 
####################################################### 
#                                                     # 
#                        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: 36 , MODEL 36 , TARGET 241 
#          The number of residues possible to evaluate: 36 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP    40     K     C     C             1.00 
 SSP    41     Y     C     C             1.00 
 SSP    42     P     C     C             1.00 
 SSP    43     Y     H     C             1.00 
 SSP    44     N     H     C             1.00 
 SSP    45     T     H     C             1.00 
 SSP    46     I     E     C             1.00 
 SSP    47     G     E     C             1.00 
 SSP    48     N     E     C             1.00 
 SSP    49     V     E     C             1.00 
 SSP    50     F     E     E             1.00 
 SSP    51     V     E     E             1.00 
 SSP    52     K     C     E             1.00 
 SSP    53     G     C     E             1.00 
 SSP    54     Q     C     C             1.00 
 SSP    55     T     E     C             1.00 
 SSP    56     S     E     C             1.00 
 SSP    57     A     E     E             1.00 
 SSP    58     T     E     E             1.00 
 SSP    59     G     E     E             1.00 
 SSP    60     V     E     E             1.00 
 SSP    61     L     E     E             1.00 
 SSP    62     I     C     E             1.00 
 SSP    63     G     C     E             1.00 
 SSP    64     K     C     C             1.00 
 SSP    65     N     C     C             1.00 
 SSP    66     T     E     E             1.00 
 SSP    67     V     E     E             1.00 
 SSP    68     L     E     E             1.00 
 SSP    69     T     E     C             1.00 
 SSP    70     N     C     C             1.00 
 SSP    71     R     H     H             1.00 
 SSP    72     H     H     H             1.00 
 SSP    73     I     H     H             1.00 
 SSP    74     A     H     C             1.00 
 SSP    75     K     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              55.6      37.5     58.8     63.6     14.9 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        64.2      50.0     77.8     53.6     14.9 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            5              80.0               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      36    100.0     55.6 
 
 BIN  0.00 - 1.00      1.00      36    100.0     55.6 
 
 
 
 
              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          33              33            33            241 
 ALL CONTACTS (< 8.0A)      92             100            92           1230 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        92         71   77.17   71.00    5.77       0     0.00         100      1230  |   1-9999 
 RES CONTACTS        59         55   93.22   80.88    9.53       0     0.00          68       577  |   1-4    
 RES CONTACTS        14          9   64.29   81.82   11.25       0     0.00          11        80  |   5-8    
 RES CONTACTS        19          7   36.84   33.33    1.22       0     0.00          21       573  |   9-9999 
 
 
 
# WARNING! TARGET 1878 atoms, MODEL 1802 atoms, 1775 common with TARGET 
           Number of atoms possible to evaluate: 173 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    69.91           62.9    70    14.6   480     ARMSMC  
     SECONDARY STRUCTURE . .    63.17           72.1    43    19.9   216     ARMSMC  
     SURFACE . . . . . . . .    75.83           50.0    18     7.5   240     ARMSMC  
     BURIED  . . . . . . . .    67.73           67.3    52    21.7   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   40 - 75   36   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    30     46 - 75       4.97     7.89 
  LCS LOCAL_SCORE:             75.31 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1   40 - 75   36   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    22     54 - 75       1.93     7.48 
  LCS LOCAL_SCORE:             42.98 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1   40 - 75   36   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    20     56 - 75       0.79     7.59 
  LCS LOCAL_SCORE:             37.11 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS      40       K     0    0   10       C        0   0   0   0   0   0   0   1   1   1   1   1   1   3   4   4   4   4   4   6  
 LCS      41       Y     3    3   11       C        0   1   1   1   1   1   2   3   3   3   3   3   3   4   4   8   9  10  12  14  
 LCS      42       P     3    4   13       C        0   1   1   1   1   1   2   3   3   3   3   5   6   8  11  12  12  14  14  14  
 LCS      43       Y     5    6   14       H        1   2   2   2   2   2   2   3   4   7   9  11  11  11  12  13  13  14  14  14  
 LCS      44       N     5    6   14       H        1   2   2   2   2   2   2   3   4   7   9  11  11  11  12  13  13  14  14  14  
 LCS      45       T     5    6   14       H        1   2   2   2   2   2   2   3   3   6   7  11  11  11  12  13  13  14  14  14  
 LCS      46       I     5    6   30       E        1   2   2   2   2   2   2   3   3   5   9  11  11  11  12  13  13  14  14  14  
 LCS      47       G     5    6   30       E        1   2   2   2   2   2   2   3   7   9   9  11  11  11  12  13  13  14  14  14  
 LCS      48       N     3    6   30       E        1   1   1   2   2   2   2   3   3   4   4   5   8  11  12  13  13  14  14  14  
 LCS      49       V     5    6   30       E        1   2   2   2   2   2   2   3   3   4   4   7   8  11  12  13  13  14  14  14  
 LCS      50       F     5    6   30       E        1   2   2   2   2   2   2   3   3   4   4   7   9  11  12  13  13  14  14  14  
 LCS      51       V     5    6   30       E        1   2   2   2   2   2   2   3   4   4   4   7   9  11  12  13  13  14  14  14  
 LCS      52       K     5    6   30       C        1   2   2   2   2   2   2   3   4   4   4   7   9  11  12  13  13  14  14  14  
 LCS      53       G     5    6   30       C        1   2   2   2   2   2   2   3   4   4   4   7   8  10  12  13  13  14  14  14  
 LCS      54       Q     3   22   30       C        1   1   1   2   2   2   3   6   7   9   9  11  11  11  12  13  13  14  14  14  
 LCS      55       T    19   22   30       E        1   2   4   6   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      56       S    20   22   30       E        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      57       A    20   22   30       E        2   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      58       T    20   22   30       E        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      59       G    20   22   30       E        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      60       V    20   22   30       E        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      61       L    20   22   30       E        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      62       I    20   22   30       C        3   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      63       G    20   22   30       C        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      64       K    20   22   30       C        2   2   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      65       N    20   22   30       C        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      66       T    20   22   30       E        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      67       V    20   22   30       E        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      68       L    20   22   30       E        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      69       T    20   22   30       E        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      70       N    20   22   30       C        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      71       R    20   22   30       H        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      72       H    20   22   30       H        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      73       I    20   22   30       H        6   7   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      74       A    20   22   30       H        1   3   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS      75       K    20   22   30       H        0   3   7   8   8   8   8   8   8   9   9  11  11  11  12  13  13  14  14  14  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.83 
 
 NUMBER_OF_CA_Tg:  241      NUMBER_OF_CA_Pr:   36      PERCENT_OF_CA:  14.94  
 
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      15      17      19      20      20      21      21      21      21      23      24      27      27      28      31      33      33      34      34      35  
 GDT PERCENT_OF_CA_Pr   41.67   47.22   52.78   55.56   55.56   58.33   58.33   58.33   58.33   63.89   66.67   75.00   75.00   77.78   86.11   91.67   91.67   94.44   94.44   97.22 
 GDT PERCENT_OF_CA_Tg    6.22    7.05    7.88    8.30    8.30    8.71    8.71    8.71    8.71    9.54    9.96   11.20   11.20   11.62   12.86   13.69   13.69   14.11   14.11   14.52 
 GDT FRAGMENT: Beg-End  56-73   56-73   56-74   56-75   56-75   55-75   55-75   55-75   55-75   47-75   43-75   43-75   43-75   47-75   44-75   43-75   43-75   42-75   42-75   41-75  
 GDT RMS_LOCAL           0.32    0.44    0.71    0.79    0.79    1.05    1.05    1.05    1.05    2.54    2.74    3.77    3.77    4.58    5.21    5.51    5.51    5.75    5.75    6.14 
 GDT RMS_ALL_CA          7.61    7.63    7.60    7.59    7.59    7.58    7.58    7.58    7.58    7.41    7.34    7.11    7.11    8.09    7.27    7.18    7.18    7.01    7.01    6.86 
 
 
 TEST (CA)  RMS =   6.80               (Number of atoms:   36) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    6.80         36    14.9   241     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1889                            CRMSCA  
     SECONDARY STRUCTURE . .    5.61         22    20.4   108     CRMSCA  
     SURFACE . . . . . . . .    9.24         10     8.3   121     CRMSCA  
     BURIED  . . . . . . . .    5.58         26    21.7   120     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    6.81        173    14.7  1180     CRMSMC  
     SECONDARY STRUCTURE . .    5.73        106    19.9   533     CRMSMC  
     SURFACE . . . . . . . .    9.04         49     8.3   593     CRMSMC  
     BURIED  . . . . . . . .    5.69        124    21.1   587     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    7.28         29     3.2   914     CRMSSC  
     RELIABLE SIDE CHAINS  .    7.28         29     3.8   764     CRMSSC  
     SECONDARY STRUCTURE . .    6.28         18     4.0   449     CRMSSC  
     SURFACE . . . . . . . .    9.38          9     2.0   461     CRMSSC  
     BURIED  . . . . . . . .    6.10         20     4.4   453     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    6.81        173     9.2  1878     CRMSALL 
     SECONDARY STRUCTURE . .    5.73        106    12.0   881     CRMSALL 
     SURFACE . . . . . . . .    9.04         49     5.2   945     CRMSALL 
     BURIED  . . . . . . . .    5.69        124    13.3   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 . . . . . . . . . .    5.715      1.000       0.500     36    14.9   241     ERRCA  
     SECONDARY STRUCTURE . .    4.633      1.000       0.500     22    20.4   108     ERRCA  
     SURFACE . . . . . . . .    7.893      1.000       0.500     10     8.3   121     ERRCA  
     BURIED  . . . . . . . .    4.877      1.000       0.500     26    21.7   120     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.758      1.000       0.500    173    14.7  1180     ERRMC  
     SECONDARY STRUCTURE . .    4.770      1.000       0.500    106    19.9   533     ERRMC  
     SURFACE . . . . . . . .    7.766      1.000       0.500     49     8.3   593     ERRMC  
     BURIED  . . . . . . . .    4.965      1.000       0.500    124    21.1   587     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.095      1.000       0.500     29     3.2   914     ERRSC  
     RELIABLE SIDE CHAINS  .    6.095      1.000       0.500     29     3.8   764     ERRSC  
     SECONDARY STRUCTURE . .    5.200      1.000       0.500     18     4.0   449     ERRSC  
     SURFACE . . . . . . . .    7.980      1.000       0.500      9     2.0   461     ERRSC  
     BURIED  . . . . . . . .    5.247      1.000       0.500     20     4.4   453     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.758      1.000       0.500    173     9.2  1878     ERRALL 
     SECONDARY STRUCTURE . .    4.770      1.000       0.500    106    12.0   881     ERRALL 
     SURFACE . . . . . . . .    7.766      1.000       0.500     49     5.2   945     ERRALL 
     BURIED  . . . . . . . .    4.965      1.000       0.500    124    13.3   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         6        10        16        29      36     241   DISTCA 
CA  (P)      0.00      2.49      4.15      6.64     12.03             241   DISTCA 
CA  (RMS)    0.00      1.71      1.92      2.83      4.81                   DISTCA 
 
ALL (N)         0        25        49        82       145     173    1878   DISTALL 
ALL (P)      0.00      1.33      2.61      4.37      7.72            1878   DISTALL 
ALL (RMS)    0.00      1.72      2.08      3.08      5.11                   DISTALL 
 
 
 
 
END of the results output 
