
#######################################################
#                                                     #
#                        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   37 (  286),  selected   37 , name one
# Molecule2: number of CA atoms   83 (  623),  selected   37 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:E  -ch2:E  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37      21_E - 57_E        2.92     2.92
  LCS_AVERAGE:     44.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      23_E - 45_E        1.97     4.50
  LONGEST_CONTINUOUS_SEGMENT:    23      35_E - 57_E        1.92     3.96
  LCS_AVERAGE:     27.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      23_E - 42_E        0.88     6.11
  LCS_AVERAGE:     21.10

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   37
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     A    21_E     A    21_E      4    4   37      3    3   15   18   21   25   29   33   35   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     S    22_E     S    22_E      4   22   37      3    3    4    4   10   23   27   33   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     A    23_E     A    23_E     20   23   37     15   17   19   19   20   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     K    24_E     K    24_E     20   23   37     15   17   19   19   20   23   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     E    25_E     E    25_E     20   23   37     15   17   19   19   20   23   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    26_E     L    26_E     20   23   37     15   17   19   19   20   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     Q    27_E     Q    27_E     20   23   37     15   17   19   19   20   25   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    28_E     L    28_E     20   23   37     15   17   19   19   20   23   32   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     E    29_E     E    29_E     20   23   37     15   17   19   19   20   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    30_E     L    30_E     20   23   37     13   17   19   19   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     I    31_E     I    31_E     20   23   37     15   17   19   19   20   24   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     K    32_E     K    32_E     20   23   37     15   17   19   19   20   23   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     Q    33_E     Q    33_E     20   23   37     15   17   19   19   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     F    34_E     F    34_E     20   23   37     15   17   19   19   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     M    35_E     M    35_E     20   23   37     15   17   19   19   20   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     A    36_E     A    36_E     20   23   37     15   17   19   19   20   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     E    37_E     E    37_E     20   23   37     15   17   19   19   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     A    38_E     A    38_E     20   23   37     15   17   19   19   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     M    39_E     M    39_E     20   23   37     12   17   19   19   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     K    40_E     K    40_E     20   23   37      4   17   19   19   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     I    41_E     I    41_E     20   23   37      4   13   19   19   20   25   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     G    42_E     G    42_E     20   23   37      3   16   17   19   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     N    43_E     N    43_E     16   23   37     13   16   17   18   20   25   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     K    44_E     K    44_E     16   23   37     13   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     E    45_E     E    45_E     16   23   37      7   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     G    46_E     G    46_E     16   23   37     13   16   17   18   21   25   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    47_E     L    47_E     16   23   37     13   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    48_E     L    48_E     16   23   37     13   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    49_E     L    49_E     16   23   37     13   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    50_E     L    50_E     16   23   37     13   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     A    51_E     A    51_E     16   23   37     13   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     E    52_E     E    52_E     16   23   37     13   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     R    53_E     R    53_E     16   23   37     13   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    54_E     L    54_E     16   23   37     13   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     E    55_E     E    55_E     16   23   37     13   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     A    56_E     A    56_E     16   23   37     13   16   17   18   21   26   33   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    57_E     L    57_E     16   23   37     12   16   17   18   21   26   31   35   36   37   37   37   37   37   37   37   37   37   37   37 
LCS_AVERAGE  LCS_A:  30.91  (  21.10   27.06   44.58 )

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     15     17     19     19     21     26     33     35     36     37     37     37     37     37     37     37     37     37     37     37 
GDT PERCENT_AT  18.07  20.48  22.89  22.89  25.30  31.33  39.76  42.17  43.37  44.58  44.58  44.58  44.58  44.58  44.58  44.58  44.58  44.58  44.58  44.58
GDT RMS_LOCAL    0.34   0.38   0.55   0.55   1.56   2.27   2.71   2.77   2.85   2.92   2.92   2.92   2.92   2.92   2.92   2.92   2.92   2.92   2.92   2.92
GDT RMS_ALL_AT   6.33   6.23   6.46   6.46   3.77   2.98   2.97   2.97   2.94   2.92   2.92   2.92   2.92   2.92   2.92   2.92   2.92   2.92   2.92   2.92

# Checking swapping
#   possible swapping detected:  E    25_E      E    25_E
#   possible swapping detected:  E    37_E      E    37_E
#   possible swapping detected:  E    52_E      E    52_E

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    21_E      A    21_E     5.481     0    0.265   0.280     7.570   30.238   25.619
LGA    S    22_E      S    22_E     5.272     0    0.140   0.766     6.222   30.238   27.381
LGA    A    23_E      A    23_E     2.501     0    0.508   0.479     2.906   59.048   60.190
LGA    K    24_E      K    24_E     3.960     0    0.062   0.428     7.504   43.452   29.101
LGA    E    25_E      E    25_E     3.876     0    0.036   0.760     5.872   45.000   36.402
LGA    L    26_E      L    26_E     1.991     0    0.072   0.180     2.455   70.833   70.833
LGA    Q    27_E      Q    27_E     2.893     0    0.042   0.083     5.247   57.262   44.392
LGA    L    28_E      L    28_E     3.969     0    0.072   1.392     8.723   45.000   32.202
LGA    E    29_E      E    29_E     2.725     0    0.076   0.982     5.122   60.952   51.640
LGA    L    30_E      L    30_E     1.274     0    0.118   0.221     1.707   77.143   79.286
LGA    I    31_E      I    31_E     3.205     0    0.032   0.653     6.964   51.786   40.774
LGA    K    32_E      K    32_E     3.750     0    0.026   0.747     9.765   48.333   29.630
LGA    Q    33_E      Q    33_E     2.214     0    0.074   1.082     4.346   66.786   56.243
LGA    F    34_E      F    34_E     2.222     0    0.089   1.279     8.796   66.786   38.139
LGA    M    35_E      M    35_E     2.894     0    0.068   0.747     3.770   57.262   54.643
LGA    A    36_E      A    36_E     3.116     0    0.025   0.038     3.693   55.357   52.952
LGA    E    37_E      E    37_E     1.864     0    0.035   0.951     2.487   70.833   72.963
LGA    A    38_E      A    38_E     2.319     0    0.119   0.128     2.792   64.881   63.333
LGA    M    39_E      M    39_E     2.426     0    0.129   1.034     3.854   68.810   62.321
LGA    K    40_E      K    40_E     1.594     0    0.219   1.038     2.845   69.048   68.519
LGA    I    41_E      I    41_E     3.315     0    0.566   1.027     6.665   52.262   42.619
LGA    G    42_E      G    42_E     1.019     0    0.103   0.103     2.072   72.976   72.976
LGA    N    43_E      N    43_E     3.462     0    0.214   0.945     7.692   51.786   38.036
LGA    K    44_E      K    44_E     2.782     0    0.030   0.850     4.837   57.262   52.011
LGA    E    45_E      E    45_E     3.364     0    0.116   0.832     5.589   51.786   39.471
LGA    G    46_E      G    46_E     3.348     0    0.031   0.031     3.349   53.571   53.571
LGA    L    47_E      L    47_E     2.111     0    0.024   1.403     3.886   62.857   59.345
LGA    L    48_E      L    48_E     1.971     0    0.044   0.117     2.243   66.786   69.821
LGA    L    49_E      L    49_E     2.786     0    0.021   1.421     6.725   57.143   41.845
LGA    L    50_E      L    50_E     2.776     0    0.016   0.142     3.067   57.143   57.202
LGA    A    51_E      A    51_E     2.278     0    0.099   0.105     2.450   64.762   64.762
LGA    E    52_E      E    52_E     2.389     0    0.041   1.158     2.988   64.762   67.619
LGA    R    53_E      R    53_E     2.642     0    0.045   1.110     7.158   57.143   38.485
LGA    L    54_E      L    54_E     2.735     0    0.043   0.482     3.615   57.143   59.405
LGA    E    55_E      E    55_E     2.174     0    0.025   0.601     2.435   64.762   70.265
LGA    A    56_E      A    56_E     2.683     0    0.053   0.053     2.883   57.143   57.143
LGA    L    57_E      L    57_E     3.038     0    0.666   0.539     4.481   51.786   47.619

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       37     148    148  100.00     286    286  100.00                83
SUMMARY(RMSD_GDC):     2.924          2.808                  3.590           25.785   23.238

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   37   83    4.0     35    2.77    32.530    32.616     1.220

LGA_LOCAL      RMSD:   2.768  Number of atoms:   35  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.969  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   2.924  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.447553 * X  +  -0.887388 * Y  +   0.110626 * Z  + -25.911167
  Y_new =   0.716519 * X  +   0.281827 * Y  +  -0.638102 * Z  + -40.021980
  Z_new =   0.535067 * X  +   0.364850 * Y  +   0.761963 * Z  + -149.584045 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.012469 -0.564588  0.446568   [DEG:   58.0102  -32.3485   25.5865 ]
ZXZ:  0.171660  0.704458  0.972337   [DEG:    9.8354   40.3625   55.7108 ]
 
# END of job
