
#######################################################
#                                                     #
#                        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   26 (  207),  selected   26 , name one
# Molecule2: number of CA atoms   37 (  291),  selected   26 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26       5_B - 30_B        2.23     2.23
  LCS_AVERAGE:     70.27

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25       6_B - 30_B        1.47     2.36
  LCS_AVERAGE:     65.28

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       7_B - 30_B        0.56     2.56
  LCS_AVERAGE:     60.50

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   26
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     E     5_C     E     5_B      3    3   26      3    3    3    3    4    4    5    7   10   13   16   20   24   26   26   26   26   26   26   26 
LCS_GDT     Q     6_C     Q     6_B      3   25   26      3    3    3    6    8   12   16   20   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     E     7_C     E     7_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     K     8_C     K     8_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     D     9_C     D     9_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     Q    10_C     Q    10_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     L    11_C     L    11_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     R    12_C     R    12_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     T    13_C     T    13_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     Q    14_C     Q    14_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     V    15_C     V    15_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     V    16_C     V    16_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     R    17_C     R    17_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     L    18_C     L    18_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     Q    19_C     Q    19_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     A    20_C     A    20_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     E    21_C     E    21_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     K    22_C     K    22_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     A    23_C     A    23_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     D    24_C     D    24_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     L    25_C     L    25_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     L    26_C     L    26_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     G    27_C     G    27_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     I    28_C     I    28_B     24   25   26     18   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     V    29_C     V    29_B     24   25   26      9   23   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_GDT     S    30_C     S    30_B     24   25   26      9   22   24   24   24   24   24   24   25   25   25   25   25   26   26   26   26   26   26   26 
LCS_AVERAGE  LCS_A:  65.35  (  60.50   65.28   70.27 )

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     18     23     24     24     24     24     24     24     25     25     25     25     25     26     26     26     26     26     26     26 
GDT PERCENT_AT  48.65  62.16  64.86  64.86  64.86  64.86  64.86  64.86  67.57  67.57  67.57  67.57  67.57  70.27  70.27  70.27  70.27  70.27  70.27  70.27
GDT RMS_LOCAL    0.27   0.50   0.56   0.56   0.56   0.56   0.56   0.56   1.47   1.47   1.47   1.47   1.47   2.23   2.23   2.23   2.23   2.23   2.23   2.23
GDT RMS_ALL_AT   2.54   2.54   2.56   2.56   2.56   2.56   2.56   2.56   2.36   2.36   2.36   2.36   2.36   2.23   2.23   2.23   2.23   2.23   2.23   2.23

# Checking swapping
#   possible swapping detected:  E     5_C      E     5_B
#   possible swapping detected:  E     7_C      E     7_B
#   possible swapping detected:  D     9_C      D     9_B
#   possible swapping detected:  E    21_C      E    21_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E     5_C      E     5_B    10.431     0    0.570   1.247    13.264    1.071    0.476
LGA    Q     6_C      Q     6_B     7.380     0    0.603   1.327    14.915   16.429    7.831
LGA    E     7_C      E     7_B     0.312     0    0.536   1.395     7.304   86.905   54.868
LGA    K     8_C      K     8_B     0.402     0    0.092   1.391     7.572  100.000   70.582
LGA    D     9_C      D     9_B     0.843     0    0.031   0.116     1.831   90.476   84.881
LGA    Q    10_C      Q    10_B     0.742     0    0.012   0.184     2.021   90.476   85.608
LGA    L    11_C      L    11_B     0.415     0    0.021   1.397     3.301   97.619   83.810
LGA    R    12_C      R    12_B     0.652     0    0.042   0.945     3.336   92.857   78.182
LGA    T    13_C      T    13_B     0.381     0    0.055   0.995     2.471   97.619   88.367
LGA    Q    14_C      Q    14_B     0.514     0    0.026   0.943     4.363   92.857   75.873
LGA    V    15_C      V    15_B     0.630     0    0.044   0.064     0.830   95.238   93.197
LGA    V    16_C      V    16_B     0.303     0    0.058   0.082     0.449  100.000  100.000
LGA    R    17_C      R    17_B     0.237     0    0.020   1.942     8.019  100.000   67.273
LGA    L    18_C      L    18_B     0.480     0    0.031   0.138     1.182   97.619   92.917
LGA    Q    19_C      Q    19_B     0.559     0    0.007   0.106     0.641   92.857   93.651
LGA    A    20_C      A    20_B     0.400     0    0.061   0.062     0.490  100.000  100.000
LGA    E    21_C      E    21_B     0.393     0    0.018   0.896     2.876  100.000   83.492
LGA    K    22_C      K    22_B     0.609     0    0.024   0.826     5.143   92.857   69.841
LGA    A    23_C      A    23_B     0.522     0    0.049   0.050     0.651   90.476   90.476
LGA    D    24_C      D    24_B     0.461     0    0.009   0.219     1.221  100.000   94.107
LGA    L    25_C      L    25_B     0.310     0    0.015   0.045     0.661  100.000   96.429
LGA    L    26_C      L    26_B     0.377     0    0.064   0.076     0.828   97.619   94.048
LGA    G    27_C      G    27_B     0.435     0    0.041   0.041     0.468  100.000  100.000
LGA    I    28_C      I    28_B     0.202     0    0.020   0.089     1.094   95.238   92.917
LGA    V    29_C      V    29_B     0.974     0    0.057   0.096     1.423   85.952   87.891
LGA    S    30_C      S    30_B     1.183     0    0.138   0.178     3.236   67.500   70.714

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       26     104    104  100.00     207    207  100.00                37
SUMMARY(RMSD_GDC):     2.227          2.123                  3.382           61.667   55.606

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   26   37    4.0     24    0.56    65.541    65.787     3.621

LGA_LOCAL      RMSD:   0.563  Number of atoms:   24  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.564  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   2.227  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.289655 * X  +   0.935387 * Y  +  -0.202855 * Z  + -40.984352
  Y_new =  -0.954200 * X  +   0.265634 * Y  +  -0.137628 * Z  +  11.838407
  Z_new =  -0.074851 * X  +   0.233429 * Y  +   0.969489 * Z  + -56.933769 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.276078  0.074921  0.236278   [DEG:  -73.1139    4.2926   13.5377 ]
ZXZ: -0.974676  0.247660 -0.310299   [DEG:  -55.8448   14.1898  -17.7788 ]
 
# END of job
