
#######################################################
#                                                     #
#                        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   14 (   56),  selected   14 , name T0378TS383_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   14 , name T0378_D1.pdb
# PARAMETERS: T0378TS383_4-D1.T0378_D1.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:    11        76 - 86          4.90     7.32
  LCS_AVERAGE:     12.12

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        76 - 79          1.27    18.30
  LONGEST_CONTINUOUS_SEGMENT:     4        78 - 81          0.20    14.64
  LONGEST_CONTINUOUS_SEGMENT:     4        81 - 84          1.57    10.19
  LONGEST_CONTINUOUS_SEGMENT:     4        82 - 85          0.99    10.23
  LCS_AVERAGE:      4.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        78 - 81          0.20    14.64
  LONGEST_CONTINUOUS_SEGMENT:     4        82 - 85          0.99    10.23
  LCS_AVERAGE:      4.01

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:   89
LCS_GDT     S      76     S      76      3    4   11     3    3    4    4    4    4    5    6    6    7    7   10   11   12   14   14   14   14   14   14 
LCS_GDT     T      77     T      77      3    4   11     3    3    3    4    4    4    6    6    7    8    9   10   11   12   14   14   14   14   14   14 
LCS_GDT     Q      78     Q      78      4    4   11     4    4    4    4    4    4    6    6    7    8    9   10   11   12   14   14   14   14   14   14 
LCS_GDT     T      79     T      79      4    4   11     4    4    4    4    4    4    6    6    7    8    9   10   11   12   14   14   14   14   14   14 
LCS_GDT     T      80     T      80      4    4   11     4    4    4    4    4    4    6    6    7    8    9   10   11   12   14   14   14   14   14   14 
LCS_GDT     P      81     P      81      4    4   11     4    4    4    4    4    5    6    6    7    8    9   10   11   12   14   14   14   14   14   14 
LCS_GDT     Q      82     Q      82      4    4   11     3    3    4    4    4    5    6    6    7    8    9   10   11   12   14   14   14   14   14   14 
LCS_GDT     P      83     P      83      4    4   11     3    3    4    4    4    5    5    6    7    8    9   10   11   12   14   14   14   14   14   14 
LCS_GDT     L      84     L      84      4    4   11     3    3    4    4    4    5    5    5    7    8    9   10   11   12   14   14   14   14   14   14 
LCS_GDT     M      85     M      85      4    4   11     3    3    4    4    4    5    5    6    7    8    9   10   11   12   14   14   14   14   14   14 
LCS_GDT     A      86     A      86      3    3   11     3    3    3    4    4    4    5    6    7    8    9   10   11   12   14   14   14   14   14   14 
LCS_GDT     V      87     V      87      3    3   10     3    3    3    3    3    3    5    6    7    8    9   10   11   12   14   14   14   14   14   14 
LCS_GDT     F      88     F      88      3    3   10     3    3    3    4    4    4    5    6    6    8    8   10   11   12   14   14   14   14   14   14 
LCS_GDT     D      89     D      89      3    3   10     0    3    3    3    3    3    4    4    6    6    7    8   10   12   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:   6.77  (   4.01    4.17   12.12 )

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      4      4      4      4      5      6      6      7      8      9     10     11     12     14     14     14     14     14     14 
GDT PERCENT_CA   4.49   4.49   4.49   4.49   4.49   5.62   6.74   6.74   7.87   8.99  10.11  11.24  12.36  13.48  15.73  15.73  15.73  15.73  15.73  15.73
GDT RMS_LOCAL    0.20   0.20   0.20   0.20   0.20   2.04   2.87   2.50   3.42   3.84   4.16   4.47   4.89   5.12   5.67   5.67   5.67   5.67   5.67   5.67
GDT RMS_ALL_CA  14.64  14.64  14.64  14.64  14.64   8.61  13.57  12.86  12.18   7.85   6.83   7.21   5.97   6.00   5.67   5.67   5.67   5.67   5.67   5.67

#      Molecule1      Molecule2       DISTANCE
LGA    S      76      S      76          2.542
LGA    T      77      T      77          3.804
LGA    Q      78      Q      78          3.332
LGA    T      79      T      79          9.125
LGA    T      80      T      80          6.400
LGA    P      81      P      81          0.993
LGA    Q      82      Q      82          2.021
LGA    P      83      P      83          3.283
LGA    L      84      L      84          4.676
LGA    M      85      M      85         10.523
LGA    A      86      A      86         13.736
LGA    V      87      V      87         16.279
LGA    F      88      F      88         21.909
LGA    D      89      D      89         27.673

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14   89    4.0      6    2.50     7.865     6.765     0.231

LGA_LOCAL      RMSD =  2.500  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.965  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  5.675  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.860518 * X  +  -0.304995 * Y  +  -0.408028 * Z  + -18.975643
  Y_new =   0.503900 * X  +   0.392025 * Y  +   0.769676 * Z  +   3.947907
  Z_new =  -0.074789 * X  +  -0.867925 * Y  +   0.491032 * Z  +  37.483807 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.055939    2.085654  [ DEG:   -60.5008    119.4992 ]
  Theta =   0.074859    3.066733  [ DEG:     4.2891    175.7109 ]
  Phi   =   0.529747   -2.611845  [ DEG:    30.3523   -149.6477 ]
 
# 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: T0378TS383_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS383_4-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14   89   4.0    6   2.50   6.765     5.67
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS383_4-D1
PFRMAT TS
TARGET T0378
MODEL 4
PARENT 1v2xA
ATOM      1  N   SER    76      12.446  27.666  41.707  1.00  0.00
ATOM      2  CA  SER    76      11.482  28.789  41.505  1.00  0.00
ATOM      3  C   SER    76      10.376  28.450  40.511  1.00  0.00
ATOM      4  O   SER    76       9.202  28.720  40.768  1.00  0.00
ATOM      5  N   THR    77      10.746  27.875  39.369  1.00  0.00
ATOM      6  CA  THR    77       9.742  27.528  38.375  1.00  0.00
ATOM      7  C   THR    77       9.126  26.177  38.736  1.00  0.00
ATOM      8  O   THR    77       8.044  25.827  38.272  1.00  0.00
ATOM      9  N   GLN    78       9.813  25.417  39.575  1.00  0.00
ATOM     10  CA  GLN    78       9.288  24.127  39.997  1.00  0.00
ATOM     11  C   GLN    78       8.124  24.448  40.943  1.00  0.00
ATOM     12  O   GLN    78       7.093  23.769  40.974  1.00  0.00
ATOM     13  N   THR    79       8.314  25.524  41.696  1.00  0.00
ATOM     14  CA  THR    79       7.349  26.022  42.663  1.00  0.00
ATOM     15  C   THR    79       6.174  26.717  41.974  1.00  0.00
ATOM     16  O   THR    79       5.026  26.627  42.414  1.00  0.00
ATOM     17  N   THR    80       6.462  27.395  40.872  1.00  0.00
ATOM     18  CA  THR    80       5.431  28.134  40.172  1.00  0.00
ATOM     19  C   THR    80       5.040  27.481  38.836  1.00  0.00
ATOM     20  O   THR    80       3.875  27.151  38.615  1.00  0.00
ATOM     21  N   PRO    81       6.015  27.258  37.966  1.00  0.00
ATOM     22  CA  PRO    81       5.748  26.663  36.660  1.00  0.00
ATOM     23  C   PRO    81       5.043  25.322  36.773  1.00  0.00
ATOM     24  O   PRO    81       4.318  24.928  35.868  1.00  0.00
ATOM     25  N   GLN    82       5.231  24.626  37.884  1.00  0.00
ATOM     26  CA  GLN    82       4.602  23.322  38.030  1.00  0.00
ATOM     27  C   GLN    82       3.367  23.310  38.921  1.00  0.00
ATOM     28  O   GLN    82       2.242  23.443  38.443  1.00  0.00
ATOM     29  N   PRO    83       3.592  23.133  40.218  1.00  0.00
ATOM     30  CA  PRO    83       2.524  23.074  41.194  1.00  0.00
ATOM     31  C   PRO    83       1.497  24.170  40.936  1.00  0.00
ATOM     32  O   PRO    83       0.322  23.892  40.715  1.00  0.00
ATOM     33  N   LEU    84       1.968  25.413  40.952  1.00  0.00
ATOM     34  CA  LEU    84       1.134  26.586  40.744  1.00  0.00
ATOM     35  C   LEU    84       0.258  26.513  39.485  1.00  0.00
ATOM     36  O   LEU    84      -0.957  26.672  39.568  1.00  0.00
ATOM     37  N   MET    85       0.882  26.268  38.338  1.00  0.00
ATOM     38  CA  MET    85       0.192  26.188  37.044  1.00  0.00
ATOM     39  C   MET    85      -0.770  25.004  36.913  1.00  0.00
ATOM     40  O   MET    85      -1.889  25.180  36.423  1.00  0.00
ATOM     41  N   ALA    86      -0.363  23.808  37.335  1.00  0.00
ATOM     42  CA  ALA    86      -1.265  22.664  37.219  1.00  0.00
ATOM     43  C   ALA    86      -2.490  22.799  38.134  1.00  0.00
ATOM     44  O   ALA    86      -3.595  22.429  37.753  1.00  0.00
ATOM     45  N   VAL    87      -2.301  23.329  39.338  1.00  0.00
ATOM     46  CA  VAL    87      -3.416  23.495  40.257  1.00  0.00
ATOM     47  C   VAL    87      -4.458  24.496  39.726  1.00  0.00
ATOM     48  O   VAL    87      -5.674  24.314  39.891  1.00  0.00
ATOM     49  N   PHE    88      -3.989  25.568  39.102  1.00  0.00
ATOM     50  CA  PHE    88      -4.924  26.563  38.613  1.00  0.00
ATOM     51  C   PHE    88      -5.608  25.979  37.411  1.00  0.00
ATOM     52  O   PHE    88      -6.792  26.214  37.206  1.00  0.00
ATOM     53  N   ASP    89      -4.866  25.232  36.611  1.00  0.00
ATOM     54  CA  ASP    89      -5.458  24.623  35.424  1.00  0.00
ATOM     55  C   ASP    89      -6.680  23.812  35.826  1.00  0.00
ATOM     56  O   ASP    89      -7.731  23.891  35.189  1.00  0.00
TER
END
