -0.579  1.00  0.00              
ATOM      5  N   VAL    41      -2.633  -7.228  -1.078  1.00  0.00              
ATOM      6  CA  VAL    41      -2.764  -7.953  -2.335  1.00  0.00              
ATOM      7  C   VAL    41      -3.388  -9.351  -2.176  1.00  0.00              
ATOM      8  O   VAL    41      -3.951  -9.929  -3.119  1.00  0.00              
ATOM      9  N   ARG    42      -3.284  -9.877  -0.963  1.00  0.00              
ATOM     10  CA  ARG    42      -3.686 -11.223  -0.616  1.00  0.00              
ATOM     11  C   ARG    42      -5.126 -11.239  -0.078  1.00  0.00              
ATOM     12  O   ARG    42      -5.767 -12.294   0.002  1.00  0.00              
ATOM     13  N   ASP    43      -5.629 -10.072   0.308  1.00  0.00              
ATOM     14  CA  ASP    43      -6.893  -9.981   1.052  1.00  0.00              
ATOM     15  C   ASP    43      -8.150  -9.985   0.177  1.00  0.00              
ATOM     16  O   ASP    43      -8.069  -9.965  -1.053  1.00  0.00              
ATOM     17  N   GLU    45      -9.306 -10.013   0.839  1.00  0.00              
ATOM     18  CA  GLU    45     -10.601  -9.856   0.173  1.00  0.00              
ATOM     19  C   GLU    45     -10.966  -8.374  -0.041  1.00  0.00              
ATOM     20  O   GLU    45     -12.019  -8.064  -0.600  1.00  0.00              
ATOM     21  N   GLY    46     -10.074  -7.477   0.389  1.00  0.00              
ATOM     22  CA  GLY    46     -10.333  -6.041   0.461  1.00  0.00              
ATOM     23  C   GLY    46     -11.208  -5.693   1.661  1.00  0.00              
ATOM     24  O   GLY    46     -11.370  -6.506   2.573  1.00  0.00              
ATOM     25  N   ARG    47     -11.793  -4.492   1.665  1.00  0.00              
ATOM     26  CA  ARG    47     -12.793  -4.158   2.666  1.00  0.00              
ATOM     27  C   ARG    47     -12.337  -3.278   3.807  1.00  0.00              
ATOM     28  O   ARG    47     -13.130  -2.996   4.697  1.00  0.00              
ATOM     29  N   MET    48     -11.078  -2.836   3.780  1.00  0.00              
ATOM     30  CA  MET    48     -10.504  -2.060   4.856  1.00  0.00              
ATOM     31  C   MET    48     -10.078  -0.671   4.355  1.00  0.00              
ATOM     32  O   MET    48      -9.913  -0.446   3.148  1.00  0.00              
ATOM     33  N   VAL    49      -9.922   0.253   5.295  1.00  0.00              
ATOM     34  CA  VAL    49      -9.179   1.490   5.046  1.00  0.00              
ATOM     35  C   VAL    49      -7.700   1.218   5.253  1.00  0.00              
ATOM     36  O   VAL    49      -7.302   0.773   6.326  1.00  0.00              
ATOM     37  N   TRP    50      -6.892   1.475   4.229  1.00  0.00              
ATOM     38  CA  TRP    50      -5.434   1.442   4.379  1.00  0.00              
ATOM     39  C   TRP    50      -4.907   2.870   4.483  1.00  0.00              
ATOM     40  O   TRP    50      -4.800   3.584   3.488  1.00  0.00              
ATOM     41  N   ARG    51      -4.555   3.270   5.697  1.00  0.00              
ATOM     42  CA  ARG    51      -4.010   4.584   5.962  1.00  0.00              
ATOM     43  C   ARG    51      -2.511   4.532   5.630  1.00  0.00              
ATOM     44  O   ARG    51      -1.802   3.621   6.070  1.00  0.00              
ATOM     45  N   ALA    52      -2.034   5.487   4.838  1.00  0.00              
ATOM     46  CA  ALA    52      -0.650   5.462   4.359  1.00  0.00              
ATOM     47  C   ALA    52       0.031   6.793   4.634  1.00  0.00              
ATOM     48  O   ALA    52      -0.597   7.839   4.512  1.00  0.00              
ATOM     49  N   TRP    53       1.316   6.747   4.961  1.00  0.00              
ATOM     50  CA  TRP    53       2.136   7.950   4.998  1.00  0.00              
ATOM     51  C   TRP    53       2.226   8.536   3.589  1.00  0.00              
ATOM     52  O   TRP    53       1.805   7.907   2.630  1.00  0.00              
ATOM     53  N   ASN    54       2.799   9.728   3.466  1.00  0.00              
ATOM     54  CA  ASN    54       2.666  10.539   2.257  1.00  0.00              
ATOM     55  C   ASN    54       3.118   9.857   0.928  1.00  0.00              
ATOM     56  O   ASN    54       2.334   9.729  -0.023  1.00  0.00              
ATOM     57  N   PHE    55       4.378   9.436   0.881  1.00  0.00              
ATOM     58  CA  PHE    55       4.979   8.793  -0.280  1.00  0.00              
ATOM     59  C   PHE    55       4.299   7.476  -0.670  1.00  0.00              
ATOM     60  O   PHE    55       3.889   7.305  -1.818  1.00  0.00              
ATOM     61  N   GLU    56       4.165   6.573   0.297  1.00  0.00              
ATOM     62  CA  GLU    56       3.453   5.315   0.136  1.00  0.00              
ATOM     63  C   GLU    56       2.024   5.530  -0.357  1.00  0.00              
ATOM     64  O   GLU    56       1.551   4.784  -1.198  1.00  0.00              
ATOM     65  N   PRO    57       1.336   6.530   0.196  1.00  0.00              
ATOM     66  CA  PRO    57      -0.051   6.840  -0.184  1.00  0.00              
ATOM     67  C   PRO    57      -0.121   7.364  -1.606  1.00  0.00              
ATOM     68  O   PRO    57      -1.049   7.048  -2.323  1.00  0.00              
ATOM     69  N   ASP    58       0.875   8.151  -2.016  1.00  0.00              
ATOM     70  CA  ASP    58       0.972   8.627  -3.396  1.00  0.00              
ATOM     71  C   ASP    58       1.047   7.415  -4.332  1.00  0.00              
ATOM     72  O   ASP    58       0.250   7.289  -5.255  1.00  0.00              
END
