
#######################################################
#                                                     #
#                        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   12 (   48),  selected   12 , name T0378TS383_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   12 , name T0378_D1.pdb
# PARAMETERS: T0378TS383_5-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:    10        75 - 87          4.94     6.46
  LONGEST_CONTINUOUS_SEGMENT:    10        76 - 88          4.97     5.85
  LCS_AVERAGE:     11.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        82 - 85          1.17     9.70
  LCS_AVERAGE:      3.75

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        75 - 77          0.79     9.63
  LONGEST_CONTINUOUS_SEGMENT:     3        81 - 83          0.46    14.29
  LONGEST_CONTINUOUS_SEGMENT:     3        82 - 84          0.19    10.29
  LONGEST_CONTINUOUS_SEGMENT:     3        83 - 85          0.80     9.06
  LONGEST_CONTINUOUS_SEGMENT:     3        84 - 86          0.74     9.15
  LONGEST_CONTINUOUS_SEGMENT:     3        85 - 87          0.76     8.28
  LONGEST_CONTINUOUS_SEGMENT:     3        86 - 88          0.54    12.79
  LONGEST_CONTINUOUS_SEGMENT:     3        87 - 89          0.78     8.78
  LCS_AVERAGE:      3.37

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     I      75     I      75      3    3   10     3    3    4    4    4    5    6    7    7    8    9    9   10   11   12   12   12   12   12   12 
LCS_GDT     S      76     S      76      3    3   10     3    3    4    4    4    5    6    7    7    8    9    9   10   11   12   12   12   12   12   12 
LCS_GDT     T      77     T      77      3    3   10     0    3    3    3    4    5    6    7    7    8    8    9   10   11   12   12   12   12   12   12 
LCS_GDT     P      81     P      81      3    3   10     3    3    3    3    4    4    5    6    6    8    9    9   10   11   12   12   12   12   12   12 
LCS_GDT     Q      82     Q      82      3    4   10     3    3    3    4    4    4    5    5    6    8    8    8   10   11   12   12   12   12   12   12 
LCS_GDT     P      83     P      83      3    4   10     3    3    3    4    4    4    5    6    6    7    9    9   10   11   12   12   12   12   12   12 
LCS_GDT     L      84     L      84      3    4   10     3    3    3    4    4    4    5    6    7    8    9    9   10   11   12   12   12   12   12   12 
LCS_GDT     M      85     M      85      3    4   10     0    3    3    4    4    4    5    7    7    8    9    9   10   11   12   12   12   12   12   12 
LCS_GDT     A      86     A      86      3    3   10     3    3    4    4    4    5    6    7    7    8    9    9   10   11   12   12   12   12   12   12 
LCS_GDT     V      87     V      87      3    3   10     3    3    4    4    4    5    6    7    7    8    9    9   10   11   12   12   12   12   12   12 
LCS_GDT     F      88     F      88      3    3   10     3    3    4    4    4    5    6    7    7    8    9    9   10   11   12   12   12   12   12   12 
LCS_GDT     D      89     D      89      3    3    9     0    3    3    3    3    4    4    5    7    8    9    9   10   11   12   12   12   12   12   12 
LCS_AVERAGE  LCS_A:   6.09  (   3.37    3.75   11.14 )

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      3      3      4      4      4      5      6      7      7      8      9      9     10     11     12     12     12     12     12     12 
GDT PERCENT_CA   3.37   3.37   4.49   4.49   4.49   5.62   6.74   7.87   7.87   8.99  10.11  10.11  11.24  12.36  13.48  13.48  13.48  13.48  13.48  13.48
GDT RMS_LOCAL    0.19   0.19   0.98   0.98   0.98   1.64   2.15   2.65   2.65   3.84   4.28   4.28   4.67   5.02   5.37   5.37   5.37   5.37   5.37   5.37
GDT RMS_ALL_CA  10.29  10.29   6.89   6.89   6.89   6.30   6.36   6.16   6.16   6.43   5.86   5.86   5.57   5.48   5.37   5.37   5.37   5.37   5.37   5.37

#      Molecule1      Molecule2       DISTANCE
LGA    I      75      I      75          2.015
LGA    S      76      S      76          1.102
LGA    T      77      T      77          2.963
LGA    P      81      P      81          9.630
LGA    Q      82      Q      82          7.662
LGA    P      83      P      83          9.663
LGA    L      84      L      84          9.663
LGA    M      85      M      85          3.918
LGA    A      86      A      86          1.327
LGA    V      87      V      87          3.304
LGA    F      88      F      88          2.639
LGA    D      89      D      89          8.234

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12   89    4.0      7    2.65     7.303     6.377     0.255

LGA_LOCAL      RMSD =  2.647  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.158  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  5.374  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.254040 * X  +   0.962021 * Y  +   0.099896 * Z  + -32.167530
  Y_new =  -0.194582 * X  +  -0.152008 * Y  +   0.969036 * Z  + -75.977982
  Z_new =   0.947418 * X  +   0.226736 * Y  +   0.225808 * Z  +   7.769115 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.787448   -2.354144  [ DEG:    45.1175   -134.8825 ]
  Theta =  -1.245070   -1.896523  [ DEG:   -71.3372   -108.6628 ]
  Phi   =  -2.487961    0.653631  [ DEG:  -142.5497     37.4503 ]
 
# 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_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS383_5-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12   89   4.0    7   2.65   6.377     5.37
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS383_5-D1
PFRMAT TS
TARGET T0378
MODEL 5
PARENT 1zjrA
ATOM      1  N   ILE    75       9.898  32.184  42.405  1.00  0.00
ATOM      2  CA  ILE    75       8.644  31.733  43.074  1.00  0.00
ATOM      3  C   ILE    75       8.415  30.241  42.860  1.00  0.00
ATOM      4  O   ILE    75       7.895  29.551  43.738  1.00  0.00
ATOM      5  N   SER    76       8.802  29.751  41.686  1.00  0.00
ATOM      6  CA  SER    76       8.636  28.342  41.351  1.00  0.00
ATOM      7  C   SER    76       9.322  27.454  42.383  1.00  0.00
ATOM      8  O   SER    76       8.754  26.462  42.841  1.00  0.00
ATOM      9  N   THR    77      10.547  27.819  42.747  1.00  0.00
ATOM     10  CA  THR    77      11.313  27.052  43.720  1.00  0.00
ATOM     11  C   THR    77      10.585  27.006  45.062  1.00  0.00
ATOM     12  O   THR    77      10.752  26.061  45.835  1.00  0.00
ATOM     13  N   PRO    81       9.778  28.029  45.331  1.00  0.00
ATOM     14  CA  PRO    81       9.016  28.099  46.573  1.00  0.00
ATOM     15  C   PRO    81       7.960  27.002  46.568  1.00  0.00
ATOM     16  O   PRO    81       7.659  26.405  47.603  1.00  0.00
ATOM     17  N   GLN    82       7.401  26.745  45.389  1.00  0.00
ATOM     18  CA  GLN    82       6.371  25.729  45.224  1.00  0.00
ATOM     19  C   GLN    82       6.897  24.333  45.536  1.00  0.00
ATOM     20  O   GLN    82       6.240  23.554  46.226  1.00  0.00
ATOM     21  N   PRO    83       8.084  24.019  45.025  1.00  0.00
ATOM     22  CA  PRO    83       8.681  22.708  45.255  1.00  0.00
ATOM     23  C   PRO    83       8.968  22.519  46.742  1.00  0.00
ATOM     24  O   PRO    83       8.732  21.446  47.297  1.00  0.00
ATOM     25  N   LEU    84       9.473  23.568  47.386  1.00  0.00
ATOM     26  CA  LEU    84       9.773  23.514  48.814  1.00  0.00
ATOM     27  C   LEU    84       8.482  23.366  49.605  1.00  0.00
ATOM     28  O   LEU    84       8.440  22.680  50.629  1.00  0.00
ATOM     29  N   MET    85       7.430  24.018  49.121  1.00  0.00
ATOM     30  CA  MET    85       6.124  23.958  49.760  1.00  0.00
ATOM     31  C   MET    85       5.654  22.510  49.690  1.00  0.00
ATOM     32  O   MET    85       5.168  21.942  50.668  1.00  0.00
ATOM     33  N   ALA    86       5.816  21.919  48.513  1.00  0.00
ATOM     34  CA  ALA    86       5.412  20.542  48.285  1.00  0.00
ATOM     35  C   ALA    86       6.287  19.593  49.096  1.00  0.00
ATOM     36  O   ALA    86       5.810  18.586  49.618  1.00  0.00
ATOM     37  N   VAL    87       7.567  19.929  49.208  1.00  0.00
ATOM     38  CA  VAL    87       8.513  19.112  49.957  1.00  0.00
ATOM     39  C   VAL    87       8.067  19.081  51.417  1.00  0.00
ATOM     40  O   VAL    87       8.122  18.049  52.078  1.00  0.00
ATOM     41  N   PHE    88       7.619  20.228  51.913  1.00  0.00
ATOM     42  CA  PHE    88       7.164  20.331  53.289  1.00  0.00
ATOM     43  C   PHE    88       5.968  19.413  53.538  1.00  0.00
ATOM     44  O   PHE    88       5.920  18.696  54.534  1.00  0.00
ATOM     45  N   ASP    89       5.001  19.442  52.628  1.00  0.00
ATOM     46  CA  ASP    89       3.816  18.595  52.749  1.00  0.00
ATOM     47  C   ASP    89       4.240  17.128  52.762  1.00  0.00
ATOM     48  O   ASP    89       3.705  16.315  53.517  1.00  0.00
TER
END
