 
####################################################### 
#                                                     # 
#                        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: 28 , MODEL 28 , TARGET 202 
#          The number of residues possible to evaluate: 28 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP    29     G     C     C             1.00 
 SSP    30     K     C     C             1.00 
 SSP    31     P     C     C             1.00 
 SSP    32     V     C     C             1.00 
 SSP    33     D     C     C             1.00 
 SSP    34     G     C     C             1.00 
 SSP    35     Y     E     C             1.00 
 SSP    36     E     C     C             1.00 
 SSP    37     V     C     C             1.00 
 SSP    38     N     C     E             1.00 
 SSP    39     R     C     C             1.00 
 SSP    40     I     C     C             1.00 
 SSP    41     V     E     E             1.00 
 SSP    42     G     E     C             1.00 
 SSP    43     T     E     C             1.00 
 SSP    44     Y     H     C             1.00 
 SSP    45     E     H     C             1.00 
 SSP    46     L     H     C             1.00 
 SSP    47     A     H     H             1.00 
 SSP    48     E     H     H             1.00 
 SSP    49     S     H     H             1.00 
 SSP    50     L     H     H             1.00 
 SSP    51     L     H     H             1.00 
 SSP    52     K     H     H             1.00 
 SSP    53     A     H     C             1.00 
 SSP    54     K     H     C             1.00 
 SSP    55     E     H     C             1.00 
 SSP    56     L     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              60.7      46.2     25.0     90.9     13.9 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        62.6      69.2     25.0     66.7     13.9 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            2              50.0               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      28    100.0     60.7 
 
 BIN  0.00 - 1.00      1.00      28    100.0     60.7 
 
 
 
 
              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 188 
 
# WARNING! TARGET 1650 atoms, MODEL 1545 atoms, 1545 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 . . . . . . . . . .    76.83           53.7    54    13.4   402     ARMSMC  
     SECONDARY STRUCTURE . .    58.99           61.3    31    21.8   142     ARMSMC  
     SURFACE . . . . . . . .    80.47           53.3    30    15.2   198     ARMSMC  
     BURIED  . . . . . . . .    72.02           54.2    24    11.8   204     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   173     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   163     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    59     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    89     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    84     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   137     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   105     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    48     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    76     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    61     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    49     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    45     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    19     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    39     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    10     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    23     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    23     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     9     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    19     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     4     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1   29 - 56   28   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    19     37 - 55       4.92    13.56 
  LONGEST_CONTINUOUS_SEGMENT    19     38 - 56       4.74    14.08 
  LCS LOCAL_SCORE:             61.73 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1   29 - 56   28   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    10     45 - 54       2.00    18.92 
  LONGEST_CONTINUOUS_SEGMENT    10     46 - 55       1.90    19.17 
  LCS LOCAL_SCORE:             26.28 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1   29 - 56   28   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     9     46 - 54       0.81    18.71 
  LCS LOCAL_SCORE:             21.30 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS      29       G     3    4   13       C        0   1   1   1   1   2   2   2   4   4   5   5   5   6   6   6   6   6   6   6  
 LCS      30       K     3    6   13       C        1   2   2   2   3   3   3   3   4   4   5   5   5   6   6   6   6   6   6   6  
 LCS      31       P     4    6   13       C        1   1   1   2   2   2   3   3   3   3   3   4   5   6   6   6   6   6   7   7  
 LCS      32       V     4    6   13       C        1   2   2   2   3   3   3   3   4   4   5   5   5   6   6   6   6   7   8   8  
 LCS      33       D     4    6   13       C        1   2   2   2   3   3   3   3   4   4   5   5   5   6   6   6   6   6   8   8  
 LCS      34       G     4    6   13       C        1   2   2   2   3   3   3   3   4   4   5   5   5   6   6   6   7   7   8   8  
 LCS      35       Y     4    6   13       E        1   2   2   2   3   3   3   3   4   4   5   5   5   6   6   6   7   8   9   9  
 LCS      36       E     4    6   13       C        1   1   1   1   3   3   3   3   4   4   5   5   5   6   6   7   8   8   9   9  
 LCS      37       V     4    6   19       C        1   1   1   2   3   3   3   3   4   4   5   5   6   8   8   9   9   9   9   9  
 LCS      38       N     4    5   19       C        1   1   1   1   2   3   5   5   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      39       R     4    5   19       C        1   1   1   1   2   3   5   5   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      40       I     6    6   19       C        1   2   2   2   2   2   3   3   4   4   5   6   7   9   9   9   9   9   9   9  
 LCS      41       V     6    6   19       E        1   2   2   2   2   2   3   3   4   6   6   7   8   9   9   9   9   9   9   9  
 LCS      42       G     6    6   19       E        1   1   2   2   2   2   4   4   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      43       T     6    6   19       E        1   2   2   2   2   3   4   4   4   6   6   7   8   9   9   9   9   9   9   9  
 LCS      44       Y     6    6   19       H        1   2   2   2   2   3   4   4   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      45       E     6   10   19       H        1   2   2   2   2   3   3   4   4   6   6   7   8   9   9   9   9   9   9   9  
 LCS      46       L     9   10   19       H        3   3   4   4   4   4   5   5   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      47       A     9   10   19       H        3   3   4   4   4   4   5   5   5   5   6   7   8   9   9   9   9   9   9   9  
 LCS      48       E     9   10   19       H        3   3   4   4   4   4   5   5   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      49       S     9   10   19       H        3   3   4   4   4   4   5   5   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      50       L     9   10   19       H        3   3   4   4   4   4   5   5   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      51       L     9   10   19       H        3   3   4   4   4   4   5   5   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      52       K     9   10   19       H        3   3   4   4   4   4   5   5   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      53       A     9   10   19       H        3   3   4   4   4   4   5   5   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      54       K     9   10   19       H        1   1   4   4   4   4   5   5   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      55       E     4   10   19       H        1   1   1   1   2   4   5   5   5   6   6   7   8   9   9   9   9   9   9   9  
 LCS      56       L     4    4   19       H        1   1   1   1   1   2   4   5   5   5   5   7   8   9   9   9   9   9   9   9  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.41 
 
 NUMBER_OF_CA_Tg:  202      NUMBER_OF_CA_Pr:   28      PERCENT_OF_CA:  13.86  
 
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       8       9       9       9       9      11      12      12      14      14      16      18      19      19      19      20      20      20      20  
 GDT PERCENT_OF_CA_Pr   28.57   28.57   32.14   32.14   32.14   32.14   39.29   42.86   42.86   50.00   50.00   57.14   64.29   67.86   67.86   67.86   71.43   71.43   71.43   71.43 
 GDT PERCENT_OF_CA_Tg    3.96    3.96    4.46    4.46    4.46    4.46    5.45    5.94    5.94    6.93    6.93    7.92    8.91    9.41    9.41    9.41    9.90    9.90    9.90    9.90 
 GDT FRAGMENT: Beg-End  46-53   46-53   46-54   46-54   46-54   46-54   38-54   38-55   38-55   38-55   38-55   38-55   38-56   38-56   38-56   38-56   37-56   37-56   37-56   37-56  
 GDT RMS_LOCAL           0.25    0.25    0.81    0.81    0.81    0.81    2.85    2.96    2.96    3.87    3.78    4.28    4.59    4.74    4.74    4.74    5.06    5.06    5.06    5.06 
 GDT RMS_ALL_CA         18.99   18.99   18.71   18.71   18.71   18.71   14.04   14.32   14.32   13.75   13.81   13.62   13.78   14.08   14.08   14.08   13.72   13.72   13.72   13.72 
 
 
 TEST (CA)  RMS =  10.83               (Number of atoms:   28) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   10.83         28    13.9   202     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3869                            CRMSCA  
     SECONDARY STRUCTURE . .    8.48         16    22.5    71     CRMSCA  
     SURFACE . . . . . . . .   12.08         16    16.0   100     CRMSCA  
     BURIED  . . . . . . . .    8.89         12    11.8   102     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   10.72        112    11.2   996     CRMSMC  
     SECONDARY STRUCTURE . .    8.45         64    18.1   353     CRMSMC  
     SURFACE . . . . . . . .   11.99         64    13.0   494     CRMSMC  
     BURIED  . . . . . . . .    8.75         48     9.6   502     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   842     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   740     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   302     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   422     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   420     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   10.72        112     6.8  1650     CRMSALL 
     SECONDARY STRUCTURE . .    8.45         64    10.9   586     CRMSALL 
     SURFACE . . . . . . . .   11.99         64     7.8   822     CRMSALL 
     BURIED  . . . . . . . .    8.75         48     5.8   828     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 . . . . . . . . . .    9.762      1.000       0.500     28    13.9   202     ERRCA  
     SECONDARY STRUCTURE . .    7.619      1.000       0.500     16    22.5    71     ERRCA  
     SURFACE . . . . . . . .   11.049      1.000       0.500     16    16.0   100     ERRCA  
     BURIED  . . . . . . . .    8.045      1.000       0.500     12    11.8   102     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.680      1.000       0.500    112    11.2   996     ERRMC  
     SECONDARY STRUCTURE . .    7.561      1.000       0.500     64    18.1   353     ERRMC  
     SURFACE . . . . . . . .   11.028      1.000       0.500     64    13.0   494     ERRMC  
     BURIED  . . . . . . . .    7.882      1.000       0.500     48     9.6   502     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   842     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   740     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   302     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   422     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   420     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.680      1.000       0.500    112     6.8  1650     ERRALL 
     SECONDARY STRUCTURE . .    7.561      1.000       0.500     64    10.9   586     ERRALL 
     SURFACE . . . . . . . .   11.028      1.000       0.500     64     7.8   822     ERRALL 
     BURIED  . . . . . . . .    7.882      1.000       0.500     48     5.8   828     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         1         4        17      28     202   DISTCA 
CA  (P)      0.00      0.00      0.50      1.98      8.42             202   DISTCA 
CA  (RMS)    0.00      0.00      2.81      3.74      6.83                   DISTCA 
 
ALL (N)         0         0         6        18        63     112    1650   DISTALL 
ALL (P)      0.00      0.00      0.36      1.09      3.82            1650   DISTALL 
ALL (RMS)    0.00      0.00      2.56      3.72      6.47                   DISTALL 
 
 
 
 
END of the results output 
