
#######################################################
#                                                     #
#                        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 (  112),  selected   14 , name T0318TS193_3_2-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected   14 , name T0318_D1.pdb
# PARAMETERS: T0318TS193_3_2-D1.T0318_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       142 - 152         4.27     7.05
  LCS_AVERAGE:      6.91

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       142 - 147         1.43     9.53
  LCS_AVERAGE:      3.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       142 - 146         0.82    10.18
  LCS_AVERAGE:      2.64

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:  154
LCS_GDT     R     142     R     142      5    6   11     3    4    5    5    6    6    6    8    9   10   10   10   12   12   12   13   13   13   14   14 
LCS_GDT     E     143     E     143      5    6   11     3    4    5    5    6    6    6    6    9   10   10   10   12   12   12   13   13   13   14   14 
LCS_GDT     L     144     L     144      5    6   11     3    4    5    5    6    6    6    8    9   10   10   10   12   12   12   13   13   13   14   14 
LCS_GDT     N     145     N     145      5    6   11     3    4    5    5    6    6    6    8    9   10   10   10   12   12   12   13   13   13   14   14 
LCS_GDT     V     146     V     146      5    6   11     3    4    5    5    6    6    6    8    9   10   10   10   12   12   12   13   13   13   14   14 
LCS_GDT     N     147     N     147      3    6   11     3    3    3    5    6    6    6    8    9   10   10   10   12   12   12   13   13   13   14   14 
LCS_GDT     I     148     I     148      3    5   11     3    3    3    4    5    5    6    6    9   10   10   10   12   12   12   13   13   13   14   14 
LCS_GDT     D     149     D     149      3    5   11     3    3    3    4    5    6    6    8    9   10   10   10   12   12   12   13   13   13   14   14 
LCS_GDT     V     150     V     150      4    5   11     3    3    4    5    5    6    6    8    9   10   10   10   12   12   12   13   13   13   14   14 
LCS_GDT     V     151     V     151      4    5   11     3    4    5    5    5    6    6    8    9   10   10   10   12   12   12   13   13   13   14   14 
LCS_GDT     C     152     C     152      4    5   11     3    4    5    5    5    5    6    7    8    8    9   10   12   12   12   13   13   13   14   14 
LCS_GDT     D     153     D     153      4    5   10     3    4    5    5    5    5    6    7    8    8    8    8    8   10   11   13   13   13   14   14 
LCS_GDT     K     154     K     154      4    5    9     3    4    5    5    5    5    6    7    8    8    8    8    8    8    8    8   10   10   14   14 
LCS_GDT     L     155     L     155      3    5    9     0    3    5    5    5    5    6    7    8    8    9   10   12   12   12   13   13   13   14   14 
LCS_AVERAGE  LCS_A:   4.36  (   2.64    3.53    6.91 )

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      4      5      5      6      6      6      8      9     10     10     10     12     12     12     13     13     13     14     14 
GDT PERCENT_CA   1.95   2.60   3.25   3.25   3.90   3.90   3.90   5.19   5.84   6.49   6.49   6.49   7.79   7.79   7.79   8.44   8.44   8.44   9.09   9.09
GDT RMS_LOCAL    0.04   0.44   0.82   0.82   1.43   1.43   1.43   3.30   3.46   3.63   3.63   3.63   4.67   4.67   4.67   5.22   5.22   5.22   5.87   5.87
GDT RMS_ALL_CA  11.12  18.85  10.18  10.18   9.53   9.53   9.53   7.67   7.83   7.74   7.74   7.74   6.17   6.17   6.17   5.96   5.96   5.96   5.87   5.87

#      Molecule1      Molecule2       DISTANCE
LGA    R     142      R     142          3.884
LGA    E     143      E     143          5.248
LGA    L     144      L     144          2.449
LGA    N     145      N     145          3.468
LGA    V     146      V     146          3.990
LGA    N     147      N     147          2.935
LGA    I     148      I     148          4.395
LGA    D     149      D     149          3.778
LGA    V     150      V     150          2.983
LGA    V     151      V     151          3.087
LGA    C     152      C     152          8.613
LGA    D     153      D     153         12.391
LGA    K     154      K     154         16.962
LGA    L     155      L     155         12.536

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  154    4.0      8    3.30     4.870     4.587     0.235

LGA_LOCAL      RMSD =  3.304  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.605  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  5.868  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.373338 * X  +   0.922986 * Y  +  -0.093356 * Z  +  39.728786
  Y_new =   0.152222 * X  +   0.160217 * Y  +   0.975274 * Z  +  54.757751
  Z_new =   0.915121 * X  +   0.349896 * Y  +  -0.200314 * Z  +  21.341150 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.090747   -1.050845  [ DEG:   119.7910    -60.2090 ]
  Theta =  -1.155809   -1.985784  [ DEG:   -66.2230   -113.7770 ]
  Phi   =   2.754438   -0.387155  [ DEG:   157.8176    -22.1824 ]
 
# 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: T0318TS193_3_2-D1                             
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS193_3_2-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14  154   4.0    8   3.30   4.587     5.87
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS193_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1097  N   ARG   142      35.428  55.776  15.006  1.00  0.00
ATOM   1098  CA  ARG   142      34.213  55.259  14.390  1.00  0.00
ATOM   1099  C   ARG   142      34.147  53.740  14.490  1.00  0.00
ATOM   1100  O   ARG   142      35.142  53.086  14.800  1.00  0.00
ATOM   1101  CB  ARG   142      34.159  55.638  12.908  1.00  0.00
ATOM   1102  CG  ARG   142      33.972  57.126  12.655  1.00  0.00
ATOM   1103  CD  ARG   142      33.999  57.440  11.168  1.00  0.00
ATOM   1104  NE  ARG   142      35.302  57.157  10.572  1.00  0.00
ATOM   1105  CZ  ARG   142      35.556  57.213   9.269  1.00  0.00
ATOM   1106  NH1 ARG   142      36.773  56.938   8.818  1.00  0.00
ATOM   1107  NH2 ARG   142      34.593  57.542   8.420  1.00  0.00
ATOM   1108  N   GLU   143      32.969  53.184  14.226  1.00  0.00
ATOM   1109  CA  GLU   143      32.792  51.738  14.202  1.00  0.00
ATOM   1110  C   GLU   143      33.082  51.170  12.818  1.00  0.00
ATOM   1111  O   GLU   143      32.854  51.833  11.806  1.00  0.00
ATOM   1112  CB  GLU   143      31.355  51.368  14.576  1.00  0.00
ATOM   1113  CG  GLU   143      30.949  51.794  15.977  1.00  0.00
ATOM   1114  CD  GLU   143      29.534  51.377  16.325  1.00  0.00
ATOM   1115  OE1 GLU   143      28.854  50.795  15.454  1.00  0.00
ATOM   1116  OE2 GLU   143      29.104  51.631  17.470  1.00  0.00
ATOM   1117  N   LEU   144      33.585  49.942  12.782  1.00  0.00
ATOM   1118  CA  LEU   144      33.795  49.237  11.523  1.00  0.00
ATOM   1119  C   LEU   144      32.796  48.099  11.356  1.00  0.00
ATOM   1120  O   LEU   144      32.814  47.386  10.352  1.00  0.00
ATOM   1121  CB  LEU   144      35.204  48.643  11.470  1.00  0.00
ATOM   1122  CG  LEU   144      36.361  49.622  11.677  1.00  0.00
ATOM   1123  CD1 LEU   144      37.690  48.884  11.705  1.00  0.00
ATOM   1124  CD2 LEU   144      36.408  50.645  10.553  1.00  0.00
ATOM   1125  N   ASN   145      31.749  46.034  11.802  1.00  0.00
ATOM   1126  CA  ASN   145      32.964  45.638  12.504  1.00  0.00
ATOM   1127  C   ASN   145      33.173  44.131  12.437  1.00  0.00
ATOM   1128  O   ASN   145      32.242  43.356  12.654  1.00  0.00
ATOM   1129  CB  ASN   145      32.888  46.043  13.978  1.00  0.00
ATOM   1130  CG  ASN   145      32.969  47.543  14.176  1.00  0.00
ATOM   1131  OD1 ASN   145      33.423  48.272  13.293  1.00  0.00
ATOM   1132  ND2 ASN   145      32.527  48.010  15.337  1.00  0.00
ATOM   1133  N   VAL   146      34.400  43.722  12.136  1.00  0.00
ATOM   1134  CA  VAL   146      34.777  42.314  12.203  1.00  0.00
ATOM   1135  C   VAL   146      35.699  42.045  13.385  1.00  0.00
ATOM   1136  O   VAL   146      36.537  42.877  13.732  1.00  0.00
ATOM   1137  CB  VAL   146      35.514  41.866  10.927  1.00  0.00
ATOM   1138  CG1 VAL   146      35.952  40.414  11.047  1.00  0.00
ATOM   1139  CG2 VAL   146      34.607  41.997   9.714  1.00  0.00
ATOM   1140  N   ASN   147      35.540  40.878  13.999  1.00  0.00
ATOM   1141  CA  ASN   147      36.426  40.451  15.075  1.00  0.00
ATOM   1142  C   ASN   147      36.375  41.422  16.248  1.00  0.00
ATOM   1143  O   ASN   147      37.390  41.684  16.893  1.00  0.00
ATOM   1144  CB  ASN   147      37.873  40.380  14.581  1.00  0.00
ATOM   1145  CG  ASN   147      38.776  39.621  15.533  1.00  0.00
ATOM   1146  OD1 ASN   147      38.313  38.787  16.312  1.00  0.00
ATOM   1147  ND2 ASN   147      40.071  39.908  15.473  1.00  0.00
ATOM   1148  N   ILE   148      35.941  43.165  16.015  1.00  0.00
ATOM   1149  CA  ILE   148      35.143  43.276  17.231  1.00  0.00
ATOM   1150  C   ILE   148      34.141  42.135  17.339  1.00  0.00
ATOM   1151  O   ILE   148      33.894  41.419  16.368  1.00  0.00
ATOM   1152  CB  ILE   148      34.350  44.596  17.266  1.00  0.00
ATOM   1153  CG1 ILE   148      35.302  45.789  17.362  1.00  0.00
ATOM   1154  CG2 ILE   148      33.418  44.625  18.467  1.00  0.00
ATOM   1155  CD1 ILE   148      34.627  47.128  17.157  1.00  0.00
ATOM   1156  N   ASP   149      33.566  41.969  18.525  1.00  0.00
ATOM   1157  CA  ASP   149      32.615  40.892  18.772  1.00  0.00
ATOM   1158  C   ASP   149      31.219  41.268  18.291  1.00  0.00
ATOM   1159  O   ASP   149      30.357  40.405  18.124  1.00  0.00
ATOM   1160  CB  ASP   149      32.534  40.583  20.268  1.00  0.00
ATOM   1161  CG  ASP   149      31.782  39.298  20.557  1.00  0.00
ATOM   1162  OD1 ASP   149      31.505  38.543  19.600  1.00  0.00
ATOM   1163  OD2 ASP   149      31.471  39.045  21.740  1.00  0.00
ATOM   1164  N   VAL   150      30.823  38.227  17.796  1.00  0.00
ATOM   1165  CA  VAL   150      30.324  37.809  19.101  1.00  0.00
ATOM   1166  C   VAL   150      31.470  37.450  20.038  1.00  0.00
ATOM   1167  O   VAL   150      31.270  36.775  21.049  1.00  0.00
ATOM   1168  CB  VAL   150      29.412  36.573  18.987  1.00  0.00
ATOM   1169  CG1 VAL   150      28.971  36.108  20.366  1.00  0.00
ATOM   1170  CG2 VAL   150      28.172  36.900  18.170  1.00  0.00
ATOM   1171  N   VAL   151      30.542  34.648  20.946  1.00  0.00
ATOM   1172  CA  VAL   151      31.581  34.220  20.017  1.00  0.00
ATOM   1173  C   VAL   151      31.136  34.400  18.572  1.00  0.00
ATOM   1174  O   VAL   151      30.042  33.985  18.192  1.00  0.00
ATOM   1175  CB  VAL   151      31.935  32.734  20.211  1.00  0.00
ATOM   1176  CG1 VAL   151      32.918  32.276  19.144  1.00  0.00
ATOM   1177  CG2 VAL   151      32.570  32.511  21.576  1.00  0.00
ATOM   1178  N   CYS   152      31.991  35.024  17.768  1.00  0.00
ATOM   1179  CA  CYS   152      31.683  35.270  16.364  1.00  0.00
ATOM   1180  C   CYS   152      32.827  34.824  15.463  1.00  0.00
ATOM   1181  O   CYS   152      33.993  34.870  15.855  1.00  0.00
ATOM   1182  CB  CYS   152      31.442  36.761  16.122  1.00  0.00
ATOM   1183  SG  CYS   152      31.055  37.187  14.408  1.00  0.00
ATOM   1184  N   ASP   153      32.486  34.392  14.254  1.00  0.00
ATOM   1185  CA  ASP   153      33.484  33.935  13.293  1.00  0.00
ATOM   1186  C   ASP   153      33.643  34.927  12.148  1.00  0.00
ATOM   1187  O   ASP   153      34.168  34.588  11.088  1.00  0.00
ATOM   1188  CB  ASP   153      33.076  32.585  12.698  1.00  0.00
ATOM   1189  CG  ASP   153      33.188  31.451  13.697  1.00  0.00
ATOM   1190  OD1 ASP   153      33.778  31.665  14.777  1.00  0.00
ATOM   1191  OD2 ASP   153      32.686  30.346  13.400  1.00  0.00
ATOM   1192  N   LYS   154      34.883  36.122  12.571  1.00  0.00
ATOM   1193  CA  LYS   154      36.183  36.296  11.933  1.00  0.00
ATOM   1194  C   LYS   154      37.039  35.045  12.078  1.00  0.00
ATOM   1195  O   LYS   154      38.119  34.948  11.495  1.00  0.00
ATOM   1196  CB  LYS   154      36.939  37.464  12.567  1.00  0.00
ATOM   1197  CG  LYS   154      38.184  37.886  11.804  1.00  0.00
ATOM   1198  CD  LYS   154      38.774  39.166  12.374  1.00  0.00
ATOM   1199  CE  LYS   154      39.968  39.634  11.558  1.00  0.00
ATOM   1200  NZ  LYS   154      40.504  40.932  12.053  1.00  0.00
ATOM   1201  N   LEU   155      36.552  34.087  12.861  1.00  0.00
ATOM   1202  CA  LEU   155      37.255  32.825  13.056  1.00  0.00
ATOM   1203  C   LEU   155      36.755  31.760  12.089  1.00  0.00
ATOM   1204  O   LEU   155      37.367  30.703  11.943  1.00  0.00
ATOM   1205  CB  LEU   155      37.044  32.309  14.481  1.00  0.00
ATOM   1206  CG  LEU   155      37.488  33.239  15.612  1.00  0.00
ATOM   1207  CD1 LEU   155      37.185  32.620  16.967  1.00  0.00
ATOM   1208  CD2 LEU   155      38.984  33.503  15.533  1.00  0.00
TER
END
