
#######################################################
#                                                     #
#                        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   34 (  238),  selected   34 , name one
# Molecule2: number of CA atoms   34 (  235),  selected   34 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        0.86     0.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        0.86     0.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        0.86     0.86
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   34
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     S     1_B     S     1_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A     34   34   34     16   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A     34   34   34      4   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A     34   34   34      3   12   30   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A     34   34   34      3   12   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     34   34   34     12   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     34   34   34     12   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     34   34   34     10   16   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     34   34   34     11   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     34   34   34     13   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     34   34   34     16   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     34   34   34     13   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     34   34   34     16   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     34   34   34     16   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     34   34   34     12   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     34   34   34     10   17   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     34   34   34     13   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     34   34   34     17   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     34   34   34     16   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
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     17     30     32     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34 
GDT PERCENT_AT  50.00  88.24  94.12 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.58   0.69   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86
GDT RMS_ALL_AT   1.05   0.90   0.90   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86

# Checking swapping
#   possible swapping detected:  D    20_B      D    20_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A     0.581     0    0.116   0.704     2.427   92.857   87.778
LGA    G     2_B      G     2_A     0.886     0    0.067   0.067     0.886   90.476   90.476
LGA    P     3_B      P     3_A     0.296     0    0.208   0.197     1.501   90.595   88.095
LGA    N     4_B      N     4_A     0.839     0    0.687   1.177     5.433   82.143   67.024
LGA    G     5_B      G     5_A     2.240     0    0.674   0.674     2.842   66.905   66.905
LGA    G     6_B      G     6_A     1.744     0    0.062   0.062     2.337   72.976   72.976
LGA    V     7_B      V     7_A     0.476     0    0.134   0.186     0.754   97.619   94.558
LGA    C     8_B      C     8_A     0.538     0    0.014   0.047     0.588   95.238   95.238
LGA    P     9_B      P     9_A     0.608     0    0.043   0.278     1.478   92.857   90.544
LGA    V    10_B      V    10_A     0.843     0    0.330   0.982     3.137   88.214   79.728
LGA    L    11_B      L    11_A     1.744     3    0.097   0.127     1.848   75.000   46.607
LGA    I    12_B      I    12_A     0.600     0    0.016   0.656     2.437   95.238   88.512
LGA    Y    13_B      Y    13_A     0.569     0    0.028   0.343     3.460   95.238   75.317
LGA    L    14_B      L    14_A     0.785     0    0.031   1.381     3.845   90.476   76.250
LGA    C    15_B      C    15_A     0.593     0    0.020   0.038     0.658   90.476   93.651
LGA    R    16_B      R    16_A     0.401     0    0.102   1.474     8.555   97.619   54.935
LGA    R    17_B      R    17_A     0.535     0    0.028   1.002     4.596   95.238   79.957
LGA    D    18_B      D    18_A     0.754     0    0.020   0.051     0.899   90.476   90.476
LGA    S    19_B      S    19_A     1.061     0    0.013   0.080     1.247   85.952   85.952
LGA    D    20_B      D    20_A     0.778     0    0.059   0.136     1.065   88.214   91.726
LGA    C    21_B      C    21_A     0.252     0    0.020   0.072     0.476  100.000  100.000
LGA    P    22_B      P    22_A     0.615     0    0.060   0.159     0.917   92.857   91.837
LGA    G    23_B      G    23_A     0.433     0    0.045   0.045     0.496  100.000  100.000
LGA    E    24_B      E    24_A     0.503     0    0.041   0.231     1.363   97.619   92.646
LGA    C    25_B      C    25_A     0.314     0    0.021   0.040     0.692   95.238   96.825
LGA    I    26_B      I    26_A     0.720     0    0.057   0.080     1.259   90.476   88.214
LGA    C    27_B      C    27_A     0.490     0    0.022   0.054     0.643   92.857   95.238
LGA    L    28_B      L    28_A     0.708     0    0.032   0.095     1.731   92.857   85.000
LGA    G    29_B      G    29_A     0.802     0    0.029   0.029     1.269   85.952   85.952
LGA    N    30_B      N    30_A     1.551     0    0.050   0.122     2.101   79.286   76.131
LGA    G    31_B      G    31_A     0.762     0    0.077   0.077     0.856   90.476   90.476
LGA    Y    32_B      Y    32_A     0.189     0    0.028   0.132     0.851  100.000   95.238
LGA    C    33_B      C    33_A     0.331     0    0.029   0.047     0.368  100.000  100.000
LGA    G    34_B      G    34_A     0.525     0    0.304   0.304     1.271   92.976   92.976

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       34     136    136  100.00     235    235  100.00                34
SUMMARY(RMSD_GDC):     0.863          0.889                  1.548           90.718   85.507

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     34    0.86    97.059    98.633     3.532

LGA_LOCAL      RMSD:   0.863  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.863  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   0.863  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.335094 * X  +   0.766812 * Y  +   0.547460 * Z  + -36.049950
  Y_new =   0.560469 * X  +  -0.629299 * Y  +   0.538385 * Z  + -30.905804
  Z_new =   0.757355 * X  +   0.126425 * Y  +  -0.640648 * Z  + -23.252178 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.031936 -0.859253  2.946757   [DEG:   59.1256  -49.2316  168.8367 ]
ZXZ:  2.347837  2.266138  1.405392   [DEG:  134.5212  129.8401   80.5230 ]
 
# END of job
