 
####################################################### 
#                                                     # 
#                        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: 30 , MODEL 30 , TARGET 156 
#          The number of residues possible to evaluate: 30 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP    81     R     C     C             1.00 
 SSP    82     G     C     C             1.00 
 SSP    83     C     C     C             1.00 
 SSP    84     I     C     C             1.00 
 SSP    85     D     C     C             1.00 
 SSP    86     D     C     C             1.00 
 SSP    87     R     C     C             1.00 
 SSP    88     I     C     C             1.00 
 SSP    89     P     C     C             1.00 
 SSP    90     T     C     C             1.00 
 SSP    91     D     C     C             1.00 
 SSP    92     P     H     H             1.00 
 SSP    93     T     H     H             1.00 
 SSP    94     M     H     H             1.00 
 SSP    95     Y     H     H             1.00 
 SSP    96     R     H     H             1.00 
 SSP    97     F     H     H             1.00 
 SSP    98     Y     H     H             1.00 
 SSP    99     E     H     H             1.00 
 SSP   100     M     H     H             1.00 
 SSP   101     L     H     H             1.00 
 SSP   102     Q     H     H             1.00 
 SSP   103     V     H     H             1.00 
 SSP   104     Y     H     C             1.00 
 SSP   105     G     H     C             1.00 
 SSP   106     T     H     C             1.00 
 SSP   107     T     H     C             1.00 
 SSP   108     L     H     C             1.00 
 SSP   109     K     H     C             1.00 
 SSP   110     A     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              76.7      63.2      0.0    100.0     19.2 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        96.7      94.7    100.0    100.0     19.2 
 
           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      30    100.0     76.7 
 
 BIN  0.00 - 1.00      1.00      30    100.0     76.7 
 
 
 
 
              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 145 
 
# WARNING! TARGET 1197 atoms, MODEL 1070 atoms, 1068 common with TARGET 
           Number of atoms possible to evaluate: 120 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    73.82           67.2    58    18.7   310     ARMSMC  
     SECONDARY STRUCTURE . .    58.93           78.4    37    19.5   190     ARMSMC  
     SURFACE . . . . . . . .    72.55           67.9    56    23.3   240     ARMSMC  
     BURIED  . . . . . . . .   103.42           50.0     2     2.9    70     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   120     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    77     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   101     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    26     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   102     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    76     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    60     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    84     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    31     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    25     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    20     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    27     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     4     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    18     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    14     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    16     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1   81 - 110  30   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    25     82 - 106      4.85     7.50 
  LONGEST_CONTINUOUS_SEGMENT    25     83 - 107      4.78     7.40 
  LONGEST_CONTINUOUS_SEGMENT    25     84 - 108      4.90     7.32 
  LCS LOCAL_SCORE:             81.67 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1   81 - 110  30   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    16     90 - 105      1.89     8.69 
  LONGEST_CONTINUOUS_SEGMENT    16     91 - 106      1.75     8.85 
  LCS LOCAL_SCORE:             37.33 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1   81 - 110  30   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    12     92 - 103      1.00     9.19 
  LONGEST_CONTINUOUS_SEGMENT    12     93 - 104      0.94     9.21 
  LCS LOCAL_SCORE:             25.00 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS      81       R     4    5   18       C        1   2   2   3   3   3   5   6   7   8   9   9  10  11  11  12  12  13  13  15  
 LCS      82       G     4    5   25       C        1   2   2   3   3   5   5   6  10  10  12  12  12  13  14  14  16  16  16  17  
 LCS      83       C     4    6   25       C        1   2   2   3   3   5   5   6   7  10  12  12  12  13  14  14  16  16  16  17  
 LCS      84       I     4    6   25       C        1   2   2   3   7   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS      85       D     4    6   25       C        1   1   2   3   3   5   8  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS      86       D     4    6   25       C        1   1   2   3   3   5   5   7   9  11  12  13  15  15  15  15  16  16  16  17  
 LCS      87       R     4    6   25       C        1   1   2   2   3   4   5   6   8   9  12  13  15  15  15  15  16  16  16  17  
 LCS      88       I     4    6   25       C        1   1   2   3   3   5   5   7   8   9  12  13  15  15  15  15  16  16  16  17  
 LCS      89       P     3    5   25       C        1   1   2   2   2   4   4   5   7   8  12  13  15  15  15  15  16  16  16  17  
 LCS      90       T     3   16   25       C        1   1   2   2   3   7   9  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS      91       D    11   16   25       C        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS      92       P    12   16   25       H        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS      93       T    12   16   25       H        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS      94       M    12   16   25       H        3   6   8   9   9   9  10  10  10  12  12  13  15  15  15  15  16  16  16  17  
 LCS      95       Y    12   16   25       H        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS      96       R    12   16   25       H        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS      97       F    12   16   25       H        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS      98       Y    12   16   25       H        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS      99       E    12   16   25       H        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS     100       M    12   16   25       H        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS     101       L    12   16   25       H        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS     102       Q    12   16   25       H        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS     103       V    12   16   25       H        3   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS     104       Y    12   16   25       H        1   6   8   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS     105       G     5   16   25       H        1   2   7   9   9   9  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS     106       T     3   16   25       H        1   1   1   3   5   8  10  10  11  12  12  13  15  15  15  15  16  16  16  17  
 LCS     107       T     3    4   25       H        0   1   1   2   2   2   5   7   8  10  10  12  15  15  15  15  16  16  16  17  
 LCS     108       L     3    3   25       H        1   1   1   1   2   3   5   7   7   8   9  10  12  13  14  15  16  16  16  17  
 LCS     109       K     3    3   23       H        1   1   1   1   2   3   5   7   7   8   9  10  11  13  14  15  16  16  16  17  
 LCS     110       A     3    3   19       H        1   1   1   1   1   2   2   3   5   5   5   7   7   8   9   9   9  10  10  11  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.92 
 
 NUMBER_OF_CA_Tg:  156      NUMBER_OF_CA_Pr:   30      PERCENT_OF_CA:  19.23  
 
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       6      10      14      15      15      15      16      17      18      19      20      21      24      24      24      24      26      26      26      27  
 GDT PERCENT_OF_CA_Pr   20.00   33.33   46.67   50.00   50.00   50.00   53.33   56.67   60.00   63.33   66.67   70.00   80.00   80.00   80.00   80.00   86.67   86.67   86.67   90.00 
 GDT PERCENT_OF_CA_Tg    3.85    6.41    8.97    9.62    9.62    9.62   10.26   10.90   11.54   12.18   12.82   13.46   15.38   15.38   15.38   15.38   16.67   16.67   16.67   17.31 
 GDT FRAGMENT: Beg-End  95-103  95-104  91-104  91-105  91-105  91-105  84-105  90-106  84-106  84-106  84-106  84-106  84-107  84-107  84-107  84-107  84-109  82-107  82-107  83-109 
 GDT RMS_LOCAL           0.22    0.63    1.07    1.17    1.17    1.17    1.99    2.19    2.87    2.95    3.32    3.64    4.43    4.43    4.43    4.43    5.27    5.10    5.10    5.53 
 GDT RMS_ALL_CA          8.97    8.94    9.01    9.12    9.12    9.12    8.49    8.42    7.98    8.00    8.10    7.93    7.57    7.57    7.57    7.57    7.18    7.30    7.30    7.08 
 
 
 TEST (CA)  RMS =   7.00               (Number of atoms:   30) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    7.00         30    19.2   156     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2332                            CRMSCA  
     SECONDARY STRUCTURE . .    6.53         19    20.0    95     CRMSCA  
     SURFACE . . . . . . . .    7.02         29    24.0   121     CRMSCA  
     BURIED  . . . . . . . .    6.30          1     2.9    35     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    7.11        120    15.6   769     CRMSMC  
     SECONDARY STRUCTURE . .    6.78         76    16.1   471     CRMSMC  
     SURFACE . . . . . . . .    7.14        116    19.4   597     CRMSMC  
     BURIED  . . . . . . . .    5.99          4     2.3   172     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   573     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   493     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   359     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   468     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   105     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    7.11        120    10.0  1197     CRMSALL 
     SECONDARY STRUCTURE . .    6.78         76    10.3   739     CRMSALL 
     SURFACE . . . . . . . .    7.14        116    12.2   952     CRMSALL 
     BURIED  . . . . . . . .    5.99          4     1.6   245     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 . . . . . . . . . .    6.061      1.000       0.500     30    19.2   156     ERRCA  
     SECONDARY STRUCTURE . .    5.449      1.000       0.500     19    20.0    95     ERRCA  
     SURFACE . . . . . . . .    6.052      1.000       0.500     29    24.0   121     ERRCA  
     BURIED  . . . . . . . .    6.302      1.000       0.500      1     2.9    35     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.084      1.000       0.500    120    15.6   769     ERRMC  
     SECONDARY STRUCTURE . .    5.551      1.000       0.500     76    16.1   471     ERRMC  
     SURFACE . . . . . . . .    6.088      1.000       0.500    116    19.4   597     ERRMC  
     BURIED  . . . . . . . .    5.975      1.000       0.500      4     2.3   172     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   573     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   493     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   359     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   468     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   105     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.084      1.000       0.500    120    10.0  1197     ERRALL 
     SECONDARY STRUCTURE . .    5.551      1.000       0.500     76    10.3   739     ERRALL 
     SURFACE . . . . . . . .    6.088      1.000       0.500    116    12.2   952     ERRALL 
     BURIED  . . . . . . . .    5.975      1.000       0.500      4     1.6   245     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)         2         2         3        11        27      30     156   DISTCA 
CA  (P)      1.28      1.28      1.92      7.05     17.31             156   DISTCA 
CA  (RMS)    0.84      0.84      1.70      3.35      5.60                   DISTCA 
 
ALL (N)         6         9        15        53       106     120    1197   DISTALL 
ALL (P)      0.50      0.75      1.25      4.43      8.86            1197   DISTALL 
ALL (RMS)    0.75      1.09      1.90      3.68      5.42                   DISTALL 
 
 
 
 
END of the results output 
