 
####################################################### 
#                                                     # 
#                        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: 34 , MODEL 34 , TARGET 378 
#          The number of residues possible to evaluate: 34 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP   300     E     H     C             1.00 
 SSP   301     T     H     H             1.00 
 SSP   302     L     H     H             1.00 
 SSP   303     A     H     H             1.00 
 SSP   304     D     H     H             1.00 
 SSP   305     A     H     H             1.00 
 SSP   306     A     H     H             1.00 
 SSP   307     R     H     C             1.00 
 SSP   308     R     C     C             1.00 
 SSP   309     D     C     C             1.00 
 SSP   310     Q     C     C             1.00 
 SSP   311     A     C     C             1.00 
 SSP   312     G     C     E             1.00 
 SSP   313     V     H     E             1.00 
 SSP   314     G     H     C             1.00 
 SSP   315     A     H     C             1.00 
 SSP   316     E     C     E             1.00 
 SSP   317     T     C     E             1.00 
 SSP   318     R     C     E             1.00 
 SSP   319     G     C     C             1.00 
 SSP   320     P     C     C             1.00 
 SSP   321     G     C     C             1.00 
 SSP   322     W     E     C             1.00 
 SSP   323     G     E     E             1.00 
 SSP   324     F     E     E             1.00 
 SSP   325     G     C     C             1.00 
 SSP   326     Y     C     C             1.00 
 SSP   327     L     C     C             1.00 
 SSP   328     S     C     C             1.00 
 SSP   329     A     E     C             1.00 
 SSP   330     V     E     C             1.00 
 SSP   331     L     E     C             1.00 
 SSP   332     D     C     C             1.00 
 SSP   333     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              61.8      54.5     33.3     76.5      9.0 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        69.5      72.7     50.0     74.2      9.0 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            4              50.0              25.0 
 
         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      34    100.0     61.8 
 
 BIN  0.00 - 1.00      1.00      34    100.0     61.8 
 
 
 
 
              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 
 
 
# WARNING! The number of residues with CB atom coordinates: MODEL 0 , TARGET 336 
 
# WARNING! TARGET 2840 atoms, MODEL 2833 atoms, 2728 common with TARGET 
           Number of atoms possible to evaluate: 136 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    69.92           53.0    66     8.8   754     ARMSMC  
     SECONDARY STRUCTURE . .    40.08           81.5    27     8.7   310     ARMSMC  
     SURFACE . . . . . . . .    74.73           46.9    32     9.7   330     ARMSMC  
     BURIED  . . . . . . . .    65.08           58.8    34     8.0   424     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   278     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   249     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0   116     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   119     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0   159     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   216     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   157     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    88     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   106     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0   110     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    69     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    60     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    25     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    51     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    35     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    35     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    16     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    28     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     7     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1  300 - 333  34   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    20    300 - 319      4.82     9.84 
  LCS LOCAL_SCORE:             52.16 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1  300 - 333  34   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    15    300 - 314      1.98     9.77 
  LCS LOCAL_SCORE:             32.35 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1  300 - 333  34   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    12    300 - 311      0.89    10.11 
  LCS LOCAL_SCORE:             21.71 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS     300       E    12   15   20       H        2   2   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     301       T    12   15   20       H        2   2   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     302       L    12   15   20       H        2   2   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     303       A    12   15   20       H        2   2   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     304       D    12   15   20       H        2   2   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     305       A    12   15   20       H        2   2   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     306       A    12   15   20       H        2   2   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     307       R    12   15   20       H        2   2   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     308       R    12   15   20       C        2   2   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     309       D    12   15   20       C        1   2   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     310       Q    12   15   20       C        1   1   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     311       A    12   15   20       C        1   1   3   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     312       G     6   15   20       C        0   1   1   3   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     313       V     4   15   20       H        0   1   1   1   2   3   3   3   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     314       G     3   15   20       H        0   0   1   1   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     315       A     4    6   20       H        0   0   1   1   2   3   3   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     316       E     4    6   20       C        0   0   1   1   1   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     317       T     4    6   20       C        0   0   1   1   1   2   2   2   2   3   4   5   5   5   5   5   6   6   6   6  
 LCS     318       R     4    6   20       C        0   1   1   1   1   1   2   2   2   2   3   3   4   5   5   5   6   6   6   6  
 LCS     319       G     4    9   20       C        0   1   1   1   1   2   2   2   2   2   3   3   4   4   4   5   5   5   5   6  
 LCS     320       P     5    9   16       C        1   1   1   2   2   2   2   2   2   2   3   3   4   4   4   5   5   5   5   6  
 LCS     321       G     6    9   16       C        1   1   1   2   2   2   2   2   2   2   3   3   4   4   4   5   5   5   5   6  
 LCS     322       W     6    9   16       E        1   1   1   2   2   2   2   2   2   2   3   4   4   5   5   5   6   6   6   6  
 LCS     323       G     6    9   16       E        1   1   1   2   2   2   2   2   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     324       F     6    9   16       E        1   1   1   2   3   3   4   4   4   4   5   5   5   5   5   5   6   6   6   6  
 LCS     325       G     6    9   16       C        1   1   1   2   2   2   2   2   2   2   3   5   5   5   5   5   6   6   6   6  
 LCS     326       Y     6    9   16       C        1   1   1   2   2   2   2   2   2   2   3   3   4   4   4   5   5   5   5   6  
 LCS     327       L     5    9   16       C        0   1   1   2   2   2   2   2   2   2   3   3   4   4   4   5   6   6   6   6  
 LCS     328       S     5    8   16       C        0   1   1   1   1   2   2   2   2   2   3   3   4   4   4   5   6   6   6   6  
 LCS     329       A     5    8   15       E        1   1   1   1   1   2   2   2   2   2   2   2   5   5   5   5   6   6   6   6  
 LCS     330       V     5    8   11       E        1   1   1   1   1   2   2   2   2   2   2   2   2   3   4   5   5   5   5   6  
 LCS     331       L     5    8   11       E        1   1   1   1   1   2   2   2   2   2   2   2   2   2   3   5   5   5   6   6  
 LCS     332       D     5    8   11       C        1   1   1   1   1   2   2   2   2   2   2   2   2   2   3   5   5   5   5   6  
 LCS     333       D     3    4   11       C        0   0   0   0   1   1   1   1   1   1   2   4   4   4   5   5   6   6   6   6  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.18 
 
 NUMBER_OF_CA_Tg:  378      NUMBER_OF_CA_Pr:   34      PERCENT_OF_CA:   8.99  
 
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       8      10      12      13      13      14      16      17      17      18      19      19      20      20      22      22      24      24      24      25  
 GDT PERCENT_OF_CA_Pr   23.53   29.41   35.29   38.24   38.24   41.18   47.06   50.00   50.00   52.94   55.88   55.88   58.82   58.82   64.71   64.71   70.59   70.59   70.59   73.53 
 GDT PERCENT_OF_CA_Tg    2.12    2.65    3.17    3.44    3.44    3.70    4.23    4.50    4.50    4.76    5.03    5.03    5.29    5.29    5.82    5.82    6.35    6.35    6.35    6.61 
 GDT FRAGMENT: Beg-End 301-308 300-309 300-311 300-312 300-312 300-314 300-324 300-324 300-324 300-324 300-324 300-324 300-324 300-324 300-324 300-329 300-329 300-329 300-329 300-329 
 GDT RMS_LOCAL           0.12    0.46    0.89    1.27    1.27    1.69    2.13    2.36    2.36    2.69    2.93    2.93    3.23    3.23    4.36    4.14    4.95    4.95    4.95    5.27 
 GDT RMS_ALL_CA         10.80   10.46   10.11    9.85    9.85    9.66    9.63    9.70    9.70    9.63    9.57    9.57    9.61    9.61    9.73    9.79   10.25   10.25   10.25   10.42 
 
 
 TEST (CA)  RMS =   9.34               (Number of atoms:   34) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    9.34         34     9.0   378     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2747                            CRMSCA  
     SECONDARY STRUCTURE . .    7.00         14     9.0   155     CRMSCA  
     SURFACE . . . . . . . .    8.50         17    10.2   166     CRMSCA  
     BURIED  . . . . . . . .   10.11         17     8.0   212     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    9.27        136     7.4  1848     CRMSMC  
     SECONDARY STRUCTURE . .    7.00         56     7.3   769     CRMSMC  
     SURFACE . . . . . . . .    8.41         68     8.4   809     CRMSMC  
     BURIED  . . . . . . . .   10.06         68     6.5  1039     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0  1328     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0  1118     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   560     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   583     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   745     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.27        136     4.8  2840     CRMSALL 
     SECONDARY STRUCTURE . .    7.00         56     4.7  1180     CRMSALL 
     SURFACE . . . . . . . .    8.41         68     5.5  1247     CRMSALL 
     BURIED  . . . . . . . .   10.06         68     4.3  1593     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 . . . . . . . . . .    7.913      1.000       0.500     34     9.0   378     ERRCA  
     SECONDARY STRUCTURE . .    6.185      1.000       0.500     14     9.0   155     ERRCA  
     SURFACE . . . . . . . .    6.893      1.000       0.500     17    10.2   166     ERRCA  
     BURIED  . . . . . . . .    8.933      1.000       0.500     17     8.0   212     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.852      1.000       0.500    136     7.4  1848     ERRMC  
     SECONDARY STRUCTURE . .    6.158      1.000       0.500     56     7.3   769     ERRMC  
     SURFACE . . . . . . . .    6.815      1.000       0.500     68     8.4   809     ERRMC  
     BURIED  . . . . . . . .    8.889      1.000       0.500     68     6.5  1039     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.000      0.000       0.000      0     0.0  1328     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0  1118     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   560     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   583     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   745     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.852      1.000       0.500    136     4.8  2840     ERRALL 
     SECONDARY STRUCTURE . .    6.158      1.000       0.500     56     4.7  1180     ERRALL 
     SURFACE . . . . . . . .    6.815      1.000       0.500     68     5.5  1247     ERRALL 
     BURIED  . . . . . . . .    8.889      1.000       0.500     68     4.3  1593     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         1         2        17        22      34     378   DISTCA 
CA  (P)      0.00      0.26      0.53      4.50      5.82             378   DISTCA 
CA  (RMS)    0.00      1.98      2.51      3.76      4.98                   DISTCA 
 
ALL (N)         0         4        12        64        88     136    2840   DISTALL 
ALL (P)      0.00      0.14      0.42      2.25      3.10            2840   DISTALL 
ALL (RMS)    0.00      1.74      2.37      3.63      4.94                   DISTALL 
 
 
 
 
END of the results output 
