 
####################################################### 
#                                                     # 
#                        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 28 
#          The number of residues possible to evaluate: 26 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP     2     E     H     C             1.00 
 SSP     3     A     H     H             1.00 
 SSP     4     L     H     H             1.00 
 SSP     5     E     H     H             1.00 
 SSP     6     K     H     H             1.00 
 SSP     7     K     H     H             1.00 
 SSP     8     V     H     H             1.00 
 SSP     9     A     H     H             1.00 
 SSP    10     A     H     H             1.00 
 SSP    11     L     H     H             1.00 
 SSP    12     E     H     H             1.00 
 SSP    13     S     H     H             1.00 
 SSP    14     K     H     H             1.00 
 SSP    15     V     H     H             1.00 
 SSP    16     Q     H     H             1.00 
 SSP    17     A     H     H             1.00 
 SSP    18     L     H     H             1.00 
 SSP    19     E     H     H             1.00 
 SSP    20     K     H     H             1.00 
 SSP    21     K     H     H             1.00 
 SSP    22     V     H     H             1.00 
 SSP    23     E     H     H             1.00 
 SSP    24     A     H     H             1.00 
 SSP    25     L     H     H             1.00 
 SSP    26     E     C     H             1.00 
 SSP    27     H     C     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              92.3      95.8      0.0     50.0     92.9 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        96.2     100.0    100.0     50.0     92.9 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            1             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      26    100.0     92.3 
 
 BIN  0.00 - 1.00      1.00      26    100.0     92.3 
 
 
 
 
              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          27              27            27             28 
 ALL CONTACTS (< 8.0A)      97              94            97             98 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        97         93   95.88   98.94   94.90       0     0.00          94        98  |   1-9999 
 RES CONTACTS        97         93   95.88  100.00   95.88       0     0.00          93        97  |   1-4    
 RES CONTACTS         0          0    0.00    0.00    0.00       0     0.00           1         1  |   5-8    
 RES CONTACTS         0          0    0.00    0.00    0.00       0     0.00           0         0  |   9-9999 
 
 
 
# WARNING! TARGET 213 atoms, MODEL 252 atoms, 207 common with TARGET 
           Number of atoms possible to evaluate: 207 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    35.48           92.3    52    96.3    54     ARMSMC  
     SECONDARY STRUCTURE . .     8.31          100.0    48   100.0    48     ARMSMC  
     SURFACE . . . . . . . .    35.48           92.3    52    96.3    54     ARMSMC  
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    75.25           38.1    21    95.5    22     ARMSSC1 
     RELIABLE SIDE CHAINS  .    81.22           27.8    18   100.0    18     ARMSSC1 
     SECONDARY STRUCTURE . .    72.61           36.8    19   100.0    19     ARMSSC1 
     SURFACE . . . . . . . .    75.25           38.1    21    95.5    22     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    61.85           58.8    17   100.0    17     ARMSSC2 
     RELIABLE SIDE CHAINS  .    51.36           66.7    12   100.0    12     ARMSSC2 
     SECONDARY STRUCTURE . .    65.70           53.3    15   100.0    15     ARMSSC2 
     SURFACE . . . . . . . .    61.85           58.8    17   100.0    17     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    70.21           25.0    12   100.0    12     ARMSSC3 
     RELIABLE SIDE CHAINS  .    62.19           27.3    11   100.0    11     ARMSSC3 
     SECONDARY STRUCTURE . .    72.68           27.3    11   100.0    11     ARMSSC3 
     SURFACE . . . . . . . .    70.21           25.0    12   100.0    12     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    57.49           40.0     5   100.0     5     ARMSSC4 
     RELIABLE SIDE CHAINS  .    57.49           40.0     5   100.0     5     ARMSSC4 
     SECONDARY STRUCTURE . .    57.49           40.0     5   100.0     5     ARMSSC4 
     SURFACE . . . . . . . .    57.49           40.0     5   100.0     5     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    1 - 28   28   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    28      1 - 28       1.75     1.75 
  LCS LOCAL_SCORE:            100.00 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1    1 - 28   28   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    28      1 - 28       1.75     1.75 
  LCS LOCAL_SCORE:            100.00 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1    1 - 28   28   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    24      1 - 24       0.99     2.22 
  LCS LOCAL_SCORE:             80.23 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS       1       V    24   28   28       C       35  57  71  82  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS       2       E    24   28   28       H       39  60  78  82  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS       3       A    24   28   28       H       42  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS       4       L    24   28   28       H       39  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS       5       E    24   28   28       H       42  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS       6       K    24   28   28       H       42  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS       7       K    24   28   28       H       42  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS       8       V    24   28   28       H       42  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS       9       A    24   28   28       H       46  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      10       A    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      11       L    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      12       E    24   28   28       H       50  67  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      13       S    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      14       K    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      15       V    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      16       Q    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      17       A    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      18       L    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      19       E    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      20       K    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      21       K    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      22       V    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      23       E    24   28   28       H       50  71  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      24       A    24   28   28       H       25  57  78  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      25       L    23   28   28       H       17  57  75  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      26       E    22   28   28       C       17  53  71  85  92  92  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      27       H     4   28   28       C       10  10  35  50  67  82  96 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS      28       G     4   28   28       C       10  10  25  32  46  60  85 100 100 100 100 100 100 100 100 100 100 100 100 100  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):  80.23 
 
 NUMBER_OF_CA_Tg:   28      NUMBER_OF_CA_Pr:   28      PERCENT_OF_CA: 100.00  
 
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      14      20      22      24      26      26      27      28      28      28      28      28      28      28      28      28      28      28      28      28  
 GDT PERCENT_OF_CA_Pr   50.00   71.43   78.57   85.71   92.86   92.86   96.43  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00 
 GDT PERCENT_OF_CA_Tg   50.00   71.43   78.57   85.71   92.86   92.86   96.43  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00  100.00 
 GDT FRAGMENT: Beg-End  10-23    3-23    2-23    3-26    1-26    1-26    1-27    1-28    1-28    1-28    1-28    1-28    1-28    1-28    1-28    1-28    1-28    1-28    1-28    1-28  
 GDT RMS_LOCAL           0.32    0.71    0.79    1.08    1.25    1.25    1.55    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75 
 GDT RMS_ALL_CA          2.49    2.22    2.29    2.04    2.00    2.00    1.81    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75    1.75 
 
 
 TEST (CA)  RMS =   1.75               (Number of atoms:   28) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.75         28   100.0    28     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0626                            CRMSCA  
     SECONDARY STRUCTURE . .    1.43         24   100.0    24     CRMSCA  
     SURFACE . . . . . . . .    1.75         28   100.0    28     CRMSCA  
     BURIED  . . . . . . . .    0.00          0     0.0     0     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.69        135    97.1   139     CRMSMC  
     SECONDARY STRUCTURE . .    1.42        120   100.0   120     CRMSMC  
     SURFACE . . . . . . . .    1.69        135    97.1   139     CRMSMC  
     BURIED  . . . . . . . .    0.00          0     0.0     0     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.62         98    97.0   101     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.46         78    98.7    79     CRMSSC  
     SECONDARY STRUCTURE . .    2.42         87   100.0    87     CRMSSC  
     SURFACE . . . . . . . .    2.62         98    97.0   101     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0     0     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.17        207    97.2   213     CRMSALL 
     SECONDARY STRUCTURE . .    1.94        183   100.0   183     CRMSALL 
     SURFACE . . . . . . . .    2.17        207    97.2   213     CRMSALL 
     BURIED  . . . . . . . .    0.00          0     0.0     0     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 . . . . . . . . . .    1.537      1.000       0.500     28   100.0    28     ERRCA  
     SECONDARY STRUCTURE . .    1.310      1.000       0.500     24   100.0    24     ERRCA  
     SURFACE . . . . . . . .    1.537      1.000       0.500     28   100.0    28     ERRCA  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.477      1.000       0.500    135    97.1   139     ERRMC  
     SECONDARY STRUCTURE . .    1.302      1.000       0.500    120   100.0   120     ERRMC  
     SURFACE . . . . . . . .    1.477      1.000       0.500    135    97.1   139     ERRMC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.345      1.000       0.500     98    97.0   101     ERRSC  
     RELIABLE SIDE CHAINS  .    2.219      1.000       0.500     78    98.7    79     ERRSC  
     SECONDARY STRUCTURE . .    2.189      1.000       0.500     87   100.0    87     ERRSC  
     SURFACE . . . . . . . .    2.345      1.000       0.500     98    97.0   101     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.877      1.000       0.500    207    97.2   213     ERRALL 
     SECONDARY STRUCTURE . .    1.702      1.000       0.500    183   100.0   183     ERRALL 
     SURFACE . . . . . . . .    1.877      1.000       0.500    207    97.2   213     ERRALL 
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0     0     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)         7        22        26        28        28      28      28   DISTCA 
CA  (P)     25.00     78.57     92.86    100.00    100.00              28   DISTCA 
CA  (RMS)    0.62      1.32      1.48      1.75      1.75                   DISTCA 
 
ALL (N)        47       129       180       203       207     207     213   DISTALL 
ALL (P)     22.07     60.56     84.51     95.31     97.18             213   DISTALL 
ALL (RMS)    0.70      1.30      1.71      2.06      2.17                   DISTALL 
 
 
 
 
END of the results output 
