 
####################################################### 
#                                                     # 
#                        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:      # 
#                        # 
########################## 
 
 
 
# WARNING! The number of residues in SS section: 32 , MODEL 32 , TARGET 252 
#          The number of residues possible to evaluate: 32 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP     1     M     C     C             1.00 
 SSP     2     K     C     C             1.00 
 SSP     3     T     C     C             1.00 
 SSP     4     V     E     C             1.00 
 SSP     5     T     E     C             1.00 
 SSP     6     V     E     C             1.00 
 SSP     7     K     C     C             1.00 
 SSP     8     N     C     C             1.00 
 SSP     9     L     E     C             1.00 
 SSP    10     I     E     E             1.00 
 SSP    11     I     E     C             1.00 
 SSP    12     G     C     C             1.00 
 SSP    13     E     C     C             1.00 
 SSP    14     G     C     E             1.00 
 SSP    15     M     C     C             1.00 
 SSP    16     P     C     C             1.00 
 SSP    17     K     E     C             1.00 
 SSP    18     I     E     C             1.00 
 SSP    19     I     E     C             1.00 
 SSP    20     V     E     C             1.00 
 SSP    21     S     E     C             1.00 
 SSP    22     L     E     C             1.00 
 SSP    23     M     C     C             1.00 
 SSP    24     G     C     C             1.00 
 SSP    25     R     C     C             1.00 
 SSP    26     D     C     C             1.00 
 SSP    27     I     H     H             1.00 
 SSP    28     N     H     H             1.00 
 SSP    29     S     H     H             1.00 
 SSP    30     V     H     H             1.00 
 SSP    31     K     H     H             1.00 
 SSP    32     A     H     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              59.4      83.3      8.3     92.9     12.7 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        40.1     100.0      8.3     41.2     12.7 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            4              25.0               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      32    100.0     59.4 
 
 BIN  0.00 - 1.00      1.00      32    100.0     59.4 
 
 
 
 
              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            252 
 ALL CONTACTS (< 8.0A)      90              86            90           1350 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        90         63   70.00   73.26    4.67       0     0.00          86      1350  |   1-9999 
 RES CONTACTS        68         61   89.71   88.41    8.65       0     0.00          69       705  |   1-4    
 RES CONTACTS         7          2   28.57   14.29    2.56       0     0.00          14        78  |   5-8    
 RES CONTACTS        15          0    0.00    0.00    0.00       0     0.00           3       567  |   9-9999 
 
 
 
# WARNING! TARGET 1934 atoms, MODEL 1933 atoms, 1933 common with TARGET 
           Number of atoms possible to evaluate: 238 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    52.85           64.5    62    12.4   502     ARMSMC  
     SECONDARY STRUCTURE . .    19.29           88.6    35    12.2   288     ARMSMC  
     SURFACE . . . . . . . .    68.01           55.9    34    14.7   232     ARMSMC  
     BURIED  . . . . . . . .    23.81           75.0    28    10.4   270     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    75.08           53.6    28    13.4   209     ARMSSC1 
     RELIABLE SIDE CHAINS  .    76.70           54.2    24    12.8   187     ARMSSC1 
     SECONDARY STRUCTURE . .    64.13           58.8    17    13.4   127     ARMSSC1 
     SURFACE . . . . . . . .    76.12           60.0    15    15.3    98     ARMSSC1 
     BURIED  . . . . . . . .    73.86           46.2    13    11.7   111     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    69.36           60.0    20    13.0   154     ARMSSC2 
     RELIABLE SIDE CHAINS  .    74.39           56.2    16    13.8   116     ARMSSC2 
     SECONDARY STRUCTURE . .    76.66           60.0    10    10.9    92     ARMSSC2 
     SURFACE . . . . . . . .    61.30           66.7    12    15.4    78     ARMSSC2 
     BURIED  . . . . . . . .    79.94           50.0     8    10.5    76     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    83.58           44.4     9    15.3    59     ARMSSC3 
     RELIABLE SIDE CHAINS  .    83.58           44.4     9    18.4    49     ARMSSC3 
     SECONDARY STRUCTURE . .    66.31           50.0     2     6.1    33     ARMSSC3 
     SURFACE . . . . . . . .    94.28           28.6     7    18.9    37     ARMSSC3 
     BURIED  . . . . . . . .    17.99          100.0     2     9.1    22     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    93.26           20.0     5    21.7    23     ARMSSC4 
     RELIABLE SIDE CHAINS  .    93.26           20.0     5    21.7    23     ARMSSC4 
     SECONDARY STRUCTURE . .   112.67            0.0     2    14.3    14     ARMSSC4 
     SURFACE . . . . . . . .    81.68           25.0     4    25.0    16     ARMSSC4 
     BURIED  . . . . . . . .   129.62            0.0     1    14.3     7     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1    1 - 32   32   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    19      6 - 24       4.75    13.32 
  LONGEST_CONTINUOUS_SEGMENT    19      7 - 25       4.70    13.39 
  LONGEST_CONTINUOUS_SEGMENT    19      8 - 26       4.97    13.49 
  LCS LOCAL_SCORE:             52.15 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1    1 - 32   32   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     9     14 - 22       1.77    15.37 
  LCS LOCAL_SCORE:             23.73 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1    1 - 32   32   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     7     26 - 32       0.47    18.42 
  LCS LOCAL_SCORE:             17.68 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS       1       M     3    5   10       C        1   1   1   1   2   2   3   3   3   3   3   3   3   3   4   5   5   5   5   5  
 LCS       2       K     3    5   10       C        1   1   1   1   2   2   3   3   3   3   3   3   3   3   4   5   5   5   5   5  
 LCS       3       T     5    6   10       C        1   1   1   1   1   2   3   3   3   3   3   3   3   3   4   4   5   5   5   5  
 LCS       4       V     5    6   10       E        1   1   1   1   2   2   3   3   3   3   3   3   3   3   4   5   5   5   6   7  
 LCS       5       T     5    6   11       E        1   1   1   1   2   2   3   3   3   3   3   4   4   5   5   6   6   7   7   8  
 LCS       6       V     5    6   19       E        1   1   1   1   1   2   3   3   3   4   5   5   5   6   7   7   7   8   9   9  
 LCS       7       K     5    6   19       C        1   1   1   1   2   2   3   3   3   3   3   5   6   7   7   7   8   8   9   9  
 LCS       8       N     6    7   19       C        1   2   2   2   2   2   3   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS       9       L     6    7   19       E        1   2   2   2   3   4   4   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      10       I     6    7   19       E        1   2   2   2   3   4   4   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      11       I     6    7   19       E        1   2   2   2   2   2   2   2   3   5   5   6   6   7   7   7   8   8   9   9  
 LCS      12       G     6    7   19       C        1   2   2   2   2   2   2   2   3   5   5   6   6   7   7   7   8   8   9   9  
 LCS      13       E     6    7   19       C        1   2   2   2   3   4   4   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      14       G     5    9   19       C        1   1   2   3   3   3   3   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      15       M     6    9   19       C        1   1   2   3   3   3   3   3   3   4   5   5   6   7   7   7   7   8   9   9  
 LCS      16       P     6    9   19       C        1   1   2   3   3   4   4   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      17       K     6    9   19       E        1   2   2   3   3   4   4   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      18       I     6    9   19       E        1   2   2   3   3   4   4   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      19       I     6    9   19       E        1   2   2   3   3   4   4   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      20       V     6    9   19       E        1   2   2   3   3   4   4   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      21       S     6    9   19       E        1   2   2   3   3   4   4   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      22       L     6    9   19       E        1   2   2   2   3   4   4   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      23       M     4    8   19       C        1   1   2   2   3   4   4   4   5   5   5   6   6   7   7   7   8   8   9   9  
 LCS      24       G     4    8   19       C        1   1   1   1   2   3   4   4   4   5   5   6   6   7   7   7   8   8   9   9  
 LCS      25       R     4    8   19       C        1   1   1   1   3   3   4   4   4   5   5   5   6   6   7   7   8   8   9   9  
 LCS      26       D     7    8   19       C        1   2   2   2   3   3   4   4   4   5   5   5   5   5   6   7   8   8   9   9  
 LCS      27       I     7    8   14       H        2   2   2   2   3   3   4   4   4   5   5   5   5   5   6   7   8   8   9   9  
 LCS      28       N     7    8   14       H        2   2   2   2   3   3   4   4   4   5   5   5   5   5   5   5   6   6   7   8  
 LCS      29       S     7    8   14       H        2   2   2   2   3   3   4   4   4   5   5   5   5   5   5   5   6   6   7   8  
 LCS      30       V     7    8   14       H        2   2   2   2   3   3   4   4   4   5   5   5   5   5   6   7   8   8   9   9  
 LCS      31       K     7    8   14       H        2   2   2   2   3   3   4   4   4   5   5   5   5   5   5   5   6   6   7   8  
 LCS      32       A     7    8   14       H        2   2   2   2   3   3   4   4   4   5   5   5   5   5   5   5   5   6   6   6  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.29 
 
 NUMBER_OF_CA_Tg:  252      NUMBER_OF_CA_Pr:   32      PERCENT_OF_CA:  12.70  
 
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       6       7       7       8       8      11      11      12      13      13      14      16      17      18      19      20      21      22      23      23  
 GDT PERCENT_OF_CA_Pr   18.75   21.88   21.88   25.00   25.00   34.38   34.38   37.50   40.62   40.62   43.75   50.00   53.12   56.25   59.38   62.50   65.62   68.75   71.88   71.88 
 GDT PERCENT_OF_CA_Tg    2.38    2.78    2.78    3.17    3.17    4.37    4.37    4.76    5.16    5.16    5.56    6.35    6.75    7.14    7.54    7.94    8.33    8.73    9.13    9.13 
 GDT FRAGMENT: Beg-End  27-32   26-32   26-32   14-21    9-23    9-23    9-23    8-23    8-23    8-23    8-23    8-24    8-24    7-24    7-25    6-25    7-30    6-30    6-30    6-30  
 GDT RMS_LOCAL           0.23    0.47    0.47    1.45    1.42    2.30    2.30    2.50    2.74    2.74    3.12    3.90    4.12    4.43    4.70    5.02    5.91    6.28    6.30    6.30 
 GDT RMS_ALL_CA         18.75   18.42   18.42   15.99   14.06   13.52   13.52   13.51   13.65   13.65   13.76   13.45   13.51   13.41   13.39   13.25   13.22   12.98   13.02   13.02 
 
 
 TEST (CA)  RMS =  11.24               (Number of atoms:   32) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   11.24         32    12.7   252     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3514                            CRMSCA  
     SECONDARY STRUCTURE . .   10.00         18    12.5   144     CRMSCA  
     SURFACE . . . . . . . .   12.47         18    15.4   117     CRMSCA  
     BURIED  . . . . . . . .    9.44         14    10.4   135     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   11.26        157    12.6  1247     CRMSMC  
     SECONDARY STRUCTURE . .   10.14         90    12.5   720     CRMSMC  
     SURFACE . . . . . . . .   12.39         88    15.2   578     CRMSMC  
     BURIED  . . . . . . . .    9.63         69    10.3   669     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   12.41        110    11.9   926     CRMSSC  
     RELIABLE SIDE CHAINS  .   12.58         94    12.2   768     CRMSSC  
     SECONDARY STRUCTURE . .   10.80         62    11.0   563     CRMSSC  
     SURFACE . . . . . . . .   13.32         64    14.2   452     CRMSSC  
     BURIED  . . . . . . . .   11.01         46     9.7   474     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   11.70        238    12.3  1934     CRMSALL 
     SECONDARY STRUCTURE . .   10.39        134    11.8  1139     CRMSALL 
     SURFACE . . . . . . . .   12.72        136    14.8   920     CRMSALL 
     BURIED  . . . . . . . .   10.18        102    10.1  1014     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 . . . . . . . . . .    6.520      0.418       0.209     32    12.7   252     ERRCA  
     SECONDARY STRUCTURE . .    5.855      0.413       0.207     18    12.5   144     ERRCA  
     SURFACE . . . . . . . .    7.442      0.438       0.219     18    15.4   117     ERRCA  
     BURIED  . . . . . . . .    5.335      0.393       0.197     14    10.4   135     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.531      0.417       0.208    157    12.6  1247     ERRMC  
     SECONDARY STRUCTURE . .    5.947      0.414       0.207     90    12.5   720     ERRMC  
     SURFACE . . . . . . . .    7.386      0.436       0.218     88    15.2   578     ERRMC  
     BURIED  . . . . . . . .    5.442      0.392       0.196     69    10.3   669     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.552      0.448       0.224    110    11.9   926     ERRSC  
     RELIABLE SIDE CHAINS  .    7.668      0.450       0.225     94    12.2   768     ERRSC  
     SECONDARY STRUCTURE . .    6.543      0.435       0.217     62    11.0   563     ERRSC  
     SURFACE . . . . . . . .    8.123      0.452       0.226     64    14.2   452     ERRSC  
     BURIED  . . . . . . . .    6.758      0.443       0.222     46     9.7   474     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.903      0.428       0.214    238    12.3  1934     ERRALL 
     SECONDARY STRUCTURE . .    6.172      0.422       0.211    134    11.8  1139     ERRALL 
     SURFACE . . . . . . . .    7.625      0.440       0.220    136    14.8   920     ERRALL 
     BURIED  . . . . . . . .    5.942      0.412       0.206    102    10.1  1014     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         0         0         0        18      32     252   DISTCA 
CA  (P)      0.00      0.00      0.00      0.00      7.14             252   DISTCA 
CA  (RMS)    0.00      0.00      0.00      0.00      8.28                   DISTCA 
 
ALL (N)         0         0         0         1       117     238    1934   DISTALL 
ALL (P)      0.00      0.00      0.00      0.05      6.05            1934   DISTALL 
ALL (RMS)    0.00      0.00      0.00      4.98      8.08                   DISTALL 
 
 
 
 
END of the results output 
