
#######################################################
#                                                     #
#                        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   38 (  321),  selected   38 , name one
# Molecule2: number of CA atoms   39 (  326),  selected   38 , 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:    38       1_A - 38_A        0.67     0.67
  LCS_AVERAGE:     97.44

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    38       1_A - 38_A        0.67     0.67
  LCS_AVERAGE:     97.44

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    38       1_A - 38_A        0.67     0.67
  LCS_AVERAGE:     97.44

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   38
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     D     1_A     D     1_A     38   38   38      5   14   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     K     2_A     K     2_A     38   38   38      5   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     L     3_A     L     3_A     38   38   38     23   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     W     4_A     W     4_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     I     5_A     I     5_A     38   38   38     17   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     L     6_A     L     6_A     38   38   38     19   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     Q     7_A     Q     7_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     K     8_A     K     8_A     38   38   38     17   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     I     9_A     I     9_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     Y    10_A     Y    10_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     E    11_A     E    11_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     I    12_A     I    12_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     M    13_A     M    13_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     V    14_A     V    14_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     R    15_A     R    15_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     L    16_A     L    16_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     D    17_A     D    17_A     38   38   38     13   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     E    18_A     E    18_A     38   38   38     17   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     E    19_A     E    19_A     38   38   38     15   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     G    20_A     G    20_A     38   38   38     21   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     H    21_A     H    21_A     38   38   38     15   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     G    22_A     G    22_A     38   38   38     18   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     E    23_A     E    23_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     A    24_A     A    24_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     S    25_A     S    25_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     L    26_A     L    26_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     M    27_A     M    27_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     V    28_A     V    28_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     S    29_A     S    29_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     D    30_A     D    30_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     L    31_A     L    31_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     I    32_A     I    32_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     Y    33_A     Y    33_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     E    34_A     E    34_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     F    35_A     F    35_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     M    36_A     M    36_A     38   38   38     24   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     K    37_A     K    37_A     38   38   38     16   34   37   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_GDT     R    38_A     R    38_A     38   38   38      3   29   36   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38   38 
LCS_AVERAGE  LCS_A:  97.44  (  97.44   97.44   97.44 )

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     24     34     37     38     38     38     38     38     38     38     38     38     38     38     38     38     38     38     38     38 
GDT PERCENT_AT  61.54  87.18  94.87  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44  97.44
GDT RMS_LOCAL    0.34   0.50   0.61   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67
GDT RMS_ALL_AT   0.68   0.68   0.68   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     1.653     0    0.539   1.475     4.794   67.619   57.679
LGA    K     2_A      K     2_A     1.023     0    0.034   0.207     1.609   85.952   82.487
LGA    L     3_A      L     3_A     0.492     0    0.022   0.075     0.641   95.238   96.429
LGA    W     4_A      W     4_A     0.517     0    0.092   1.137     7.441   92.857   53.469
LGA    I     5_A      I     5_A     1.265     0    0.064   1.388     5.343   88.214   72.738
LGA    L     6_A      L     6_A     0.709     0    0.000   0.044     0.996   95.238   92.857
LGA    Q     7_A      Q     7_A     0.181     0    0.078   0.101     0.564  100.000   97.884
LGA    K     8_A      K     8_A     0.688     0    0.059   0.875     6.074   92.857   73.651
LGA    I     9_A      I     9_A     0.488     0    0.009   0.115     1.224   97.619   92.917
LGA    Y    10_A      Y    10_A     0.117     0    0.013   0.052     0.678  100.000   97.619
LGA    E    11_A      E    11_A     0.396     0    0.000   0.102     0.978  100.000   94.709
LGA    I    12_A      I    12_A     0.478     0    0.055   0.787     2.262  100.000   87.619
LGA    M    13_A      M    13_A     0.527     0    0.037   0.722     1.960   97.619   89.583
LGA    V    14_A      V    14_A     0.358     0    0.024   0.045     0.724  100.000   95.918
LGA    R    15_A      R    15_A     0.405     0    0.008   1.269     7.569  100.000   67.100
LGA    L    16_A      L    16_A     0.294     0    0.054   0.080     0.565  100.000   98.810
LGA    D    17_A      D    17_A     0.678     0    0.000   0.906     2.352   92.857   81.905
LGA    E    18_A      E    18_A     0.988     0    0.020   0.260     2.302   88.214   77.937
LGA    E    19_A      E    19_A     0.791     0    0.109   0.735     2.235   90.476   82.646
LGA    G    20_A      G    20_A     0.690     0    0.010   0.010     1.358   90.595   90.595
LGA    H    21_A      H    21_A     0.966     0    0.042   0.457     2.671   90.476   77.571
LGA    G    22_A      G    22_A     0.621     0    0.036   0.036     0.739   92.857   92.857
LGA    E    23_A      E    23_A     0.411     0    0.019   0.351     1.635   97.619   92.751
LGA    A    24_A      A    24_A     0.371     0    0.032   0.029     0.576  100.000   98.095
LGA    S    25_A      S    25_A     0.278     0    0.048   0.050     0.378  100.000  100.000
LGA    L    26_A      L    26_A     0.246     0    0.060   0.065     0.599  100.000   98.810
LGA    M    27_A      M    27_A     0.443     0    0.030   0.149     0.498  100.000  100.000
LGA    V    28_A      V    28_A     0.418     0    0.029   0.079     0.453  100.000  100.000
LGA    S    29_A      S    29_A     0.238     0    0.000   0.090     0.915  100.000   98.413
LGA    D    30_A      D    30_A     0.247     0    0.037   0.078     0.463  100.000  100.000
LGA    L    31_A      L    31_A     0.394     0    0.024   0.954     3.703   97.619   84.940
LGA    I    32_A      I    32_A     0.343     0    0.045   0.115     0.588  100.000   98.810
LGA    Y    33_A      Y    33_A     0.286     0    0.012   0.105     0.710  100.000   96.032
LGA    E    34_A      E    34_A     0.372     0    0.050   0.726     3.610  100.000   85.714
LGA    F    35_A      F    35_A     0.447     0    0.000   0.450     1.715  100.000   89.870
LGA    M    36_A      M    36_A     0.237     0    0.072   0.110     0.430  100.000  100.000
LGA    K    37_A      K    37_A     0.751     0    0.058   0.564     1.559   85.952   86.561
LGA    R    38_A      R    38_A     1.628     0    0.133   1.130     8.844   67.143   46.450

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       38     152    152  100.00     321    321  100.00                39
SUMMARY(RMSD_GDC):     0.668          0.733                  1.747           92.488   85.421

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   39    4.0     38    0.67    94.872    96.435     4.947

LGA_LOCAL      RMSD:   0.668  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.668  Number of assigned atoms:   38 
Std_ASGN_ATOMS RMSD:   0.668  Standard rmsd on all 38 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.290253 * X  +  -0.758892 * Y  +  -0.582954 * Z  + 184.698990
  Y_new =  -0.926482 * X  +  -0.375344 * Y  +   0.027329 * Z  + 279.516937
  Z_new =  -0.239548 * X  +   0.532165 * Y  +  -0.812045 * Z  + 103.915565 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.267196  0.241900  2.561473   [DEG:  -72.6050   13.8599  146.7616 ]
ZXZ: -1.617642  2.518444 -0.422970   [DEG:  -92.6840  144.2962  -24.2344 ]
 
# END of job
