
#######################################################
#                                                     #
#                        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   10 (   78),  selected   10 , name T0356TS213_1_3-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected   10 , name T0356_D2.pdb
# PARAMETERS: T0356TS213_1_3-D2.T0356_D2.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       122 - 131         1.54     1.54
  LCS_AVERAGE:      5.21

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       122 - 131         1.54     1.54
  LCS_AVERAGE:      5.21

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       126 - 131         0.65     3.40
  LCS_AVERAGE:      2.71

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:  192
LCS_GDT     T     122     T     122      4   10   10     2    6    7    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     K     123     K     123      4   10   10     3    6    7    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     R     124     R     124      4   10   10     3    4    5    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     L     125     L     125      4   10   10     3    4    4    5    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     R     126     R     126      6   10   10     3    6    6    6    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     G     127     G     127      6   10   10     5    6    7    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     A     128     A     128      6   10   10     5    6    7    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     P     129     P     129      6   10   10     5    6    7    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     C     130     C     130      6   10   10     5    6    7    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     Q     131     Q     131      6   10   10     5    6    7    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   4.38  (   2.71    5.21    5.21 )

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      5      6      7      8      9     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   2.60   3.12   3.65   4.17   4.69   5.21   5.21   5.21   5.21   5.21   5.21   5.21   5.21   5.21   5.21   5.21   5.21   5.21   5.21   5.21
GDT RMS_LOCAL    0.34   0.65   0.76   0.98   1.22   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54
GDT RMS_ALL_CA   2.26   3.40   1.58   1.59   1.62   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54   1.54

#      Molecule1      Molecule2       DISTANCE
LGA    T     122      T     122          0.760
LGA    K     123      K     123          0.881
LGA    R     124      R     124          1.991
LGA    L     125      L     125          2.526
LGA    R     126      R     126          2.882
LGA    G     127      G     127          0.454
LGA    A     128      A     128          0.654
LGA    P     129      P     129          1.137
LGA    C     130      C     130          1.249
LGA    Q     131      Q     131          0.332

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  192    4.0     10    1.54     4.427     4.820     0.611

LGA_LOCAL      RMSD =  1.536  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.536  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  1.536  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.170477 * X  +   0.964535 * Y  +  -0.201517 * Z  +  78.489563
  Y_new =   0.842181 * X  +   0.248794 * Y  +   0.478364 * Z  +  66.699661
  Z_new =   0.511535 * X  +  -0.088164 * Y  +  -0.854727 * Z  +  86.628693 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.038807    0.102786  [ DEG:  -174.1108      5.8892 ]
  Theta =  -0.536970   -2.604622  [ DEG:   -30.7661   -149.2339 ]
  Phi   =   1.770520   -1.371072  [ DEG:   101.4433    -78.5567 ]
 
# 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: T0356TS213_1_3-D2                             
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS213_1_3-D2.T0356_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  192   4.0   10   1.54   4.820     1.54
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS213_1_3-D2
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1r8j_A
ATOM    959  N   THR   122      84.354  77.528  71.858  1.00108.26       1SG 960
ATOM    960  CA  THR   122      85.384  76.556  72.071  1.00108.26       1SG 961
ATOM    961  CB  THR   122      85.884  75.912  70.808  1.00108.26       1SG 962
ATOM    962  OG1 THR   122      86.857  74.922  71.110  1.00108.26       1SG 963
ATOM    963  CG2 THR   122      86.475  76.987  69.880  1.00108.26       1SG 964
ATOM    964  C   THR   122      86.523  77.278  72.716  1.00108.26       1SG 965
ATOM    965  O   THR   122      86.981  78.308  72.227  1.00108.26       1SG 966
ATOM    966  N   LYS   123      86.995  76.772  73.868  1.00 68.78       1SG 967
ATOM    967  CA  LYS   123      88.074  77.450  74.519  1.00 68.78       1SG 968
ATOM    968  CB  LYS   123      87.617  78.493  75.556  1.00 68.78       1SG 969
ATOM    969  CG  LYS   123      86.854  79.668  74.943  1.00 68.78       1SG 970
ATOM    970  CD  LYS   123      86.097  80.503  75.978  1.00 68.78       1SG 971
ATOM    971  CE  LYS   123      85.326  81.684  75.382  1.00 68.78       1SG 972
ATOM    972  NZ  LYS   123      84.593  82.400  76.452  1.00 68.78       1SG 973
ATOM    973  C   LYS   123      88.869  76.423  75.248  1.00 68.78       1SG 974
ATOM    974  O   LYS   123      88.516  75.244  75.275  1.00 68.78       1SG 975
ATOM    975  N   ARG   124      89.999  76.863  75.829  1.00122.16       1SG 976
ATOM    976  CA  ARG   124      90.840  75.997  76.601  1.00122.16       1SG 977
ATOM    977  CB  ARG   124      92.255  76.547  76.839  1.00122.16       1SG 978
ATOM    978  CG  ARG   124      93.215  76.369  75.664  1.00122.16       1SG 979
ATOM    979  CD  ARG   124      92.828  77.117  74.388  1.00122.16       1SG 980
ATOM    980  NE  ARG   124      93.953  76.923  73.431  1.00122.16       1SG 981
ATOM    981  CZ  ARG   124      94.030  75.763  72.719  1.00122.16       1SG 982
ATOM    982  NH1 ARG   124      93.069  74.807  72.876  1.00122.16       1SG 983
ATOM    983  NH2 ARG   124      95.078  75.547  71.869  1.00122.16       1SG 984
ATOM    984  C   ARG   124      90.217  75.832  77.946  1.00122.16       1SG 985
ATOM    985  O   ARG   124      89.428  76.669  78.380  1.00122.16       1SG 986
ATOM    986  N   LEU   125      90.561  74.730  78.642  1.00 76.19       1SG 987
ATOM    987  CA  LEU   125      89.987  74.479  79.930  1.00 76.19       1SG 988
ATOM    988  CB  LEU   125      90.350  73.103  80.520  1.00 76.19       1SG 989
ATOM    989  CG  LEU   125      89.727  72.848  81.907  1.00 76.19       1SG 990
ATOM    990  CD1 LEU   125      88.190  72.852  81.842  1.00 76.19       1SG 991
ATOM    991  CD2 LEU   125      90.297  71.573  82.554  1.00 76.19       1SG 992
ATOM    992  C   LEU   125      90.490  75.516  80.875  1.00 76.19       1SG 993
ATOM    993  O   LEU   125      91.652  75.921  80.830  1.00 76.19       1SG 994
ATOM    994  N   ARG   126      89.592  75.987  81.755  1.00176.40       1SG 995
ATOM    995  CA  ARG   126      89.955  76.948  82.747  1.00176.40       1SG 996
ATOM    996  CB  ARG   126      89.032  78.179  82.794  1.00176.40       1SG 997
ATOM    997  CG  ARG   126      88.993  78.987  81.498  1.00176.40       1SG 998
ATOM    998  CD  ARG   126      88.141  80.253  81.596  1.00176.40       1SG 999
ATOM    999  NE  ARG   126      89.047  81.367  81.993  1.00176.40       1SG1000
ATOM   1000  CZ  ARG   126      89.725  82.056  81.030  1.00176.40       1SG1001
ATOM   1001  NH1 ARG   126      89.555  81.739  79.715  1.00176.40       1SG1002
ATOM   1002  NH2 ARG   126      90.571  83.070  81.384  1.00176.40       1SG1003
ATOM   1003  C   ARG   126      89.759  76.234  84.036  1.00176.40       1SG1004
ATOM   1004  O   ARG   126      89.146  75.168  84.069  1.00176.40       1SG1005
ATOM   1005  N   GLY   127      90.307  76.775  85.135  1.00 23.35       1SG1006
ATOM   1006  CA  GLY   127      90.066  76.104  86.373  1.00 23.35       1SG1007
ATOM   1007  C   GLY   127      88.589  76.165  86.566  1.00 23.35       1SG1008
ATOM   1008  O   GLY   127      87.979  77.223  86.416  1.00 23.35       1SG1009
ATOM   1009  N   ALA   128      87.973  75.023  86.916  1.00 32.69       1SG1010
ATOM   1010  CA  ALA   128      86.551  75.027  87.064  1.00 32.69       1SG1011
ATOM   1011  CB  ALA   128      85.857  73.800  86.449  1.00 32.69       1SG1012
ATOM   1012  C   ALA   128      86.259  75.019  88.518  1.00 32.69       1SG1013
ATOM   1013  O   ALA   128      86.904  74.333  89.309  1.00 32.69       1SG1014
ATOM   1014  N   PRO   129      85.309  75.834  88.876  1.00128.81       1SG1015
ATOM   1015  CA  PRO   129      84.859  75.925  90.230  1.00128.81       1SG1016
ATOM   1016  CD  PRO   129      84.953  77.005  88.096  1.00128.81       1SG1017
ATOM   1017  CB  PRO   129      83.997  77.188  90.312  1.00128.81       1SG1018
ATOM   1018  CG  PRO   129      83.741  77.580  88.845  1.00128.81       1SG1019
ATOM   1019  C   PRO   129      84.143  74.669  90.583  1.00128.81       1SG1020
ATOM   1020  O   PRO   129      84.017  74.362  91.767  1.00128.81       1SG1021
ATOM   1021  N   CYS   130      83.646  73.933  89.576  1.00 22.38       1SG1022
ATOM   1022  CA  CYS   130      82.976  72.712  89.896  1.00 22.38       1SG1023
ATOM   1023  CB  CYS   130      82.485  71.956  88.649  1.00 22.38       1SG1024
ATOM   1024  SG  CYS   130      81.121  72.802  87.791  1.00 22.38       1SG1025
ATOM   1025  C   CYS   130      83.996  71.850  90.564  1.00 22.38       1SG1026
ATOM   1026  O   CYS   130      83.737  71.239  91.599  1.00 22.38       1SG1027
ATOM   1027  N   GLN   131      85.207  71.829  89.980  1.00 75.87       1SG1028
ATOM   1028  CA  GLN   131      86.307  71.040  90.453  1.00 75.87       1SG1029
ATOM   1029  CB  GLN   131      87.023  71.624  91.685  1.00 75.87       1SG1030
ATOM   1030  CG  GLN   131      86.169  71.614  92.955  1.00 75.87       1SG1031
ATOM   1031  CD  GLN   131      87.001  72.199  94.086  1.00 75.87       1SG1032
ATOM   1032  OE1 GLN   131      87.209  71.561  95.118  1.00 75.87       1SG1033
ATOM   1033  NE2 GLN   131      87.488  73.453  93.892  1.00 75.87       1SG1034
ATOM   1034  C   GLN   131      85.819  69.641  90.807  1.00 75.87       1SG1035
ATOM   1035  O   GLN   131      86.529  68.967  91.598  1.00 75.87       1SG1036
ATOM   1036  OXT GLN   131      84.747  69.224  90.290  1.00 75.87       1SG1037
TER
END
