 
####################################################### 
#                                                     # 
#                        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: 26 , MODEL 26 , TARGET 252 
#          The number of residues possible to evaluate: 26 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP    34     A     H     C             1.00 
 SSP    35     L     H     H             1.00 
 SSP    36     A     H     H             1.00 
 SSP    37     Y     H     H             1.00 
 SSP    38     R     H     H             1.00 
 SSP    39     E     H     H             1.00 
 SSP    40     A     C     H             1.00 
 SSP    41     T     C     H             1.00 
 SSP    42     F     C     C             1.00 
 SSP    43     D     C     C             1.00 
 SSP    44     I     E     C             1.00 
 SSP    45     L     E     C             1.00 
 SSP    46     E     E     C             1.00 
 SSP    47     W     E     C             1.00 
 SSP    48     R     E     C             1.00 
 SSP    49     V     H     C             1.00 
 SSP    50     D     H     C             1.00 
 SSP    51     H     H     C             1.00 
 SSP    52     F     C     C             1.00 
 SSP    53     M     C     C             1.00 
 SSP    54     D     C     H             1.00 
 SSP    55     I     C     H             1.00 
 SSP    56     A     C     H             1.00 
 SSP    57     S     C     H             1.00 
 SSP    58     T     H     H             1.00 
 SSP    59     Q     H     C             1.00 
 SSP  BREAK 
 
 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              38.5      54.5      0.0     40.0     10.3 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        35.8      60.6      0.0     26.4     10.3 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            4              50.0               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      26    100.0     38.5 
 
 BIN  0.00 - 1.00      1.00      26    100.0     38.5 
 
 
 
 
              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          26              26            26            252 
 ALL CONTACTS (< 8.0A)      78              61            78           1350 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        78         52   66.67   85.25    3.85       0     0.00          61      1350  |   1-9999 
 RES CONTACTS        66         51   77.27   89.47    7.23       0     0.00          57       705  |   1-4    
 RES CONTACTS         4          1   25.00   25.00    1.28       0     0.00           4        78  |   5-8    
 RES CONTACTS         8          0    0.00    0.00    0.00       0     0.00           0       567  |   9-9999 
 
 
 
# WARNING! TARGET 1934 atoms, MODEL 1933 atoms, 1933 common with TARGET 
           Number of atoms possible to evaluate: 218 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    59.15           64.0    50    10.0   502     ARMSMC  
     SECONDARY STRUCTURE . .    34.87           83.3    24     8.3   288     ARMSMC  
     SURFACE . . . . . . . .    55.24           65.2    23     9.9   232     ARMSMC  
     BURIED  . . . . . . . .    62.29           63.0    27    10.0   270     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.84           45.5    22    10.5   209     ARMSSC1 
     RELIABLE SIDE CHAINS  .    81.71           42.9    21    11.2   187     ARMSSC1 
     SECONDARY STRUCTURE . .    62.81           54.5    11     8.7   127     ARMSSC1 
     SURFACE . . . . . . . .    73.14           50.0    10    10.2    98     ARMSSC1 
     BURIED  . . . . . . . .    85.02           41.7    12    10.8   111     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    78.17           44.4    18    11.7   154     ARMSSC2 
     RELIABLE SIDE CHAINS  .    73.67           40.0    15    12.9   116     ARMSSC2 
     SECONDARY STRUCTURE . .    92.71           30.0    10    10.9    92     ARMSSC2 
     SURFACE . . . . . . . .    90.58           28.6     7     9.0    78     ARMSSC2 
     BURIED  . . . . . . . .    69.13           54.5    11    14.5    76     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.16           33.3     6    10.2    59     ARMSSC3 
     RELIABLE SIDE CHAINS  .    85.64           40.0     5    10.2    49     ARMSSC3 
     SECONDARY STRUCTURE . .    91.45           20.0     5    15.2    33     ARMSSC3 
     SURFACE . . . . . . . .    88.93           25.0     4    10.8    37     ARMSSC3 
     BURIED  . . . . . . . .    73.69           50.0     2     9.1    22     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    70.18            0.0     2     8.7    23     ARMSSC4 
     RELIABLE SIDE CHAINS  .    70.18            0.0     2     8.7    23     ARMSSC4 
     SECONDARY STRUCTURE . .    70.18            0.0     2    14.3    14     ARMSSC4 
     SURFACE . . . . . . . .    83.97            0.0     1     6.2    16     ARMSSC4 
     BURIED  . . . . . . . .    52.91            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   34 - 59   26   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    18     34 - 51       4.84    10.70 
  LONGEST_CONTINUOUS_SEGMENT    18     35 - 52       4.61    10.40 
  LCS LOCAL_SCORE:             67.16 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1   34 - 59   26   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     9     34 - 42       1.98    23.57 
  LONGEST_CONTINUOUS_SEGMENT     9     40 - 48       1.77    14.70 
  LCS LOCAL_SCORE:             29.29 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1   34 - 59   26   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     6     34 - 39       0.69    23.44 
  LCS LOCAL_SCORE:             18.93 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS      34       A     6    9   18       H        1   1   2   3   3   3   3   3   3   4   4   5   5   6   6   7   7   7   8   8  
 LCS      35       L     6    9   18       H        1   1   2   3   3   3   3   3   4   5   5   5   6   7   7   7   7   7   8   8  
 LCS      36       A     6    9   18       H        1   1   2   3   3   3   3   4   5   5   5   5   6   7   7   7   7   7   8   8  
 LCS      37       Y     6    9   18       H        1   1   2   3   3   3   3   4   5   5   5   5   6   7   7   7   7   7   8   8  
 LCS      38       R     6    9   18       H        1   1   2   3   3   3   3   3   4   5   5   5   6   7   7   7   7   7   8   8  
 LCS      39       E     6    9   18       H        1   1   2   3   3   3   3   3   3   4   5   5   6   7   7   7   7   7   7   8  
 LCS      40       A     5    9   18       C        1   1   2   3   3   3   3   3   5   5   5   5   6   7   7   7   7   7   7   8  
 LCS      41       T     5    9   18       C        1   1   2   3   3   3   3   4   5   5   5   5   6   7   7   7   7   7   7   8  
 LCS      42       F     5    9   18       C        1   1   2   2   3   3   3   4   5   5   5   5   6   7   7   7   7   7   8   8  
 LCS      43       D     5    9   18       C        1   1   1   2   3   3   3   4   5   5   5   5   6   7   7   7   7   7   8   8  
 LCS      44       I     5    9   18       E        1   1   1   2   2   3   3   4   5   5   5   5   6   7   7   7   7   7   8   8  
 LCS      45       L     5    9   18       E        1   1   2   2   3   3   3   4   5   5   5   5   6   7   7   7   7   7   8   8  
 LCS      46       E     5    9   18       E        1   1   2   2   3   3   3   4   5   5   5   5   6   7   7   7   7   7   8   8  
 LCS      47       W     5    9   18       E        1   1   1   2   3   3   3   3   4   5   5   5   6   7   7   7   7   7   8   8  
 LCS      48       R     4    9   18       E        1   1   2   2   3   3   3   4   5   5   5   5   6   7   7   7   7   7   8   8  
 LCS      49       V     4    6   18       H        1   1   1   1   2   3   3   4   5   5   5   5   6   7   7   7   7   7   8   8  
 LCS      50       D     4    6   18       H        1   1   1   1   2   3   3   4   5   5   5   5   6   7   7   7   7   7   8   8  
 LCS      51       H     4    6   18       H        1   1   1   1   2   3   3   3   5   5   5   5   6   7   7   7   7   7   8   8  
 LCS      52       F     4    6   18       C        1   1   1   1   2   3   3   3   4   5   5   5   6   7   7   7   7   7   8   8  
 LCS      53       M     4    6   16       C        1   1   1   1   2   2   3   3   4   4   5   5   5   6   6   7   7   7   8   8  
 LCS      54       D     5    6   16       C        1   1   1   1   2   2   3   3   4   4   5   5   5   6   6   7   7   7   8   8  
 LCS      55       I     5    6   16       C        1   1   1   1   2   2   2   3   3   4   5   5   5   5   5   6   7   7   8   8  
 LCS      56       A     5    6   16       C        1   1   1   1   2   2   2   3   3   4   5   5   5   5   5   5   6   7   7   7  
 LCS      57       S     5    6   16       C        1   1   1   1   2   2   3   3   4   4   5   5   5   6   6   7   7   7   8   8  
 LCS      58       T     5    6   16       H        1   1   1   1   2   2   2   3   4   4   5   5   5   6   6   7   7   7   8   8  
 LCS      59       Q     3    3   16       H        1   1   1   1   2   2   3   3   4   4   5   5   5   6   6   7   7   7   8   8  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.20 
 
 NUMBER_OF_CA_Tg:  252      NUMBER_OF_CA_Pr:   26      PERCENT_OF_CA:  10.32  
 
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       5       6       8       8       9       9      11      13      14      15      15      16      18      18      19      20      20      22      22  
 GDT PERCENT_OF_CA_Pr   19.23   19.23   23.08   30.77   30.77   34.62   34.62   42.31   50.00   53.85   57.69   57.69   61.54   69.23   69.23   73.08   76.92   76.92   84.62   84.62 
 GDT PERCENT_OF_CA_Tg    1.98    1.98    2.38    3.17    3.17    3.57    3.57    4.37    5.16    5.56    5.95    5.95    6.35    7.14    7.14    7.54    7.94    7.94    8.73    8.73 
 GDT FRAGMENT: Beg-End  34-38   34-38   34-39   34-41   34-41   40-48   40-48   36-50   36-51   36-52   35-49   36-52   36-52   35-52   35-52   34-59   34-59   34-59   34-59   34-59  
 GDT RMS_LOCAL           0.28    0.28    0.69    1.28    1.28    1.77    1.77    3.14    3.44    3.64    3.92    3.88    4.14    4.61    4.61    5.91    6.07    6.07    6.50    6.50 
 GDT RMS_ALL_CA         23.28   23.28   23.44   23.68   23.68   14.70   14.70   10.73   10.77   10.43   12.32   10.68   10.40   10.40   10.40    8.01    8.06    8.06    7.96    7.96 
 
 
 TEST (CA)  RMS =   7.81               (Number of atoms:   26) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    7.81         26    10.3   252     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3003                            CRMSCA  
     SECONDARY STRUCTURE . .    7.24         13     9.0   144     CRMSCA  
     SURFACE . . . . . . . .    8.79         12    10.3   117     CRMSCA  
     BURIED  . . . . . . . .    6.86         14    10.4   135     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    7.91        130    10.4  1247     CRMSMC  
     SECONDARY STRUCTURE . .    7.50         65     9.0   720     CRMSMC  
     SURFACE . . . . . . . .    8.91         60    10.4   578     CRMSMC  
     BURIED  . . . . . . . .    6.94         70    10.5   669     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    9.78        114    12.3   926     CRMSSC  
     RELIABLE SIDE CHAINS  .    9.83        102    13.3   768     CRMSSC  
     SECONDARY STRUCTURE . .   10.90         64    11.4   563     CRMSSC  
     SURFACE . . . . . . . .   11.17         43     9.5   452     CRMSSC  
     BURIED  . . . . . . . .    8.84         71    15.0   474     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    8.85        218    11.3  1934     CRMSALL 
     SECONDARY STRUCTURE . .    9.41        116    10.2  1139     CRMSALL 
     SURFACE . . . . . . . .    9.92         91     9.9   920     CRMSALL 
     BURIED  . . . . . . . .    7.99        127    12.5  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 . . . . . . . . . .    3.603      0.300       0.177     26    10.3   252     ERRCA  
     SECONDARY STRUCTURE . .    2.913      0.242       0.121     13     9.0   144     ERRCA  
     SURFACE . . . . . . . .    4.432      0.333       0.166     12    10.3   117     ERRCA  
     BURIED  . . . . . . . .    2.893      0.272       0.186     14    10.4   135     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.614      0.291       0.163    130    10.4  1247     ERRMC  
     SECONDARY STRUCTURE . .    3.119      0.251       0.125     65     9.0   720     ERRMC  
     SURFACE . . . . . . . .    4.507      0.333       0.166     60    10.4   578     ERRMC  
     BURIED  . . . . . . . .    2.848      0.255       0.160     70    10.5   669     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.096      0.342       0.178    114    12.3   926     ERRSC  
     RELIABLE SIDE CHAINS  .    5.119      0.341       0.178    102    13.3   768     ERRSC  
     SECONDARY STRUCTURE . .    6.282      0.400       0.200     64    11.4   563     ERRSC  
     SURFACE . . . . . . . .    6.723      0.429       0.214     43     9.5   452     ERRSC  
     BURIED  . . . . . . . .    4.110      0.289       0.155     71    15.0   474     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.297      0.312       0.167    218    11.3  1934     ERRALL 
     SECONDARY STRUCTURE . .    4.740      0.326       0.163    116    10.2  1139     ERRALL 
     SURFACE . . . . . . . .    5.431      0.373       0.186     91     9.9   920     ERRALL 
     BURIED  . . . . . . . .    3.484      0.269       0.153    127    12.5  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)         1         2         2         5        21      26     252   DISTCA 
CA  (P)      0.40      0.79      0.79      1.98      8.33             252   DISTCA 
CA  (RMS)    0.93      1.56      1.56      3.79      6.41                   DISTCA 
 
ALL (N)         2         6         9        45       153     218    1934   DISTALL 
ALL (P)      0.10      0.31      0.47      2.33      7.91            1934   DISTALL 
ALL (RMS)    0.85      1.46      1.94      3.98      6.40                   DISTALL 
 
 
 
 
END of the results output 
