 
####################################################### 
#                                                     # 
#                        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: 37 , MODEL 37 , TARGET 241 
#          The number of residues possible to evaluate: 37 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP   206     L     E     C             1.00 
 SSP   207     V     E     C             1.00 
 SSP   208     G     E     C             1.00 
 SSP   209     I     E     C             1.00 
 SSP   210     H     E     E             1.00 
 SSP   211     S     E     E             1.00 
 SSP   212     S     E     E             1.00 
 SSP   213     K     E     E             1.00 
 SSP   214     V     E     E             1.00 
 SSP   215     S     E     C             1.00 
 SSP   216     H     C     C             1.00 
 SSP   217     L     C     C             1.00 
 SSP   218     D     C     C             1.00 
 SSP   219     R     C     C             1.00 
 SSP   220     E     C     C             1.00 
 SSP   221     H     C     C             1.00 
 SSP   222     Q     E     C             1.00 
 SSP   223     I     E     C             1.00 
 SSP   224     N     E     C             1.00 
 SSP   225     Y     E     E             1.00 
 SSP   226     G     E     E             1.00 
 SSP   227     V     E     E             1.00 
 SSP   228     G     E     E             1.00 
 SSP   229     I     C     H             1.00 
 SSP   230     G     C     H             1.00 
 SSP   231     N     H     H             1.00 
 SSP   232     Y     H     H             1.00 
 SSP   233     V     H     H             1.00 
 SSP   234     K     H     H             1.00 
 SSP   235     R     H     H             1.00 
 SSP   236     I     H     H             1.00 
 SSP   237     I     H     H             1.00 
 SSP   238     N     H     H             1.00 
 SSP   239     E     H     H             1.00 
 SSP   240     K     H     H             1.00 
 SSP   241     N     C     H             1.00 
 SSP   242     E     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              70.3     100.0     52.9     70.0     15.4 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        79.5     100.0     76.5     64.0     15.4 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            3             100.0               0.0 
 
         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      37    100.0     70.3 
 
 BIN  0.00 - 1.00      1.00      37    100.0     70.3 
 
 
 
 
              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 
 
 
 
 CONSIDERED - explicitly provided contacts (with positive confidence) or 
              non contacts (with negative confidence) possible to evaluate 
 SEP      - Minimum separation between residues considered 
 NPC      - Number of contacts predicted correctly 
 PC(P)    - Percent of contacts predicted correctly from CONSIDERED in PREDICTION 
 PC(T)    - Percent of contacts predicted correctly from CONSIDERED in TARGET with SEP limit 
 PC(TT)   - Percent of contacts predicted correctly from TOTAL in TARGET with SEP limit 
 
                        CONSIDERED     CONSIDERED       TOTAL          TOTAL 
                      in PREDICTION    in TARGET    in PREDICTION    in TARGET 
 ALL RESIDUES USED          32              32            32            241 
 ALL CONTACTS (< 8.0A)      86              94            86           1230 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        86         67   77.91   71.28    5.45       0     0.00          94      1230  |   1-9999 
 RES CONTACTS        69         58   84.06   84.06   10.05       0     0.00          69       577  |   1-4    
 RES CONTACTS         3          1   33.33   20.00    1.25       0     0.00           5        80  |   5-8    
 RES CONTACTS        14          8   57.14   40.00    1.40       0     0.00          20       573  |   9-9999 
 
 
 
# WARNING! TARGET 1878 atoms, MODEL 1783 atoms, 1762 common with TARGET 
           Number of atoms possible to evaluate: 176 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    69.64           56.9    72    15.0   480     ARMSMC  
     SECONDARY STRUCTURE . .    64.30           66.0    53    24.5   216     ARMSMC  
     SURFACE . . . . . . . .    74.18           51.2    41    17.1   240     ARMSMC  
     BURIED  . . . . . . . .    63.14           64.5    31    12.9   240     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   204     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   187     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    94     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   103     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0   101     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   158     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   113     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    72     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    83     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    75     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    52     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    46     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    27     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    43     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     9     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    29     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    29     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    17     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    23     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1  206 - 242  37   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    37    206 - 242      4.91     4.91 
  LCS LOCAL_SCORE:            100.00 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1  206 - 242  37   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    13    230 - 242      1.87    18.27 
  LCS LOCAL_SCORE:             27.25 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1  206 - 242  37   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    10    232 - 241      0.56    18.65 
  LCS LOCAL_SCORE:             17.24 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS     206       L     3    6   37       E        0   1   1   2   2   3   4   4   5   7  12  13  13  14  14  14  14  15  15  15  
 LCS     207       V     4    6   37       E        0   1   1   2   2   4   6   7   9  11  12  13  13  14  14  14  14  15  15  15  
 LCS     208       G     4    6   37       E        1   1   2   2   4   5   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     209       I     5    8   37       E        1   1   2   2   3   4   6   8  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     210       H     5    8   37       E        1   1   2   2   2   4   6   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     211       S     5    8   37       E        1   1   2   2   2   4   6   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     212       S     5    8   37       E        1   1   2   2   2   4   6   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     213       K     5    8   37       E        1   1   2   2   2   3   4   4   6   6   7   9  12  14  14  14  14  15  15  15  
 LCS     214       V     3    8   37       E        1   1   1   2   2   4   7   8  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     215       S     4    8   37       E        1   1   1   2   2   3   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     216       H     5    8   37       C        1   1   2   2   2   4   6   8   9  11  12  12  13  14  14  14  14  15  15  15  
 LCS     217       L     5    7   37       C        1   1   2   2   2   3   4   6   7   7   8   9  12  12  13  14  14  15  15  15  
 LCS     218       D     5    6   37       C        1   1   2   2   2   2   4   6   7   7   8   9  11  13  13  14  14  15  15  15  
 LCS     219       R     5    6   37       C        1   1   2   2   2   3   6   6   7   7   8  11  12  13  13  14  14  15  15  15  
 LCS     220       E     5    6   37       C        1   1   2   2   3   4   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     221       H     3   10   37       C        1   1   2   3   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     222       Q     3   10   37       E        0   1   1   2   3   4   6   8  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     223       I     6   11   37       E        0   1   3   4   4   6   7   8  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     224       N     7   11   37       E        2   2   3   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     225       Y     7   11   37       E        2   2   3   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     226       G     7   11   37       E        2   2   3   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     227       V     7   11   37       E        2   2   3   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     228       G     7   11   37       E        2   2   3   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     229       I     7   11   37       C        1   2   3   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     230       G     7   13   37       C        1   2   3   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     231       N     4   13   37       H        1   1   1   3   4   5   6   8  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     232       Y    10   13   37       H        3   3   4   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     233       V    10   13   37       H        3   3   4   4   4   5   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     234       K    10   13   37       H        3   3   4   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     235       R    10   13   37       H        3   3   4   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     236       I    10   13   37       H        3   3   4   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     237       I    10   13   37       H        3   3   4   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     238       N    10   13   37       H        3   3   4   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     239       E    10   13   37       H        3   3   4   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     240       K    10   13   37       H        3   3   4   4   4   6   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     241       N    10   13   37       C        1   2   4   4   4   5   7   9  10  11  12  13  13  14  14  14  14  15  15  15  
 LCS     242       E     3   13   37       C        0   1   1   1   2   4   4   6   7   9  11  13  13  14  14  14  14  15  15  15  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.41 
 
 NUMBER_OF_CA_Tg:  241      NUMBER_OF_CA_Pr:   37      PERCENT_OF_CA:  15.35  
 
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       9       9      10      11      12      16      19      23      26      28      30      32      32      34      34      34      35      37      37      37  
 GDT PERCENT_OF_CA_Pr   24.32   24.32   27.03   29.73   32.43   43.24   51.35   62.16   70.27   75.68   81.08   86.49   86.49   91.89   91.89   91.89   94.59  100.00  100.00  100.00 
 GDT PERCENT_OF_CA_Tg    3.73    3.73    4.15    4.56    4.98    6.64    7.88    9.54   10.79   11.62   12.45   13.28   13.28   14.11   14.11   14.11   14.52   15.35   15.35   15.35 
 GDT FRAGMENT: Beg-End 232-240 232-240 232-241 223-240 230-241 221-240 208-241 208-241 208-241 208-241 207-241 206-242 206-242 206-242 206-242 206-242 206-242 206-242 206-242 206-242 
 GDT RMS_LOCAL           0.30    0.30    0.56    1.33    1.38    2.34    2.64    3.00    3.23    3.38    3.58    3.82    3.82    4.09    4.09    4.09    4.40    4.91    4.91    4.91 
 GDT RMS_ALL_CA         17.86   17.86   18.65    6.74   16.58    5.55    5.39    5.17    5.04    5.11    5.21    5.23    5.23    5.12    5.12    5.12    5.01    4.91    4.91    4.91 
 
 
 TEST (CA)  RMS =   4.91               (Number of atoms:   37) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    4.91         37    15.4   241     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1327                            CRMSCA  
     SECONDARY STRUCTURE . .    4.31         27    25.0   108     CRMSCA  
     SURFACE . . . . . . . .    5.30         21    17.4   121     CRMSCA  
     BURIED  . . . . . . . .    4.35         16    13.3   120     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    4.93        176    14.9  1180     CRMSMC  
     SECONDARY STRUCTURE . .    4.32        128    24.0   533     CRMSMC  
     SURFACE . . . . . . . .    5.30        100    16.9   593     CRMSMC  
     BURIED  . . . . . . . .    4.40         76    12.9   587     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    5.80         28     3.1   914     CRMSSC  
     RELIABLE SIDE CHAINS  .    5.80         28     3.7   764     CRMSSC  
     SECONDARY STRUCTURE . .    5.13         20     4.5   449     CRMSSC  
     SURFACE . . . . . . . .    6.25         16     3.5   461     CRMSSC  
     BURIED  . . . . . . . .    5.14         12     2.6   453     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    4.93        176     9.4  1878     CRMSALL 
     SECONDARY STRUCTURE . .    4.32        128    14.5   881     CRMSALL 
     SURFACE . . . . . . . .    5.30        100    10.6   945     CRMSALL 
     BURIED  . . . . . . . .    4.40         76     8.1   933     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 . . . . . . . . . .    4.418      1.000       0.500     37    15.4   241     ERRCA  
     SECONDARY STRUCTURE . .    3.992      1.000       0.500     27    25.0   108     ERRCA  
     SURFACE . . . . . . . .    4.665      1.000       0.500     21    17.4   121     ERRCA  
     BURIED  . . . . . . . .    4.094      1.000       0.500     16    13.3   120     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.396      1.000       0.500    176    14.9  1180     ERRMC  
     SECONDARY STRUCTURE . .    3.945      1.000       0.500    128    24.0   533     ERRMC  
     SURFACE . . . . . . . .    4.650      1.000       0.500    100    16.9   593     ERRMC  
     BURIED  . . . . . . . .    4.062      1.000       0.500     76    12.9   587     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.232      1.000       0.500     28     3.1   914     ERRSC  
     RELIABLE SIDE CHAINS  .    5.232      1.000       0.500     28     3.7   764     ERRSC  
     SECONDARY STRUCTURE . .    4.750      1.000       0.500     20     4.5   449     ERRSC  
     SURFACE . . . . . . . .    5.566      1.000       0.500     16     3.5   461     ERRSC  
     BURIED  . . . . . . . .    4.787      1.000       0.500     12     2.6   453     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.396      1.000       0.500    176     9.4  1878     ERRALL 
     SECONDARY STRUCTURE . .    3.945      1.000       0.500    128    14.5   881     ERRALL 
     SURFACE . . . . . . . .    4.650      1.000       0.500    100    10.6   945     ERRALL 
     BURIED  . . . . . . . .    4.062      1.000       0.500     76     8.1   933     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         4        10        26        37      37     241   DISTCA 
CA  (P)      0.00      1.66      4.15     10.79     15.35             241   DISTCA 
CA  (RMS)    0.00      1.81      2.29      3.37      4.91                   DISTCA 
 
ALL (N)         4        20        50       121       173     176    1878   DISTALL 
ALL (P)      0.21      1.06      2.66      6.44      9.21            1878   DISTALL 
ALL (RMS)    0.68      1.47      2.20      3.34      4.75                   DISTALL 
 
 
 
 
END of the results output 
