
#######################################################
#                                                     #
#                        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 T0356TS418_1_3-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected   10 , name T0356_D2.pdb
# PARAMETERS: T0356TS418_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         3.02     3.02
  LCS_AVERAGE:      5.21

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       125 - 131         1.99     8.03
  LCS_AVERAGE:      3.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       126 - 131         0.99     9.61
  LCS_AVERAGE:      2.92

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      5    5   10     4    4    5    5    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     K     123     K     123      5    5   10     4    4    5    5    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     R     124     R     124      5    5   10     4    4    5    5    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     L     125     L     125      5    7   10     4    4    5    5    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     R     126     R     126      6    7   10     3    4    6    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     G     127     G     127      6    7   10     3    5    6    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     A     128     A     128      6    7   10     3    5    6    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     P     129     P     129      6    7   10     3    5    6    6    6    7    8    9   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     C     130     C     130      6    7   10     3    5    6    6    6    7    8    9   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     Q     131     Q     131      6    7   10     3    5    6    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   3.82  (   2.92    3.33    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      4      5      6      6      6      8      8      9     10     10     10     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   2.08   2.60   3.12   3.12   3.12   4.17   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
GDT RMS_LOCAL    0.36   0.51   0.99   0.99   0.99   2.22   2.22   2.70   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02
GDT RMS_ALL_CA  13.73   9.13   9.61   9.61   9.61   3.50   3.50   3.21   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02

#      Molecule1      Molecule2       DISTANCE
LGA    T     122      T     122          1.711
LGA    K     123      K     123          2.088
LGA    R     124      R     124          2.707
LGA    L     125      L     125          2.595
LGA    R     126      R     126          1.907
LGA    G     127      G     127          3.858
LGA    A     128      A     128          1.101
LGA    P     129      P     129          3.513
LGA    C     130      C     130          3.493
LGA    Q     131      Q     131          6.128

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  192    4.0      9    2.70     3.906     3.945     0.321

LGA_LOCAL      RMSD =  2.700  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.212  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  3.023  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.937129 * X  +   0.159376 * Y  +  -0.310464 * Z  +  89.929008
  Y_new =   0.054269 * X  +   0.945357 * Y  +   0.321489 * Z  +  62.556980
  Z_new =   0.344737 * X  +   0.284428 * Y  +  -0.894571 * Z  +  82.721809 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.833751   -0.307842  [ DEG:   162.3620    -17.6380 ]
  Theta =  -0.351959   -2.789634  [ DEG:   -20.1658   -159.8342 ]
  Phi   =   3.083748   -0.057845  [ DEG:   176.6857     -3.3143 ]
 
# 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: T0356TS418_1_3-D2                             
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS418_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    9   2.70   3.945     3.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS418_1_3-D2
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1r8j_A
ATOM    959  N   THR   122      85.361  76.030  71.106  1.00108.94       1SG 960
ATOM    960  CA  THR   122      86.679  76.354  71.561  1.00108.94       1SG 961
ATOM    961  CB  THR   122      87.076  77.775  71.290  1.00108.94       1SG 962
ATOM    962  OG1 THR   122      88.458  77.958  71.559  1.00108.94       1SG 963
ATOM    963  CG2 THR   122      86.232  78.704  72.178  1.00108.94       1SG 964
ATOM    964  C   THR   122      86.659  76.160  73.041  1.00108.94       1SG 965
ATOM    965  O   THR   122      85.620  76.310  73.683  1.00108.94       1SG 966
ATOM    966  N   LYS   123      87.816  75.805  73.631  1.00104.18       1SG 967
ATOM    967  CA  LYS   123      87.808  75.516  75.034  1.00104.18       1SG 968
ATOM    968  CB  LYS   123      88.450  74.161  75.382  1.00104.18       1SG 969
ATOM    969  CG  LYS   123      87.761  72.951  74.748  1.00104.18       1SG 970
ATOM    970  CD  LYS   123      88.618  71.683  74.800  1.00104.18       1SG 971
ATOM    971  CE  LYS   123      89.826  71.726  73.859  1.00104.18       1SG 972
ATOM    972  NZ  LYS   123      90.774  70.639  74.192  1.00104.18       1SG 973
ATOM    973  C   LYS   123      88.606  76.546  75.757  1.00104.18       1SG 974
ATOM    974  O   LYS   123      89.573  77.092  75.228  1.00104.18       1SG 975
ATOM    975  N   ARG   124      88.177  76.850  76.997  1.00141.86       1SG 976
ATOM    976  CA  ARG   124      88.904  77.741  77.851  1.00141.86       1SG 977
ATOM    977  CB  ARG   124      88.037  78.451  78.903  1.00141.86       1SG 978
ATOM    978  CG  ARG   124      88.848  79.388  79.802  1.00141.86       1SG 979
ATOM    979  CD  ARG   124      87.999  80.407  80.563  1.00141.86       1SG 980
ATOM    980  NE  ARG   124      86.723  79.743  80.950  1.00141.86       1SG 981
ATOM    981  CZ  ARG   124      85.629  79.861  80.142  1.00141.86       1SG 982
ATOM    982  NH1 ARG   124      85.714  80.583  78.989  1.00141.86       1SG 983
ATOM    983  NH2 ARG   124      84.453  79.259  80.488  1.00141.86       1SG 984
ATOM    984  C   ARG   124      89.912  76.903  78.564  1.00141.86       1SG 985
ATOM    985  O   ARG   124      89.703  75.710  78.775  1.00141.86       1SG 986
ATOM    986  N   LEU   125      91.052  77.509  78.937  1.00158.91       1SG 987
ATOM    987  CA  LEU   125      92.111  76.749  79.531  1.00158.91       1SG 988
ATOM    988  CB  LEU   125      93.388  77.578  79.750  1.00158.91       1SG 989
ATOM    989  CG  LEU   125      94.567  76.743  80.284  1.00158.91       1SG 990
ATOM    990  CD1 LEU   125      94.989  75.671  79.265  1.00158.91       1SG 991
ATOM    991  CD2 LEU   125      95.741  77.637  80.717  1.00158.91       1SG 992
ATOM    992  C   LEU   125      91.699  76.185  80.858  1.00158.91       1SG 993
ATOM    993  O   LEU   125      91.915  75.003  81.122  1.00158.91       1SG 994
ATOM    994  N   ARG   126      91.065  76.990  81.732  1.00201.26       1SG 995
ATOM    995  CA  ARG   126      90.785  76.457  83.036  1.00201.26       1SG 996
ATOM    996  CB  ARG   126      91.239  77.362  84.192  1.00201.26       1SG 997
ATOM    997  CG  ARG   126      92.752  77.508  84.358  1.00201.26       1SG 998
ATOM    998  CD  ARG   126      93.451  78.179  83.177  1.00201.26       1SG 999
ATOM    999  NE  ARG   126      94.812  78.574  83.642  1.00201.26       1SG1000
ATOM   1000  CZ  ARG   126      95.820  77.662  83.693  1.00201.26       1SG1001
ATOM   1001  NH1 ARG   126      95.577  76.361  83.341  1.00201.26       1SG1002
ATOM   1002  NH2 ARG   126      97.067  78.033  84.101  1.00201.26       1SG1003
ATOM   1003  C   ARG   126      89.316  76.299  83.220  1.00201.26       1SG1004
ATOM   1004  O   ARG   126      88.535  77.209  82.945  1.00201.26       1SG1005
ATOM   1005  N   GLY   127      88.902  75.110  83.697  1.00 20.25       1SG1006
ATOM   1006  CA  GLY   127      87.520  74.905  84.006  1.00 20.25       1SG1007
ATOM   1007  C   GLY   127      87.358  75.325  85.428  1.00 20.25       1SG1008
ATOM   1008  O   GLY   127      88.331  75.679  86.094  1.00 20.25       1SG1009
ATOM   1009  N   ALA   128      86.115  75.298  85.940  1.00 30.45       1SG1010
ATOM   1010  CA  ALA   128      85.937  75.659  87.313  1.00 30.45       1SG1011
ATOM   1011  CB  ALA   128      84.802  76.671  87.555  1.00 30.45       1SG1012
ATOM   1012  C   ALA   128      85.586  74.407  88.037  1.00 30.45       1SG1013
ATOM   1013  O   ALA   128      84.713  73.642  87.628  1.00 30.45       1SG1014
ATOM   1014  N   PRO   129      86.297  74.169  89.096  1.00 55.92       1SG1015
ATOM   1015  CA  PRO   129      86.027  73.004  89.882  1.00 55.92       1SG1016
ATOM   1016  CD  PRO   129      87.694  74.567  89.158  1.00 55.92       1SG1017
ATOM   1017  CB  PRO   129      87.201  72.882  90.847  1.00 55.92       1SG1018
ATOM   1018  CG  PRO   129      88.365  73.524  90.068  1.00 55.92       1SG1019
ATOM   1019  C   PRO   129      84.687  73.110  90.526  1.00 55.92       1SG1020
ATOM   1020  O   PRO   129      84.054  72.082  90.765  1.00 55.92       1SG1021
ATOM   1021  N   CYS   130      84.247  74.345  90.828  1.00 20.71       1SG1022
ATOM   1022  CA  CYS   130      82.962  74.552  91.422  1.00 20.71       1SG1023
ATOM   1023  CB  CYS   130      82.710  76.015  91.823  1.00 20.71       1SG1024
ATOM   1024  SG  CYS   130      83.826  76.560  93.150  1.00 20.71       1SG1025
ATOM   1025  C   CYS   130      81.940  74.166  90.406  1.00 20.71       1SG1026
ATOM   1026  O   CYS   130      80.902  73.598  90.739  1.00 20.71       1SG1027
ATOM   1027  N   GLN   131      82.236  74.464  89.124  1.00 71.49       1SG1028
ATOM   1028  CA  GLN   131      81.350  74.204  88.027  1.00 71.49       1SG1029
ATOM   1029  CB  GLN   131      81.265  72.714  87.625  1.00 71.49       1SG1030
ATOM   1030  CG  GLN   131      80.639  71.802  88.683  1.00 71.49       1SG1031
ATOM   1031  CD  GLN   131      80.587  70.385  88.133  1.00 71.49       1SG1032
ATOM   1032  OE1 GLN   131      81.427  69.982  87.330  1.00 71.49       1SG1033
ATOM   1033  NE2 GLN   131      79.570  69.600  88.579  1.00 71.49       1SG1034
ATOM   1034  C   GLN   131      79.962  74.721  88.398  1.00 71.49       1SG1035
ATOM   1035  O   GLN   131      79.879  75.919  88.778  1.00 71.49       1SG1036
ATOM   1036  OXT GLN   131      78.972  73.946  88.307  1.00 71.49       1SG1037
TER
END
