 
####################################################### 
#                                                     # 
#                        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 98 
#          The number of residues possible to evaluate: 26 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP    62     K     H     C             1.00 
 SSP    63     I     H     E             1.00 
 SSP    64     V     H     E             1.00 
 SSP    65     T     H     E             1.00 
 SSP    66     L     H     E             1.00 
 SSP    67     N     C     C             1.00 
 SSP    68     P     C     C             1.00 
 SSP    69     P     C     C             1.00 
 SSP    70     N     C     C             1.00 
 SSP    71     C     C     C             1.00 
 SSP    72     D     E     C             1.00 
 SSP    73     L     E     C             1.00 
 SSP    74     T     E     C             1.00 
 SSP    75     V     C     C             1.00 
 SSP    76     P     C     C             1.00 
 SSP    77     T     C     C             1.00 
 SSP    78     S     C     C             1.00 
 SSP    79     G     C     C             1.00 
 SSP    80     L     C     C             1.00 
 SSP    81     V     E     C             1.00 
 SSP    82     L     E     C             1.00 
 SSP    83     N     C     E             1.00 
 SSP    84     V     H     E             1.00 
 SSP    85     Y     H     E             1.00 
 SSP    86     S     H     E             1.00 
 SSP    87     Y     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              42.3       0.0      0.0     91.7     26.5 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        21.4       0.0      0.0     46.4     26.5 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            4               0.0              50.0 
 
         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     42.3 
 
 BIN  0.00 - 1.00      1.00      26    100.0     42.3 
 
 
 
 
              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          24              24            24             98 
 ALL CONTACTS (< 8.0A)      70              72            70            462 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        70         37   52.86   51.39    8.01       0     0.00          72       462  |   1-9999 
 RES CONTACTS        40         35   87.50   71.43   11.51       0     0.00          49       304  |   1-4    
 RES CONTACTS         4          1   25.00   12.50    4.00       0     0.00           8        25  |   5-8    
 RES CONTACTS        26          1    3.85    6.67    0.75       0     0.00          15       133  |   9-9999 
 
 
 
# WARNING! TARGET 717 atoms, MODEL 646 atoms, 646 common with TARGET 
           Number of atoms possible to evaluate: 127 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    98.31           32.0    50    25.8   194     ARMSMC  
     SECONDARY STRUCTURE . .   107.63           27.3    22    17.5   126     ARMSMC  
     SURFACE . . . . . . . .   114.59           24.1    29    23.8   122     ARMSMC  
     BURIED  . . . . . . . .    69.83           42.9    21    29.2    72     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    84     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    79     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    54     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    52     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    32     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    30     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    31     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    27     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    20     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    13     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     9     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    11     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    10     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     6     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     5     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1   62 - 87   26   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    22     66 - 87       4.90     6.97 
  LCS LOCAL_SCORE:             80.33 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1   62 - 87   26   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     9     69 - 77       1.23     9.80 
  LCS LOCAL_SCORE:             23.52 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1   62 - 87   26   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     8     70 - 77       0.99    10.18 
  LCS LOCAL_SCORE:             21.30 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS      62       K     3    3   12       H        0   3   3   3   3   3   4   4   5   6  10  11  14  14  15  16  17  17  19  21  
 LCS      63       I     3    3   12       H        0   3   3   3   3   3   4   5   7   9  12  13  16  17  20  21  22  24  24  24  
 LCS      64       V     3    3   14       H        0   4   4   4   4   4   6   7   7   8  11  13  14  14  18  21  22  24  24  24  
 LCS      65       T     4    4   21       H        0   3   4   4   4   4   6   7   7   8  11  13  14  15  18  21  22  24  24  24  
 LCS      66       L     4    4   22       H        3   3   4   4   4   6   9  10  12  12  14  17  19  20  21  21  22  24  24  24  
 LCS      67       N     4    4   22       C        4   4   4   6   8   9  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      68       P     4    7   22       C        4   4   4   4   5   8  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      69       P     7    9   22       C        4   6   7   9   9  10  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      70       N     8    9   22       C        5   6   8   9   9  10  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      71       C     8    9   22       C        5   6   8   9   9  10  10  11  14  16  17  18  19  20  21  21  22  24  24  24  
 LCS      72       D     8    9   22       E        5   6   8   9   9  10  10  11  13  16  17  18  19  20  21  21  22  24  24  24  
 LCS      73       L     8    9   22       E        5   6   8   9   9  10  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      74       T     8    9   22       E        5   6   8   9   9  10  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      75       V     8    9   22       C        2   5   8   9   9  10  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      76       P     8    9   22       C        3   5   8   9   9  10  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      77       T     8    9   22       C        3   5   8   9   9  10  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      78       S     3    4   22       C        3   3   3   4   7   8  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      79       G     3    4   22       C        0   3   3   4   4   4   4   4   5   5   5   7   8   8  15  19  21  24  24  24  
 LCS      80       L     6    6   22       C        4   6   6   6   8   9  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      81       V     6    6   22       E        4   6   6   6   8   8  10  12  13  15  17  18  19  20  21  21  22  24  24  24  
 LCS      82       L     6    6   22       E        4   6   6   6   8   9  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      83       N     6    6   22       C        4   6   6   6   8   8  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      84       V     6    6   22       H        3   6   6   7   9  10  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      85       Y     6    6   22       H        3   6   6   6   8   9  10  12  15  16  17  18  19  20  21  21  22  24  24  24  
 LCS      86       S     3    3   22       H        3   4   4   4   4   4   5  10  14  16  17  18  19  20  21  21  22  24  24  24  
 LCS      87       Y     3    3   22       H        3   4   4   4   4   4   5   6   6   6   7  10  13  20  21  21  21  22  23  24  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   1.50 
 
 NUMBER_OF_CA_Tg:   98      NUMBER_OF_CA_Pr:   26      PERCENT_OF_CA:  26.53  
 
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       6       8       9       9      10      10      12      15      16      17      18      19      20      21      21      22      24      24      24  
 GDT PERCENT_OF_CA_Pr   19.23   23.08   30.77   34.62   34.62   38.46   38.46   46.15   57.69   61.54   65.38   69.23   73.08   76.92   80.77   80.77   84.62   92.31   92.31   92.31 
 GDT PERCENT_OF_CA_Tg    5.10    6.12    8.16    9.18    9.18   10.20   10.20   12.24   15.31   16.33   17.35   18.37   19.39   20.41   21.43   21.43   22.45   24.49   24.49   24.49 
 GDT FRAGMENT: Beg-End  70-74   69-74   70-77   69-77   69-77   69-84   69-84   67-85   67-85   67-85   67-86   67-86   67-86   67-87   66-87   66-87   63-86   63-86   63-86   64-87  
 GDT RMS_LOCAL           0.35    0.64    0.99    1.23    1.23    1.82    1.82    2.80    3.36    3.55    3.69    3.87    4.08    4.32    4.54    4.54    5.11    5.63    5.63    5.59 
 GDT RMS_ALL_CA         10.77   10.00   10.18    9.80    9.80    8.44    8.44    7.05    6.84    6.92    6.92    6.89    6.88    7.06    6.99    6.99    6.61    6.57    6.57    6.71 
 
 
 TEST (CA)  RMS =   6.54               (Number of atoms:   26) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    6.54         26    26.5    98     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2516                            CRMSCA  
     SECONDARY STRUCTURE . .    7.99         12    19.0    63     CRMSCA  
     SURFACE . . . . . . . .    7.06         15    24.2    62     CRMSCA  
     BURIED  . . . . . . . .    5.77         11    30.6    36     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    6.71        127    26.1   487     CRMSMC  
     SECONDARY STRUCTURE . .    8.10         60    19.1   314     CRMSMC  
     SURFACE . . . . . . . .    7.14         73    23.8   307     CRMSMC  
     BURIED  . . . . . . . .    6.09         54    30.0   180     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    7.53         23     7.1   325     CRMSSC  
     RELIABLE SIDE CHAINS  .    7.53         23     8.4   273     CRMSSC  
     SECONDARY STRUCTURE . .    8.80         12     5.4   221     CRMSSC  
     SURFACE . . . . . . . .    8.18         13     6.5   199     CRMSSC  
     BURIED  . . . . . . . .    6.59         10     7.9   126     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    6.71        127    17.7   717     CRMSALL 
     SECONDARY STRUCTURE . .    8.10         60    12.7   473     CRMSALL 
     SURFACE . . . . . . . .    7.14         73    16.3   447     CRMSALL 
     BURIED  . . . . . . . .    6.09         54    20.0   270     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 . . . . . . . . . .    5.779      1.000       0.500     26    26.5    98     ERRCA  
     SECONDARY STRUCTURE . .    7.204      1.000       0.500     12    19.0    63     ERRCA  
     SURFACE . . . . . . . .    6.168      1.000       0.500     15    24.2    62     ERRCA  
     BURIED  . . . . . . . .    5.247      1.000       0.500     11    30.6    36     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.960      1.000       0.500    127    26.1   487     ERRMC  
     SECONDARY STRUCTURE . .    7.352      1.000       0.500     60    19.1   314     ERRMC  
     SURFACE . . . . . . . .    6.262      1.000       0.500     73    23.8   307     ERRMC  
     BURIED  . . . . . . . .    5.553      1.000       0.500     54    30.0   180     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.788      1.000       0.500     23     7.1   325     ERRSC  
     RELIABLE SIDE CHAINS  .    6.788      1.000       0.500     23     8.4   273     ERRSC  
     SECONDARY STRUCTURE . .    8.146      1.000       0.500     12     5.4   221     ERRSC  
     SURFACE . . . . . . . .    7.408      1.000       0.500     13     6.5   199     ERRSC  
     BURIED  . . . . . . . .    5.981      1.000       0.500     10     7.9   126     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.960      1.000       0.500    127    17.7   717     ERRALL 
     SECONDARY STRUCTURE . .    7.352      1.000       0.500     60    12.7   473     ERRALL 
     SURFACE . . . . . . . .    6.262      1.000       0.500     73    16.3   447     ERRALL 
     BURIED  . . . . . . . .    5.553      1.000       0.500     54    20.0   270     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         5        11        24      26      98   DISTCA 
CA  (P)      0.00      0.00      5.10     11.22     24.49              98   DISTCA 
CA  (RMS)    0.00      0.00      2.44      3.15      5.66                   DISTCA 
 
ALL (N)         1         3        20        57       114     127     717   DISTALL 
ALL (P)      0.14      0.42      2.79      7.95     15.90             717   DISTALL 
ALL (RMS)    0.80      1.40      2.42      3.52      5.66                   DISTALL 
 
 
 
 
END of the results output 
