
#######################################################
#                                                     #
#                        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    6 (   47),  selected    6 , name T0378TS401_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected    6 , name T0378_D1.pdb
# PARAMETERS: T0378TS401_1-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:     6        84 - 89          3.72     3.72
  LCS_AVERAGE:      6.74

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        84 - 86          0.77     6.20
  LONGEST_CONTINUOUS_SEGMENT:     3        85 - 87          0.76     6.50
  LONGEST_CONTINUOUS_SEGMENT:     3        86 - 88          0.49     6.08
  LONGEST_CONTINUOUS_SEGMENT:     3        87 - 89          0.91     6.77
  LCS_AVERAGE:      3.37

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3        84 - 86          0.77     6.20
  LONGEST_CONTINUOUS_SEGMENT:     3        86 - 88          0.49     6.08
  LONGEST_CONTINUOUS_SEGMENT:     3        87 - 89          0.91     6.77
  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     L      84     L      84      3    3    6     0    3    3    3    3    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     M      85     M      85      3    3    6     0    3    3    3    3    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A      86     A      86      3    3    6     0    3    3    3    3    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     V      87     V      87      3    3    6     1    3    3    3    3    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     F      88     F      88      3    3    6     0    3    3    3    3    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     D      89     D      89      3    3    6     0    3    3    3    3    3    3    4    4    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   4.49  (   3.37    3.37    6.74 )

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      1      3      3      3      3      3      4      5      5      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   1.12   3.37   3.37   3.37   3.37   3.37   4.49   5.62   5.62   6.74   6.74   6.74   6.74   6.74   6.74   6.74   6.74   6.74   6.74   6.74
GDT RMS_LOCAL   31.63   0.49   0.49   0.49   0.49   0.49   2.52   3.14   3.14   3.72   3.72   3.72   3.72   3.72   3.72   3.72   3.72   3.72   3.72   3.72
GDT RMS_ALL_CA   6.08   6.08   6.08   6.08   6.08   6.08   4.69   4.06   4.06   3.72   3.72   3.72   3.72   3.72   3.72   3.72   3.72   3.72   3.72   3.72

#      Molecule1      Molecule2       DISTANCE
LGA    L      84      L      84          3.783
LGA    M      85      M      85          2.280
LGA    A      86      A      86          3.162
LGA    V      87      V      87          2.798
LGA    F      88      F      88          3.474
LGA    D      89      D      89          7.052

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6   89    4.0      5    3.14     4.775     4.475     0.154

LGA_LOCAL      RMSD =  3.143  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.065  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  3.721  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.447556 * X  +  -0.379760 * Y  +  -0.809614 * Z  +  99.486809
  Y_new =  -0.653581 * X  +   0.479011 * Y  +  -0.585987 * Z  +  72.086716
  Z_new =   0.610349 * X  +   0.791411 * Y  +  -0.033820 * Z  +  25.810200 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.613504   -1.528089  [ DEG:    92.4470    -87.5530 ]
  Theta =  -0.656501   -2.485092  [ DEG:   -37.6147   -142.3853 ]
  Phi   =  -0.970361    2.171232  [ DEG:   -55.5976    124.4024 ]
 
# 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: T0378TS401_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS401_1-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6   89   4.0    5   3.14   4.475     3.72
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS401_1-D1
PFRMAT TS
TARGET T0378
MODEL  1 REFINED
PARENT 1zjr_A
ATOM      1  N   LEU    84       1.991  22.420  48.426  1.00 57.54       1SG   2
ATOM      2  CA  LEU    84       2.452  21.606  47.278  1.00 57.54       1SG   3
ATOM      3  CB  LEU    84       2.134  22.318  45.948  1.00 57.54       1SG   4
ATOM      4  CG  LEU    84       0.626  22.448  45.642  1.00 57.54       1SG   5
ATOM      5  CD2 LEU    84       0.388  22.846  44.178  1.00 57.54       1SG   6
ATOM      6  CD1 LEU    84      -0.087  23.381  46.634  1.00 57.54       1SG   7
ATOM      7  C   LEU    84       3.924  21.372  47.356  1.00 57.54       1SG   8
ATOM      8  O   LEU    84       4.404  20.633  48.215  1.00 57.54       1SG   9
ATOM      9  N   MET    85       4.683  22.016  46.453  1.00 83.06       1SG  10
ATOM     10  CA  MET    85       6.105  21.840  46.435  1.00 83.06       1SG  11
ATOM     11  CB  MET    85       6.798  22.662  45.334  1.00 83.06       1SG  12
ATOM     12  CG  MET    85       6.434  22.244  43.906  1.00 83.06       1SG  13
ATOM     13  SD  MET    85       7.033  20.600  43.412  1.00 83.06       1SG  14
ATOM     14  CE  MET    85       6.432  20.719  41.702  1.00 83.06       1SG  15
ATOM     15  C   MET    85       6.617  22.338  47.744  1.00 83.06       1SG  16
ATOM     16  O   MET    85       7.504  21.736  48.349  1.00 83.06       1SG  17
ATOM     17  N   ALA    86       6.042  23.455  48.227  1.00 21.90       1SG  18
ATOM     18  CA  ALA    86       6.493  24.053  49.447  1.00 21.90       1SG  19
ATOM     19  CB  ALA    86       5.721  25.335  49.804  1.00 21.90       1SG  20
ATOM     20  C   ALA    86       6.299  23.084  50.567  1.00 21.90       1SG  21
ATOM     21  O   ALA    86       7.163  22.943  51.431  1.00 21.90       1SG  22
ATOM     22  N   VAL    87       5.159  22.372  50.573  1.00 34.71       1SG  23
ATOM     23  CA  VAL    87       4.908  21.475  51.658  1.00 34.71       1SG  24
ATOM     24  CB  VAL    87       3.623  20.718  51.506  1.00 34.71       1SG  25
ATOM     25  CG1 VAL    87       3.521  19.697  52.652  1.00 34.71       1SG  26
ATOM     26  CG2 VAL    87       2.459  21.723  51.456  1.00 34.71       1SG  27
ATOM     27  C   VAL    87       6.000  20.466  51.691  1.00 34.71       1SG  28
ATOM     28  O   VAL    87       6.585  20.237  52.743  1.00 34.71       1SG  29
ATOM     29  N   PHE    88       6.331  19.874  50.530  1.00126.07       1SG  30
ATOM     30  CA  PHE    88       7.328  18.846  50.458  1.00126.07       1SG  31
ATOM     31  CB  PHE    88       7.478  18.257  49.044  1.00126.07       1SG  32
ATOM     32  CG  PHE    88       8.203  16.963  49.188  1.00126.07       1SG  33
ATOM     33  CD1 PHE    88       7.499  15.811  49.466  1.00126.07       1SG  34
ATOM     34  CD2 PHE    88       9.570  16.889  49.055  1.00126.07       1SG  35
ATOM     35  CE1 PHE    88       8.146  14.606  49.607  1.00126.07       1SG  36
ATOM     36  CE2 PHE    88      10.224  15.687  49.194  1.00126.07       1SG  37
ATOM     37  CZ  PHE    88       9.512  14.544  49.471  1.00126.07       1SG  38
ATOM     38  C   PHE    88       8.625  19.471  50.844  1.00126.07       1SG  39
ATOM     39  O   PHE    88       9.462  18.857  51.506  1.00126.07       1SG  40
ATOM     40  N   ASP    89       8.807  20.737  50.436  1.00 74.26       1SG  41
ATOM     41  CA  ASP    89      10.003  21.468  50.715  1.00 74.26       1SG  42
ATOM     42  CB  ASP    89       9.932  22.918  50.208  1.00 74.26       1SG  43
ATOM     43  CG  ASP    89      11.305  23.568  50.349  1.00 74.26       1SG  44
ATOM     44  OD1 ASP    89      12.248  22.886  50.831  1.00 74.26       1SG  45
ATOM     45  OD2 ASP    89      11.432  24.761  49.968  1.00 74.26       1SG  46
ATOM     46  C   ASP    89      10.149  21.518  52.198  1.00 74.26       1SG  47
ATOM     47  O   ASP    89      11.265  21.503  52.718  1.00 74.26       1SG  48
TER
END
