
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   56 (  427),  selected   56 , name one
# Molecule2: number of CA atoms  369 ( 2890),  selected   56 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    56     318_A - 373_A       1.54     1.54
  LCS_AVERAGE:     15.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    56     318_A - 373_A       1.54     1.54
  LCS_AVERAGE:     15.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40     318_A - 357_A       0.99     1.83
  LCS_AVERAGE:      8.83

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   56
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     N   318_A     N   318_A     40   56   56     18   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     V   319_A     V   319_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     L   320_A     L   320_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     L   321_A     L   321_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     L   322_A     L   322_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     E   323_A     E   323_A     40   56   56     18   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     P   324_A     P   324_A     40   56   56     18   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     G   325_A     G   325_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     K   326_A     K   326_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     V   327_A     V   327_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     I   328_A     I   328_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     A   329_A     A   329_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     H   330_A     H   330_A     40   56   56     21   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     A   331_A     A   331_A     40   56   56      8   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     D   332_A     D   332_A     40   56   56     23   35   40   47   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     C   333_A     C   333_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     H   334_A     H   334_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     K   335_A     K   335_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     T   336_A     T   336_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     N   337_A     N   337_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     Q   338_A     Q   338_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     K   339_A     K   339_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     I   340_A     I   340_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     R   341_A     R   341_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     D   342_A     D   342_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     A   343_A     A   343_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     G   344_A     G   344_A     40   56   56     22   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     V   345_A     V   345_A     40   56   56     22   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     E   346_A     E   346_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     V   347_A     V   347_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     I   348_A     I   348_A     40   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     E   349_A     E   349_A     40   56   56      3   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     V   350_A     V   350_A     40   56   56      3   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     T   351_A     T   351_A     40   56   56     12   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     G   352_A     G   352_A     40   56   56      3   14   34   46   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     T   353_A     T   353_A     40   56   56      3    5   35   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     E   354_A     E   354_A     40   56   56      3   25   37   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     I   355_A     I   355_A     40   56   56      3    7   35   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     R   356_A     R   356_A     40   56   56      3   10   19   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     K   357_A     K   357_A     40   56   56      3   11   29   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     A   358_A     A   358_A     15   56   56      3   10   20   47   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     C   359_A     C   359_A     15   56   56      3   10   19   28   44   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     G   360_A     G   360_A     15   56   56      3   11   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     G   361_A     G   361_A     15   56   56      4   11   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     I   362_A     I   362_A     15   56   56      4   11   29   47   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     K   363_A     K   363_A     15   56   56      8   33   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     C   364_A     C   364_A     15   56   56     23   35   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     R   365_A     R   365_A     15   56   56      3   15   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     V   366_A     V   366_A     15   56   56     11   33   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     M   367_A     M   367_A     15   56   56      4   15   25   47   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     Q   368_A     Q   368_A     15   56   56      4   31   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     I   369_A     I   369_A     15   56   56      4   16   37   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     N   370_A     N   370_A     15   56   56      3   16   38   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     R   371_A     R   371_A     12   56   56     15   34   40   48   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     E   372_A     E   372_A      9   56   56      3   35   40   46   54   55   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_GDT     P   373_A     P   373_A      9   56   56      3    5   23   42   50   52   56   56   56   56   56   56   56   56   56   56   56   56   56   56 
LCS_AVERAGE  LCS_A:  13.06  (   8.83   15.18   15.18 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
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_AT     23     35     40     48     54     55     56     56     56     56     56     56     56     56     56     56     56     56     56     56 
GDT PERCENT_AT   6.23   9.49  10.84  13.01  14.63  14.91  15.18  15.18  15.18  15.18  15.18  15.18  15.18  15.18  15.18  15.18  15.18  15.18  15.18  15.18
GDT RMS_LOCAL    0.31   0.50   0.71   1.24   1.40   1.48   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_AT   1.73   1.75   1.73   1.57   1.55   1.55   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

# Checking swapping
#   possible swapping detected:  D   332_A      D   332_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    N   318_A      N   318_A     1.153     0    0.039   1.115     3.781   83.690   72.679
LGA    V   319_A      V   319_A     0.782     0    0.030   1.171     2.717   90.476   80.952
LGA    L   320_A      L   320_A     0.552     0    0.118   1.410     4.671   92.857   75.774
LGA    L   321_A      L   321_A     0.472     0    0.074   1.069     2.769   95.238   84.524
LGA    L   322_A      L   322_A     0.890     0    0.050   0.898     3.057   90.476   83.155
LGA    E   323_A      E   323_A     1.432     0    0.052   0.695     2.109   81.429   78.624
LGA    P   324_A      P   324_A     1.457     0    0.025   0.214     1.907   79.286   76.531
LGA    G   325_A      G   325_A     0.700     0    0.045   0.045     0.842   90.476   90.476
LGA    K   326_A      K   326_A     0.743     0    0.048   0.544     3.611   90.476   77.725
LGA    V   327_A      V   327_A     0.591     0    0.055   0.120     0.644   90.476   93.197
LGA    I   328_A      I   328_A     0.408     0    0.038   0.996     2.281   92.857   84.226
LGA    A   329_A      A   329_A     0.747     0    0.114   0.152     1.062   90.476   88.667
LGA    H   330_A      H   330_A     0.455     0    0.087   1.087     2.569   97.619   85.571
LGA    A   331_A      A   331_A     1.237     0    0.085   0.086     1.696   81.548   79.810
LGA    D   332_A      D   332_A     1.395     0    0.250   0.918     2.298   85.952   79.464
LGA    C   333_A      C   333_A     0.846     0    0.016   0.780     1.709   88.214   84.524
LGA    H   334_A      H   334_A     0.594     0    0.003   1.380     6.571   90.476   60.857
LGA    K   335_A      K   335_A     0.603     0    0.015   1.081     6.776   90.476   64.021
LGA    T   336_A      T   336_A     0.567     0    0.046   1.113     2.566   92.857   83.401
LGA    N   337_A      N   337_A     0.599     0    0.057   1.204     4.072   92.857   81.667
LGA    Q   338_A      Q   338_A     0.772     0    0.029   0.580     2.981   90.476   79.894
LGA    K   339_A      K   339_A     0.587     0    0.043   0.850     2.827   92.857   82.116
LGA    I   340_A      I   340_A     0.733     0    0.040   0.883     1.990   90.476   83.869
LGA    R   341_A      R   341_A     0.780     0    0.071   0.217     1.059   90.476   89.654
LGA    D   342_A      D   342_A     0.835     0    0.039   1.209     5.567   88.214   70.595
LGA    A   343_A      A   343_A     1.074     0    0.210   0.203     1.393   90.595   88.762
LGA    G   344_A      G   344_A     1.080     0    0.051   0.051     1.201   81.429   81.429
LGA    V   345_A      V   345_A     1.059     0    0.059   1.170     3.480   85.952   79.524
LGA    E   346_A      E   346_A     0.791     0    0.077   0.181     0.927   90.476   90.476
LGA    V   347_A      V   347_A     0.718     0    0.052   0.087     1.197   88.214   89.184
LGA    I   348_A      I   348_A     0.735     0    0.104   1.047     2.196   90.476   82.857
LGA    E   349_A      E   349_A     1.290     0    0.105   0.813     2.744   81.429   75.873
LGA    V   350_A      V   350_A     1.209     0    0.120   0.181     1.821   81.429   77.755
LGA    T   351_A      T   351_A     1.132     0    0.023   1.074     2.942   77.143   74.286
LGA    G   352_A      G   352_A     2.189     0    0.480   0.480     2.743   64.881   64.881
LGA    T   353_A      T   353_A     2.408     0    0.039   1.061     4.322   62.857   55.782
LGA    E   354_A      E   354_A     2.029     0    0.069   0.248     2.362   66.786   65.661
LGA    I   355_A      I   355_A     2.480     0    0.020   0.904     4.655   60.952   55.298
LGA    R   356_A      R   356_A     2.569     0    0.219   1.464     6.380   55.357   54.762
LGA    K   357_A      K   357_A     2.322     0    0.114   0.696     3.260   59.167   69.683
LGA    A   358_A      A   358_A     2.575     0    0.045   0.057     3.116   55.476   55.810
LGA    C   359_A      C   359_A     3.827     0    0.516   0.643     5.521   39.524   38.730
LGA    G   360_A      G   360_A     1.634     0    0.041   0.041     1.786   72.857   72.857
LGA    G   361_A      G   361_A     1.535     0    0.043   0.043     1.573   72.857   72.857
LGA    I   362_A      I   362_A     2.046     0    0.050   1.436     5.459   70.833   55.357
LGA    K   363_A      K   363_A     1.596     0    0.034   0.988     4.207   77.143   66.455
LGA    C   364_A      C   364_A     0.292     0    0.038   0.092     0.784   97.619   96.825
LGA    R   365_A      R   365_A     1.349     0    0.205   0.955     6.377   83.690   60.260
LGA    V   366_A      V   366_A     1.405     0    0.116   1.047     4.352   77.143   71.429
LGA    M   367_A      M   367_A     2.816     0    0.029   1.013     5.613   60.952   52.083
LGA    Q   368_A      Q   368_A     1.443     0    0.046   0.473     3.811   72.976   68.730
LGA    I   369_A      I   369_A     2.351     0    0.059   0.529     3.830   64.881   59.286
LGA    N   370_A      N   370_A     2.354     0    0.095   0.298     3.898   70.952   57.976
LGA    R   371_A      R   371_A     0.493     0    0.081   0.782     2.149   88.333   79.351
LGA    E   372_A      E   372_A     1.785     0    0.023   0.794     2.843   75.238   67.725
LGA    P   373_A      P   373_A     3.285     0    0.393   0.510     3.642   53.810   53.197

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       56     224    224  100.00     427    427  100.00               369
SUMMARY(RMSD_GDC):     1.539          1.541                  2.142           12.228   11.239

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56  369    4.0     56    1.54    13.211    14.199     3.416

LGA_LOCAL      RMSD:   1.539  Number of atoms:   56  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.540  Number of assigned atoms:   56 
Std_ASGN_ATOMS RMSD:   1.539  Standard rmsd on all 56 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.998437 * X  +   0.050767 * Y  +   0.023354 * Z  +  82.607811
  Y_new =   0.044989 * X  +   0.978155 * Y  +  -0.202948 * Z  + -98.851143
  Z_new =  -0.033147 * X  +  -0.201580 * Y  +  -0.978911 * Z  +  61.364594 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  3.096564  0.033153 -2.938508   [DEG:  177.4200    1.8995 -168.3641 ]
ZXZ:  0.114570  2.935857 -2.978615   [DEG:    6.5644  168.2122 -170.6621 ]
 
# END of job
