 
####################################################### 
#                                                     # 
#                        ACE                          # 
#                                                     # 
#        Ab-initio protein structure prediction       # 
#                         &                           # 
#               Comparative modeling                  # 
#                                                     # 
#                     Evaluator                       # 
#                                                     # 
#                ----------------- 11/1998            # 
#                                                     # 
#                         by                          # 
#           Adam Zemla & Ceslovas Venclovas           # 
#                                                     # 
#         Protein Structure Prediction Center         # 
#      Lawrence Livermore National Laboratory, CA     # 
#                                                     # 
####################################################### 
########################## 
#                        # 
#    ACE parameters:     # 
#                        # 
########################## 
# 
# MEASURES: 
# 
# For AB: 0 3 9 13 14 
# For CM: 0 1 2 3 6 7 8 9 10 11 12 13 14 18 
# 
ARMSMC  0 1 2     7 8 9    11 12 13 14 18 
ARMSSC  0 1 2 3 6 7 8 9    11 12 13 14 18 
# 
CRMSCA  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSMC  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSSC  0 1 2 3 6     9    11 12 13 14 18 
CRMSALL 0 1 2     7 8 9    11 12 13 14 18 
# 
D-E_CA  0 1 2     7 8 9    11 12 13 14 18 
D-E_MC  0 1 2     7 8 9    11 12 13 14 18 
D-E_SC  0 1 2 3 6 7 8 9    11 12 13 14 18 
D-E_ALL 0 1 2     7 8 9    11 12 13 14 18 
# 
# Output parameters 
# 
DIHED-OUTPUT        0         #    1 - ON, 0 - OFF 
RES-CONTACTS        0         #    1 - ON, 0 - OFF 
SS-OUTPUT           1         #    1 - ON, 0 - OFF 
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
# 
# Calculation parameters 
# 
SOV-METHOD          1         #    0 - SOV 94,  1 - SOV 
# 
TEMP-FACTOR         30.0      #    Target structure temperature factor cutoff 
ACCESS-CUTOFF       0.20      #    Solvent accessibility cutoff   
ANGLES-CORRECT      30.0      #    target-model  (diff < 30.0)    
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
ROTATION-MATRIX     0         #    1 - ON, 0 - OFF   
SC-SWAPPING         1         #    1 - ON, 0 - OFF    
SEP-CONTACTS        1         #    Separation interval along the chain 
RESIDUE-CONTACTS    8.0       #    Contact definition between two C-beta atoms 
# 
CRMS-METHOD         1         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
ITER-CUTOFF         2.5       #    DISTANCE cutoff (for CA (iter))  
LCS_GDT             1         #    LCS and GDT calculations (1 - ON, 0 - OFF) 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
 
 
#          The number of residues in SS section: 41 , MODEL 41 , TARGET 200 
#          The number of residues possible to evaluate: 41 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP   255     A     C     C             1.00 
 SSP   256     V     E     C             1.00 
 SSP   257     V     E     C             1.00 
 SSP   258     A     E     C             1.00 
 SSP   259     A     E     C             1.00 
 SSP   260     A     C     C             1.00 
 SSP   261     R     C     C             1.00 
 SSP   262     V     C     C             1.00 
 SSP   263     G     C     C             1.00 
 SSP   264     V     C     C             1.00 
 SSP   265     G     H     C             1.00 
 SSP   266     H     H     C             1.00 
 SSP   267     A     H     C             1.00 
 SSP   268     G     H     C             1.00 
 SSP   269     E     H     E             1.00 
 SSP   270     W     H     C             1.00 
 SSP   271     A     H     C             1.00 
 SSP   272     R     C     E             1.00 
 SSP   273     K     C     C             1.00 
 SSP   274     P     C     C             1.00 
 SSP   275     L     C     C             1.00 
 SSP   276     R     E     C             1.00 
 SSP   277     F     E     C             1.00 
 SSP   278     Y     E     H             1.00 
 SSP   279     V     E     H             1.00 
 SSP   280     R     C     H             1.00 
 SSP   281     G     C     H             1.00 
 SSP   282     S     C     H             1.00 
 SSP   283     P     C     H             1.00 
 SSP   284     W     C     H             1.00 
 SSP   285     V     C     H             1.00 
 SSP   286     S     C     H             1.00 
 SSP   287     V     C     C             1.00 
 SSP   288     V     C     C             1.00 
 SSP   289     D     C     C             1.00 
 SSP   290     R     H     C             1.00 
 SSP   291     V     H     C             1.00 
 SSP   292     A     H     C             1.00 
 SSP   293     E     H     C             1.00 
 SSP   294     Q     C     C             1.00 
 SSP   295     D     C     C             1.00 
 
 NP      - Number of predicted residues 
 PP      - Percent of predicted residues 
 Q3      - Residues predicted correctly (H, E, C) 
 Qhelix  - Residues predicted correctly (HELIX) 
 Qstrand - Residues predicted correctly (STRAND) 
 Qcoil   - Residues predicted correctly (COIL) 
 SOV     - Segment overlap quantity 
 
                     Q3      Qhelix   Qstrand   Qcoil      PP 
 Qindex              34.1       0.0      0.0     63.6     20.5 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        25.2       0.0      0.0     46.9     20.5 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            4               0.0              25.0 
 
         Number of wrong    Number of wrong 
             breaks             joins 
 B/J            0                 0 
 
  CONFIDENCE (P)     Average     NP    PP/BIN     Q3 
 BIN  0.90 - 1.00      1.00      41    100.0     34.1 
 
 BIN  0.00 - 1.00      1.00      41    100.0     34.1 
 
 
 
 
              predicted        number of target      total number   total number 
                as a         contacts possible in         of             of 
               contact         predicted subset:       contacts       contacts 
            percent  number    percent    number       in target    in prediction 
 CONTACTS:     0.0      0         0.0        0             0              0 
 
 
# WARNING! The number of residues with CB atom coordinates: MODEL 0 , TARGET 181 
 
# WARNING! TARGET 1546 atoms, MODEL 1538 atoms, 1400 common with TARGET 
           Number of atoms possible to evaluate: 164 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    82.83           39.6    48    12.2   395     ARMSMC  
     SECONDARY STRUCTURE . .    82.48           34.5    29    17.4   167     ARMSMC  
     SURFACE . . . . . . . .    93.75           37.5    24    12.8   187     ARMSMC  
     BURIED  . . . . . . . .    70.24           41.7    24    11.5   208     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   143     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   128     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    65     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    73     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    70     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   101     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    76     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    45     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    53     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    48     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    39     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    34     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    19     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    25     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    16     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    16     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     8     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1  255 - 295  41   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    23    260 - 282      4.97    11.91 
  LONGEST_CONTINUOUS_SEGMENT    23    261 - 283      4.99    12.10 
  LCS LOCAL_SCORE:             49.38 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1  255 - 295  41   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     9    255 - 263      1.52    17.76 
  LCS LOCAL_SCORE:             14.10 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1  255 - 295  41   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     7    255 - 261      0.91    17.38 
  LCS LOCAL_SCORE:             10.47 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS    BREAK 
 LCS    BREAK 
 LCS     255       A     7    9   16       C        2   3   3   3   4   4   4   5   5   6   6   7   7   7   8   8   9  10  10  10  
 LCS     256       V     7    9   16       E        2   3   3   3   4   4   4   5   5   6   6   7   7   7   8   8   9  10  10  11  
 LCS     257       V     7    9   16       E        2   3   3   3   4   4   4   5   5   6   6   7   7   7   8   8   9  10  11  13  
 LCS     258       A     7    9   16       E        2   3   3   3   4   4   4   5   5   6   6   7   7   7   8  10  11  12  13  14  
 LCS     259       A     7    9   22       E        2   3   3   3   4   4   4   5   5   6   7   8  10  11  11  12  13  14  14  15  
 LCS     260       A     7    9   23       C        2   3   3   3   4   4   4   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     261       R     7    9   23       C        1   2   3   3   4   4   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     262       V     4    9   23       C        1   2   3   3   4   5   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     263       G     4    9   23       C        2   3   3   3   4   5   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     264       V     3    6   23       C        1   1   2   2   3   5   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     265       G     3    4   23       H        1   2   3   3   4   5   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     266       H     3    4   23       H        1   1   2   2   3   4   4   5   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     267       A     3    4   23       H        1   1   2   2   3   4   4   5   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     268       G     3    4   23       H        0   1   2   2   2   2   3   3   5   6   8   9  10  11  12  13  13  14  14  15  
 LCS     269       E     3    4   23       H        1   1   2   2   3   4   4   5   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     270       W     3    5   23       H        1   1   2   2   3   4   5   5   6   7   8   9  10  11  12  13  13  14  14  15  
 LCS     271       A     3    5   23       H        1   1   2   2   3   4   5   5   6   7   7   8   9  10  12  13  13  14  14  15  
 LCS     272       R     4    5   23       C        2   2   2   2   3   4   5   5   6   7   9   9  10  11  12  13  13  14  14  15  
 LCS     273       K     4    5   23       C        2   2   2   2   3   4   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     274       P     4    6   23       C        2   2   3   3   4   5   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     275       L     5    6   23       C        2   2   2   3   4   5   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     276       R     5    6   23       E        1   2   2   2   3   4   4   5   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     277       F     5    6   23       E        1   2   2   3   4   5   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     278       Y     5    6   23       E        1   2   2   3   4   5   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     279       V     5    6   23       E        1   2   2   3   3   5   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     280       R     4    5   23       C        1   2   2   2   2   3   3   4   5   7   8   8  10  11  11  13  13  14  14  15  
 LCS     281       G     4    5   23       C        1   2   2   2   2   2   3   5   6   7   7   9  10  10  12  13  13  14  14  15  
 LCS     282       S     4    5   23       C        2   2   3   3   4   5   5   6   7   8   9   9  10  11  12  13  13  14  14  15  
 LCS     283       P     4    5   23       C        2   2   3   3   4   5   5   6   6   8   9   9  10  11  12  13  13  14  14  15  
 LCS     284       W     4    5   20       C        2   2   2   2   2   2   3   4   5   7   7   7   8  10  12  13  13  14  14  15  
 LCS     285       V     4    5   20       C        2   2   2   2   2   4   5   5   5   7   7   8   9  11  12  13  13  14  14  15  
 LCS     286       S     3    5   20       C        1   1   1   2   2   2   4   4   6   6   7   7   9  10  11  13  13  14  14  15  
 LCS     287       V     3    3   20       C        1   1   1   2   2   2   4   4   5   5   6   8  10  11  12  13  13  14  14  15  
 LCS     288       V     3    4   14       C        1   1   1   2   2   2   4   4   5   5   5   6   6   6   7   7   7   8   9  11  
 LCS     289       D     3    4   14       C        1   1   1   2   2   2   4   4   5   5   5   6   6   6   7   7   7   8   9   9  
 LCS     290       R     4    5   14       H        1   2   2   2   2   2   4   4   5   5   5   6   6   6   7   7   7   8   9   9  
 LCS     291       V     4    5   14       H        1   2   2   2   2   2   4   4   5   5   5   6   6   6   7   7   7   8   9   9  
 LCS     292       A     4    5   14       H        1   2   2   2   2   2   2   4   5   5   5   6   6   6   7   7   7   8   9   9  
 LCS     293       E     4    5   14       H        1   2   2   2   2   2   4   4   5   5   5   6   6   6   7   7   7   8   9   9  
 LCS     294       Q     3    5   14       C        0   1   1   1   2   2   2   3   4   4   5   6   7  10  11  11  12  13  14  15  
 LCS     295       D     3    3   14       C        0   1   1   1   1   1   2   2   3   3   3   5   5   8  11  11  12  13  14  15  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.44 
 
 NUMBER_OF_CA_Tg:  200      NUMBER_OF_CA_Pr:   41      PERCENT_OF_CA:  20.50  
 
GLOBAL_DISTANCE_TEST (the largest set of residues under DISTANCE_CUTOFF (using LCS results)): 
 GDT DISTANCE_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_OF_CA_max       5       7       7       7       8      10      11      12      14      17      18      19      21      22      25      26      27      29      29      30  
 GDT PERCENT_OF_CA_Pr   12.20   17.07   17.07   17.07   19.51   24.39   26.83   29.27   34.15   41.46   43.90   46.34   51.22   53.66   60.98   63.41   65.85   70.73   70.73   73.17 
 GDT PERCENT_OF_CA_Tg    2.50    3.50    3.50    3.50    4.00    5.00    5.50    6.00    7.00    8.50    9.00    9.50   10.50   11.00   12.50   13.00   13.50   14.50   14.50   15.00 
 GDT FRAGMENT: Beg-End 255-263 255-263 255-263 255-263 255-263 262-283 262-283 261-283 260-279 260-282 260-283 260-283 260-283 260-283 260-287 260-287 260-287 259-287 259-287 259-294 
 GDT RMS_LOCAL           0.17    0.47    0.47    0.47    1.12    2.10    2.27    2.53    3.20    3.71    3.86    4.04    4.42    4.62    5.27    5.41    5.59    5.92    5.92    6.35 
 GDT RMS_ALL_CA         17.91   17.92   17.92   17.92   17.77   13.59   13.54   13.34   11.86   11.84   12.01   12.08   11.90   11.85   12.38   12.36   12.33   12.26   12.26   11.46 
 
 
 TEST (CA)  RMS =  10.26               (Number of atoms:   41) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   10.26         41    20.5   200     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2502                            CRMSCA  
     SECONDARY STRUCTURE . .    8.76         15    17.9    84     CRMSCA  
     SURFACE . . . . . . . .   11.02         24    25.0    96     CRMSCA  
     BURIED  . . . . . . . .    9.08         17    16.3   104     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   10.12        164    16.7   981     CRMSMC  
     SECONDARY STRUCTURE . .    8.58         60    14.4   417     CRMSMC  
     SURFACE . . . . . . . .   10.87         96    20.5   469     CRMSMC  
     BURIED  . . . . . . . .    8.96         68    13.3   512     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   746     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   634     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   349     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   375     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   371     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   10.12        164    10.6  1546     CRMSALL 
     SECONDARY STRUCTURE . .    8.58         60     8.8   685     CRMSALL 
     SURFACE . . . . . . . .   10.87         96    12.6   759     CRMSALL 
     BURIED  . . . . . . . .    8.96         68     8.6   787     CRMSALL 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.255      1.000       0.500     41    20.5   200     ERRCA  
     SECONDARY STRUCTURE . .    7.883      1.000       0.500     15    17.9    84     ERRCA  
     SURFACE . . . . . . . .    9.970      1.000       0.500     24    25.0    96     ERRCA  
     BURIED  . . . . . . . .    8.245      1.000       0.500     17    16.3   104     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.124      1.000       0.500    164    16.7   981     ERRMC  
     SECONDARY STRUCTURE . .    7.748      1.000       0.500     60    14.4   417     ERRMC  
     SURFACE . . . . . . . .    9.783      1.000       0.500     96    20.5   469     ERRMC  
     BURIED  . . . . . . . .    8.195      1.000       0.500     68    13.3   512     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.000      0.000       0.000      0     0.0   746     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   634     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   349     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   375     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   371     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.124      1.000       0.500    164    10.6  1546     ERRALL 
     SECONDARY STRUCTURE . .    7.748      1.000       0.500     60     8.8   685     ERRALL 
     SURFACE . . . . . . . .    9.783      1.000       0.500     96    12.6   759     ERRALL 
     BURIED  . . . . . . . .    8.195      1.000       0.500     68     8.6   787     ERRALL 
 
 
 
DISTANCES: Percent of total atoms where distance (target <-> model) in global 
           superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms 
            D < 1     D < 2     D < 3     D < 5    D < 10      NP      TN 
CA  (N)         0         1         2         5        26      41     200   DISTCA 
CA  (P)      0.00      0.50      1.00      2.50     13.00             200   DISTCA 
CA  (RMS)    0.00      1.86      2.44      3.85      6.79                   DISTCA 
 
ALL (N)         0         3         7        21       111     164    1546   DISTALL 
ALL (P)      0.00      0.19      0.45      1.36      7.18            1546   DISTALL 
ALL (RMS)    0.00      1.85      2.47      3.79      6.94                   DISTALL 
 
 
 
 
END of the results output 
