
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , 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:    60       1_A - 60_A        0.37     0.37
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.37     0.37
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.37     0.37
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     60   60   60     45   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     60   60   60     50   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     60   60   60     48   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     60   60   60     31   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  100.00  100.00 )

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     54     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  90.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37
GDT RMS_ALL_AT   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37

# Checking swapping
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    37_A      E    37_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  D    53_A      D    53_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.807     0    0.227   0.814     1.633   88.214   87.202
LGA    D     2_A      D     2_A     0.394     0    0.012   0.489     2.353   97.619   90.893
LGA    K     3_A      K     3_A     0.527     0    0.019   0.568     1.683   97.619   89.683
LGA    A     4_A      A     4_A     0.520     0    0.045   0.054     0.602   95.238   94.286
LGA    A     5_A      A     5_A     0.288     0    0.046   0.062     0.503  100.000   98.095
LGA    C     6_A      C     6_A     0.164     0    0.021   0.056     0.211  100.000  100.000
LGA    A     7_A      A     7_A     0.176     0    0.036   0.047     0.268  100.000  100.000
LGA    D     8_A      D     8_A     0.277     0    0.019   0.099     0.677  100.000   96.429
LGA    G     9_A      G     9_A     0.101     0    0.050   0.050     0.215  100.000  100.000
LGA    I    10_A      I    10_A     0.214     0    0.022   0.047     0.337  100.000  100.000
LGA    A    11_A      A    11_A     0.250     0    0.035   0.046     0.289  100.000  100.000
LGA    A    12_A      A    12_A     0.091     0    0.012   0.017     0.264  100.000  100.000
LGA    V    13_A      V    13_A     0.244     0    0.023   0.049     0.378  100.000  100.000
LGA    K    14_A      K    14_A     0.251     0    0.083   0.204     0.719   97.619   96.825
LGA    A    15_A      A    15_A     0.218     0    0.044   0.041     0.424  100.000  100.000
LGA    R    16_A      R    16_A     0.319     0    0.018   1.076     4.698  100.000   85.801
LGA    V    17_A      V    17_A     0.269     0    0.035   0.047     0.315  100.000  100.000
LGA    E    18_A      E    18_A     0.170     0    0.024   0.713     3.409  100.000   83.598
LGA    K    19_A      K    19_A     0.416     0    0.048   1.069     5.178   95.238   79.365
LGA    L    20_A      L    20_A     0.385     0    0.032   0.155     0.542  100.000   98.810
LGA    A    21_A      A    21_A     0.345     0    0.019   0.025     0.393  100.000  100.000
LGA    P    22_A      P    22_A     0.504     0    0.049   0.063     0.843   92.857   94.558
LGA    E    23_A      E    23_A     0.530     0    0.081   0.897     3.094   92.857   80.265
LGA    A    24_A      A    24_A     0.397     0    0.067   0.078     0.510  100.000   98.095
LGA    V    25_A      V    25_A     0.255     0    0.039   0.068     0.347  100.000  100.000
LGA    P    26_A      P    26_A     0.233     0    0.023   0.088     0.395  100.000  100.000
LGA    Q    27_A      Q    27_A     0.254     0    0.012   1.210     4.058  100.000   77.249
LGA    K    28_A      K    28_A     0.231     0    0.051   0.827     3.537  100.000   81.217
LGA    L    29_A      L    29_A     0.261     0    0.026   1.127     2.723  100.000   89.286
LGA    K    30_A      K    30_A     0.382     0    0.017   0.102     0.699  100.000   98.942
LGA    R    31_A      R    31_A     0.374     0    0.039   1.367     7.191  100.000   67.013
LGA    A    32_A      A    32_A     0.394     0    0.037   0.052     0.411  100.000  100.000
LGA    L    33_A      L    33_A     0.354     0    0.038   0.058     0.441  100.000  100.000
LGA    K    34_A      K    34_A     0.260     0    0.060   0.951     3.994  100.000   80.317
LGA    I    35_A      I    35_A     0.370     0    0.095   0.096     0.487  100.000  100.000
LGA    A    36_A      A    36_A     0.383     0    0.017   0.017     0.463  100.000  100.000
LGA    E    37_A      E    37_A     0.272     0    0.021   0.368     0.942  100.000   97.884
LGA    R    38_A      R    38_A     0.301     0    0.073   0.550     2.134  100.000   91.688
LGA    E    39_A      E    39_A     0.398     0    0.029   1.093     3.727  100.000   84.656
LGA    Q    40_A      Q    40_A     0.320     0    0.050   0.251     0.887   97.619   96.825
LGA    G    41_A      G    41_A     0.145     0    0.042   0.042     0.239  100.000  100.000
LGA    E    42_A      E    42_A     0.453     0    0.132   0.455     1.731  100.000   93.810
LGA    G    43_A      G    43_A     0.319     0    0.055   0.055     0.470  100.000  100.000
LGA    E    44_A      E    44_A     0.279     0    0.022   0.931     4.332  100.000   82.698
LGA    F    45_A      F    45_A     0.389     0    0.016   0.060     0.504  100.000   99.134
LGA    D    46_A      D    46_A     0.512     0    0.077   1.202     4.245   97.619   80.952
LGA    E    47_A      E    47_A     0.398     0    0.032   0.358     1.733  100.000   93.810
LGA    C    48_A      C    48_A     0.038     0    0.017   0.079     0.189  100.000  100.000
LGA    L    49_A      L    49_A     0.131     0    0.029   0.121     0.377  100.000  100.000
LGA    E    50_A      E    50_A     0.108     0    0.024   0.228     0.894  100.000   98.942
LGA    A    51_A      A    51_A     0.097     0    0.013   0.026     0.214  100.000  100.000
LGA    L    52_A      L    52_A     0.254     0    0.016   0.053     0.490  100.000  100.000
LGA    D    53_A      D    53_A     0.227     0    0.041   0.288     0.994  100.000   97.619
LGA    D    54_A      D    54_A     0.184     0    0.020   0.344     1.091  100.000   94.167
LGA    A    55_A      A    55_A     0.331     0    0.004   0.012     0.441  100.000  100.000
LGA    K    56_A      K    56_A     0.629     0    0.044   0.656     1.366   97.619   90.635
LGA    R    57_A      R    57_A     0.251     0    0.017   1.130     4.649  100.000   80.606
LGA    A    58_A      A    58_A     0.603     0    0.033   0.036     0.958   92.857   92.381
LGA    L    59_A      L    59_A     0.426     0    0.053   0.236     1.071   97.619   95.298
LGA    P    60_A      P    60_A     0.938     0    0.033   0.349     1.174   90.476   89.184

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     0.365          0.369                  1.167           98.851   93.804

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.37   100.000   100.000    12.891

LGA_LOCAL      RMSD:   0.365  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.365  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.365  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.406950 * X  +  -0.043849 * Y  +   0.912398 * Z  +  13.295703
  Y_new =  -0.377573 * X  +   0.917598 * Y  +  -0.124307 * Z  +   8.523183
  Z_new =  -0.831764 * X  +  -0.395083 * Y  +  -0.389973 * Z  +   7.760220 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.393623  0.982277 -2.349685   [DEG: -137.1445   56.2804 -134.6271 ]
ZXZ:  1.435388  1.971398 -2.014240   [DEG:   82.2417  112.9528 -115.4074 ]
 
# END of job
