 
####################################################### 
#                                                     # 
#                        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: 23 , MODEL 23 , TARGET 311 
#          The number of residues possible to evaluate: 23 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP   242     V     C     C             1.00 
 SSP   243     A     C     C             1.00 
 SSP   244     V     C     C             1.00 
 SSP   245     K     C     E             1.00 
 SSP   246     R     C     E             1.00 
 SSP   247     I     C     E             1.00 
 SSP   248     G     C     C             1.00 
 SSP   249     D     C     C             1.00 
 SSP   250     E     H     C             1.00 
 SSP   251     T     H     C             1.00 
 SSP   252     F     H     C             1.00 
 SSP   253     R     H     C             1.00 
 SSP   254     L     C     C             1.00 
 SSP   255     C     H     E             1.00 
 SSP  BREAK 
 SSP   258     Y     C     E             1.00 
 SSP   259     L     C     E             1.00 
 SSP   260     D     C     C             1.00 
 SSP   261     D     E     C             1.00 
 SSP   262     I     E     C             1.00 
 SSP   263     I     E     C             1.00 
 SSP   264     T     E     C             1.00 
 SSP   265     V     E     C             1.00 
 SSP   266     D     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              34.8       0.0      0.0     61.5      7.4 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        23.9       0.0      0.0     35.3      7.4 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            3               0.0               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      23    100.0     34.8 
 
 BIN  0.00 - 1.00      1.00      23    100.0     34.8 
 
 
 
 
              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          21              21            76            308 
 ALL CONTACTS (< 8.0A)      53              40           296           1729 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        53         31   58.49   77.50    1.79       0     0.00          40      1729  |   1-9999 
 RES CONTACTS        36         30   83.33   76.92    3.44       0     0.00          39       873  |   1-4    
 RES CONTACTS         8          1   12.50  100.00    1.15       0     0.00           1        87  |   5-8    
 RES CONTACTS         9          0    0.00    0.00    0.00       0     0.00           0       769  |   9-9999 
 
 
 
# WARNING! TARGET 2227 atoms, MODEL 3689 atoms, 2186 common with TARGET 
           Number of atoms possible to evaluate: 112 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    90.14           28.6    42     6.8   620     ARMSMC  
     SECONDARY STRUCTURE . .    70.84           30.0    10     3.0   338     ARMSMC  
     SURFACE . . . . . . . .   105.34           20.0    15     5.4   276     ARMSMC  
     BURIED  . . . . . . . .    80.46           33.3    27     7.8   344     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   212     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   185     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0   124     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   101     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0   111     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   163     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   118     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    96     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    91     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    72     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    58     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    45     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    38     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    38     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    20     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    21     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    21     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    14     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    15     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  242 - 255  14   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    13    242 - 254      4.62     5.28 
  LCS LOCAL_SCORE:             91.84 
 
 FRAGMENT  2  258 - 266  9    Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     9    258 - 266      2.36     2.36 
  LCS LOCAL_SCORE:            100.00 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1  242 - 255  14   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     7    247 - 253      1.86    11.47 
  LCS LOCAL_SCORE:             44.39 
 
 FRAGMENT  2  258 - 266  9    Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     8    258 - 265      1.75     2.62 
  LCS LOCAL_SCORE:             83.95 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1  242 - 255  14   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     5    243 - 247      0.61    12.67 
  LCS LOCAL_SCORE:             29.59 
 
 FRAGMENT  2  258 - 266  9    Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     4    258 - 261      0.92    10.17 
  LONGEST_CONTINUOUS_SEGMENT     4    260 - 263      0.89     3.36 
  LONGEST_CONTINUOUS_SEGMENT     4    262 - 265      0.91     4.81 
  LCS LOCAL_SCORE:             43.21 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS     242       V     3    6   13       C        0   0   1   1   1   1   1   1   2   2   3   3   3   3   4   4   5   5   6   6  
 LCS     243       A     5    6   13       C        0   1   1   1   1   1   2   2   2   2   3   3   4   4   4   5   5   5   6   6  
 LCS     244       V     5    6   13       C        1   1   1   1   1   1   2   2   2   2   3   3   4   4   4   5   5   5   6   6  
 LCS     245       K     5    6   13       C        1   1   1   1   1   1   2   2   2   2   3   3   4   4   4   5   5   5   6   6  
 LCS     246       R     5    6   13       C        1   1   1   1   1   1   2   2   2   2   3   3   4   4   4   5   5   5   6   6  
 LCS     247       I     5    7   13       C        1   1   1   1   1   2   2   2   2   2   3   3   4   4   4   5   5   5   6   6  
 LCS     248       G     4    7   13       C        0   1   1   1   1   2   2   2   2   2   3   3   4   4   4   5   5   5   6   6  
 LCS     249       D     4    7   13       C        0   1   1   1   1   2   2   2   2   2   3   3   4   4   4   5   5   5   6   6  
 LCS     250       E     4    7   13       H        0   1   1   1   1   2   2   2   2   2   3   3   4   4   4   5   5   5   6   6  
 LCS     251       T     4    7   13       H        0   1   1   1   1   2   2   2   2   2   3   3   3   3   4   5   5   5   6   6  
 LCS     252       F     4    7   13       H        0   1   1   1   1   2   2   2   2   2   3   3   3   3   4   4   5   5   6   6  
 LCS     253       R     4    7   13       H        0   1   1   1   1   2   2   2   2   2   3   3   4   4   4   5   5   5   6   6  
 LCS     254       L     3    5   13       C        0   0   0   0   1   1   1   2   2   3   3   3   4   4   4   5   5   5   6   6  
 LCS     255       C     3    3   11       H        0   0   1   1   1   1   2   3   3   3   3   3   4   4   4   5   5   5   6   6  
 LCS     256       Q     0    0    0       H        0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  
 LCS     257       E     0    0    0       H        0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  
 LCS     258       Y     4    8    9       C        0   0   1   1   2   2   2   3   3   3   3   3   3   3   3   4   4   4   6   6  
 LCS     259       L     4    8    9       C        0   0   1   1   2   2   2   3   3   3   3   3   3   3   3   5   5   5   6   6  
 LCS     260       D     4    8    9       C        0   0   1   1   2   2   2   3   3   3   3   3   3   3   3   4   4   4   4   5  
 LCS     261       D     4    8    9       E        0   0   1   1   2   2   2   3   3   3   3   3   3   3   3   4   4   4   6   6  
 LCS     262       I     4    8    9       E        0   0   1   1   2   2   2   3   3   3   3   3   4   4   4   5   5   5   6   6  
 LCS     263       I     4    8    9       E        0   0   1   1   2   2   2   3   3   3   3   3   4   4   4   5   5   5   6   6  
 LCS     264       T     4    8    9       E        0   0   1   1   2   2   2   3   3   3   3   3   4   4   4   5   5   5   6   6  
 LCS     265       V     4    8    9       E        0   0   1   1   2   2   2   3   3   3   3   3   4   4   4   5   5   5   6   6  
 LCS     266       D     3    4    9       C        0   0   0   0   1   1   2   3   3   3   3   3   3   3   4   5   5   5   6   6  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.10 
 
 NUMBER_OF_CA_Tg:  311      NUMBER_OF_CA_Pr:   23      PERCENT_OF_CA:   7.40  
 
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       5       6       7       8       9      10      10      10      11      12      13      15      15      16      17      18      19      20  
 GDT PERCENT_OF_CA_Pr   17.39   21.74   21.74   26.09   30.43   34.78   39.13   43.48   43.48   43.48   47.83   52.17   56.52   65.22   65.22   69.57   73.91   78.26   82.61   86.96 
 GDT PERCENT_OF_CA_Tg    1.29    1.61    1.61    1.93    2.25    2.57    2.89    3.22    3.22    3.22    3.54    3.86    4.18    4.82    4.82    5.14    5.47    5.79    6.11    6.43 
 GDT FRAGMENT: Beg-End 244-247 243-247 243-247 258-265 258-265 258-265 255-266 255-266 255-266 255-266 254-266 242-253 243-265 243-265 243-265 243-265 242-266 242-266 242-266 242-266 
 GDT RMS_LOCAL           0.34    0.61    0.61    1.24    1.44    1.75    2.49    2.71    2.71    2.71    3.36    4.23    5.29    5.62    5.62    5.92    6.21    6.43    6.66    6.89 
 GDT RMS_ALL_CA         13.41   13.68   13.68   16.23   15.97   16.34   14.65   14.83   14.83   14.83   13.42   14.79    8.23    8.06    8.06    7.96    8.15    8.04    8.08    7.92 
 
 
 TEST (CA)  RMS =   7.72               (Number of atoms:   23) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    7.72         23     7.4   311     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3356                            CRMSCA  
     SECONDARY STRUCTURE . .    7.08          5     3.0   169     CRMSCA  
     SURFACE . . . . . . . .    8.76          9     6.5   139     CRMSCA  
     BURIED  . . . . . . . .    6.97         14     8.1   172     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    7.85        112     7.3  1524     CRMSMC  
     SECONDARY STRUCTURE . .    7.34         25     3.0   833     CRMSMC  
     SURFACE . . . . . . . .    8.56         44     6.5   681     CRMSMC  
     BURIED  . . . . . . . .    7.36         68     8.1   843     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    8.58         20     2.0   983     CRMSSC  
     RELIABLE SIDE CHAINS  .    8.58         20     2.5   795     CRMSSC  
     SECONDARY STRUCTURE . .    8.24          5     0.9   569     CRMSSC  
     SURFACE . . . . . . . .    9.92          8     1.6   498     CRMSSC  
     BURIED  . . . . . . . .    7.57         12     2.5   485     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    7.85        112     5.0  2227     CRMSALL 
     SECONDARY STRUCTURE . .    7.34         25     2.0  1245     CRMSALL 
     SURFACE . . . . . . . .    8.56         44     4.2  1054     CRMSALL 
     BURIED  . . . . . . . .    7.36         68     5.8  1173     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 . . . . . . . . . .    7.322      1.000       0.500     23     7.4   311     ERRCA  
     SECONDARY STRUCTURE . .    6.870      1.000       0.500      5     3.0   169     ERRCA  
     SURFACE . . . . . . . .    8.318      1.000       0.500      9     6.5   139     ERRCA  
     BURIED  . . . . . . . .    6.681      1.000       0.500     14     8.1   172     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.459      1.000       0.500    112     7.3  1524     ERRMC  
     SECONDARY STRUCTURE . .    7.132      1.000       0.500     25     3.0   833     ERRMC  
     SURFACE . . . . . . . .    8.092      1.000       0.500     44     6.5   681     ERRMC  
     BURIED  . . . . . . . .    7.049      1.000       0.500     68     8.1   843     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.023      1.000       0.500     20     2.0   983     ERRSC  
     RELIABLE SIDE CHAINS  .    8.023      1.000       0.500     20     2.5   795     ERRSC  
     SECONDARY STRUCTURE . .    7.971      1.000       0.500      5     0.9   569     ERRSC  
     SURFACE . . . . . . . .    9.571      1.000       0.500      8     1.6   498     ERRSC  
     BURIED  . . . . . . . .    6.992      1.000       0.500     12     2.5   485     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.459      1.000       0.500    112     5.0  2227     ERRALL 
     SECONDARY STRUCTURE . .    7.132      1.000       0.500     25     2.0  1245     ERRALL 
     SURFACE . . . . . . . .    8.092      1.000       0.500     44     4.2  1054     ERRALL 
     BURIED  . . . . . . . .    7.049      1.000       0.500     68     5.8  1173     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         0         4        18      23     311   DISTCA 
CA  (P)      0.00      0.00      0.00      1.29      5.79             311   DISTCA 
CA  (RMS)    0.00      0.00      0.00      4.11      6.65                   DISTCA 
 
ALL (N)         0         1         2        17        91     112    2227   DISTALL 
ALL (P)      0.00      0.04      0.09      0.76      4.09            2227   DISTALL 
ALL (RMS)    0.00      1.99      2.03      4.04      6.85                   DISTALL 
 
 
 
 
END of the results output 
