 
####################################################### 
#                                                     # 
#                        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: 7 , MODEL 7 , TARGET 182 
#          The number of residues possible to evaluate: 7 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP   320     N     C     C             1.00 
 SSP   321     F     C     C             1.00 
 SSP   322     H     C     H             1.00 
 SSP   323     G     H     H             1.00 
 SSP   324     L     H     H             1.00 
 SSP   325     R     H     H             1.00 
 SSP   326     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              71.4      75.0      0.0     66.7      3.8 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed       100.0     100.0    100.0    100.0      3.8 
 
           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       7    100.0     71.4 
 
 BIN  0.00 - 1.00      1.00       7    100.0     71.4 
 
 
 
 
              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           7               7           291            181 
 ALL CONTACTS (< 8.0A)      16              16          1490            805 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        16         14   87.50   87.50    1.74       0     0.00          16       805  |   1-9999 
 RES CONTACTS        16         14   87.50   87.50    3.12       0     0.00          16       448  |   1-4    
 RES CONTACTS         0          0    0.00    0.00    0.00       0     0.00           0        33  |   5-8    
 RES CONTACTS         0          0    0.00    0.00    0.00       0     0.00           0       324  |   9-9999 
 
 
 
# WARNING! TARGET 1362 atoms, MODEL 3106 atoms, 1332 common with TARGET 
           Number of atoms possible to evaluate: 34 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    53.35           75.0    12     3.3   359     ARMSMC  
     SECONDARY STRUCTURE . .    20.79           85.7     7     4.4   159     ARMSMC  
     SURFACE . . . . . . . .    53.35           75.0    12     5.4   223     ARMSMC  
     BURIED  . . . . . . . .     0.00            0.0     0     0.0   136     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   127     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   118     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    63     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    76     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    51     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    99     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    68     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    49     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    59     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    40     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    35     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    31     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    18     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    27     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     8     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    14     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    14     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     7     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1  320 - 326  7    Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     7    320 - 326      1.34     1.34 
  LCS LOCAL_SCORE:            100.00 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1  320 - 326  7    Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     7    320 - 326      1.34     1.34 
  LCS LOCAL_SCORE:            100.00 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1  320 - 326  7    Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     6    321 - 326      0.99     1.60 
  LCS LOCAL_SCORE:             83.67 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS     320       N     5    7    7       C        1   1   2   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3  
 LCS     321       F     6    7    7       C        2   2   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3  
 LCS     322       H     6    7    7       C        2   2   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3  
 LCS     323       G     6    7    7       H        2   2   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3  
 LCS     324       L     6    7    7       H        2   2   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3  
 LCS     325       R     6    7    7       H        2   2   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3  
 LCS     326       Y     6    7    7       H        1   2   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3  
 LCS    BREAK 
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.12 
 
 NUMBER_OF_CA_Tg:  182      NUMBER_OF_CA_Pr:    7      PERCENT_OF_CA:   3.85  
 
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       4       5       6       7       7       7       7       7       7       7       7       7       7       7       7       7       7       7       7       7  
 GDT PERCENT_OF_CA_Pr   57.14   71.43   85.71  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  100.00  100.00  100.00  100.00 
 GDT PERCENT_OF_CA_Tg    2.20    2.75    3.30    3.85    3.85    3.85    3.85    3.85    3.85    3.85    3.85    3.85    3.85    3.85    3.85    3.85    3.85    3.85    3.85    3.85 
 GDT FRAGMENT: Beg-End 321-324 321-325 321-326 320-326 320-326 320-326 320-326 320-326 320-326 320-326 320-326 320-326 320-326 320-326 320-326 320-326 320-326 320-326 320-326 320-326 
 GDT RMS_LOCAL           0.30    0.73    0.99    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34 
 GDT RMS_ALL_CA          1.79    1.70    1.60    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34    1.34 
 
 
 TEST (CA)  RMS =   1.34               (Number of atoms:    7) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.34          7     3.8   182     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1919                            CRMSCA  
     SECONDARY STRUCTURE . .    1.16          4     5.0    80     CRMSCA  
     SURFACE . . . . . . . .    1.34          7     6.2   113     CRMSCA  
     BURIED  . . . . . . . .    0.00          0     0.0    69     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.64         34     3.8   891     CRMSMC  
     SECONDARY STRUCTURE . .    1.23         19     4.8   397     CRMSMC  
     SURFACE . . . . . . . .    1.64         34     6.2   548     CRMSMC  
     BURIED  . . . . . . . .    0.00          0     0.0   343     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.28          6     0.9   634     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.28          6     1.1   534     CRMSSC  
     SECONDARY STRUCTURE . .    1.41          3     0.9   322     CRMSSC  
     SURFACE . . . . . . . .    2.28          6     1.6   379     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   255     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    1.64         34     2.5  1362     CRMSALL 
     SECONDARY STRUCTURE . .    1.23         19     3.0   642     CRMSALL 
     SURFACE . . . . . . . .    1.64         34     4.1   831     CRMSALL 
     BURIED  . . . . . . . .    0.00          0     0.0   531     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 . . . . . . . . . .    1.289      1.000       0.500      7     3.8   182     ERRCA  
     SECONDARY STRUCTURE . .    1.121      1.000       0.500      4     5.0    80     ERRCA  
     SURFACE . . . . . . . .    1.289      1.000       0.500      7     6.2   113     ERRCA  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0    69     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.415      1.000       0.500     34     3.8   891     ERRMC  
     SECONDARY STRUCTURE . .    1.151      1.000       0.500     19     4.8   397     ERRMC  
     SURFACE . . . . . . . .    1.415      1.000       0.500     34     6.2   548     ERRMC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   343     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.003      1.000       0.500      6     0.9   634     ERRSC  
     RELIABLE SIDE CHAINS  .    2.003      1.000       0.500      6     1.1   534     ERRSC  
     SECONDARY STRUCTURE . .    1.339      1.000       0.500      3     0.9   322     ERRSC  
     SURFACE . . . . . . . .    2.003      1.000       0.500      6     1.6   379     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   255     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.415      1.000       0.500     34     2.5  1362     ERRALL 
     SECONDARY STRUCTURE . .    1.151      1.000       0.500     19     3.0   642     ERRALL 
     SURFACE . . . . . . . .    1.415      1.000       0.500     34     4.1   831     ERRALL 
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   531     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         7         7         7         7       7     182   DISTCA 
CA  (P)      0.55      3.85      3.85      3.85      3.85             182   DISTCA 
CA  (RMS)    0.70      1.34      1.34      1.34      1.34                   DISTCA 
 
ALL (N)        10        31        32        34        34      34    1362   DISTALL 
ALL (P)      0.73      2.28      2.35      2.50      2.50            1362   DISTALL 
ALL (RMS)    0.78      1.26      1.30      1.64      1.64                   DISTALL 
 
 
 
 
END of the results output 
