 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0064.inter 
CONANA-PAIR            ../CONANA/T0064.pair 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0064.1r69.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0064.2cro.rot 
# 
ITER-CUTOFF            2.5       #    DISTANCE cutoff (for CA (iter))  
# 
# 
# 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 
SS-OUTPUT           0         #    1 - ON, 0 - OFF  
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
ALIGNMENT-OUTPUT    0         #    1 - ON, 0 - OFF 
# 
# Calculation parameters 
# 
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)  
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
SC-SWAPPING         1         #    1 - ON, 0 - OFF  
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
LIGAND-DIST1        4.0       #    Ligand contact: contact with ligand cutoff 
LIGAND-DIST2        6.0       #    Ligand contact: protein neighborhood cutoff 
PARENT-DIST3        2.5       #    target-parent (dist > 2.5) 
# 
CRMS-METHOD         3         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
# 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
# Reading the coordinates set (1) 
 
 
# Evaluating the coordinates set (1) 
 
# WARNING! TARGET 845 atoms, MODEL 915 atoms, 845 common with TARGET 
           Number of atoms possible to evaluate: 515 
 
 
 CA-RMS TARGET<->PARENT(1r69)	 1.473148 
 
 CA-RMS TARGET<->PARENT(2cro)	 1.394009 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    37.29           86.7   128    63.7   201     ARMSMC  
     WELL ORDERED  . . . . .    37.33           88.2   110    68.3   161     ARMSMC  
     NO INTER CONTACTS . . .    34.78           86.0    86    81.9   105     ARMSMC  
     SHIFTED CHAIN . . . . .    50.33           75.0    68    48.2   141     ARMSMC  
     ALTERNATIVE PARENT  . .    89.65           50.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    25.33           95.9    74    58.3   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    80.05           50.0    16    18.0    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    36.38           84.6    78    51.7   151     ARMSMC  
     BURIED  . . . . . . . .    38.66           90.0    50   100.0    50     ARMSMC  
     CORE  . . . . . . . . .    25.95           92.0   112   100.0   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    86.47           39.7    58    63.7    91     ARMSSC1 
     WELL ORDERED  . . . . .    81.71           44.7    38    70.4    54     ARMSSC1 
     NO INTER CONTACTS . . .    84.71           43.2    37    82.2    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .    88.92           35.8    53    63.1    84     ARMSSC1 
     CHANGED ANGLES  . . . .   100.00           21.2    33    50.0    66     ARMSSC1 
     SHIFTED CHAIN . . . . .    87.72           38.7    31    48.4    64     ARMSSC1 
     ALTERNATIVE PARENT  . .    94.34            0.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    84.48           45.5    33    57.9    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    95.80           22.2     9    21.4    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    87.66           38.9    36    52.2    69     ARMSSC1 
     BURIED  . . . . . . . .    84.50           40.9    22   100.0    22     ARMSSC1 
     CORE  . . . . . . . . .    84.65           42.9    49   100.0    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.76           44.2    43    67.2    64     ARMSSC2 
     WELL ORDERED  . . . . .    78.70           47.6    21    75.0    28     ARMSSC2 
     NO INTER CONTACTS . . .    68.10           57.7    26    78.8    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .    76.13           40.6    32    65.3    49     ARMSSC2 
     CHANGED ANGLES  . . . .    93.08           26.9    26    55.3    47     ARMSSC2 
     SHIFTED CHAIN . . . . .    78.72           43.5    23    52.3    44     ARMSSC2 
     ALTERNATIVE PARENT  . .    55.56            0.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    70.11           57.7    26    61.9    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    88.28           28.6     7    25.0    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    90.61           32.1    28    57.1    49     ARMSSC2 
     BURIED  . . . . . . . .    44.79           66.7    15   100.0    15     ARMSSC2 
     CORE  . . . . . . . . .    75.54           47.2    36   100.0    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    96.61           19.0    21    67.7    31     ARMSSC3 
     WELL ORDERED  . . . . .   100.21           16.7     6    60.0    10     ARMSSC3 
     NO INTER CONTACTS . . .   103.82           18.2    11    73.3    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    89.26           23.5    17    65.4    26     ARMSSC3 
     CHANGED ANGLES  . . . .   103.36           17.6    17    70.8    24     ARMSSC3 
     SHIFTED CHAIN . . . . .   102.77           20.0    10    50.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    85.37           26.7    15    65.2    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    95.64            0.0     4    28.6    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    89.65           22.2    18    64.3    28     ARMSSC3 
     BURIED  . . . . . . . .   130.80            0.0     3   100.0     3     ARMSSC3 
     CORE  . . . . . . . . .    96.83           23.5    17   100.0    17     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   104.98           10.0    10    83.3    12     ARMSSC4 
     WELL ORDERED  . . . . .   133.56            0.0     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .   115.35           20.0     5    83.3     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .   104.98           10.0    10    83.3    12     ARMSSC4 
     CHANGED ANGLES  . . . .    99.62           11.1     9    81.8    11     ARMSSC4 
     SHIFTED CHAIN . . . . .   109.25            0.0     4    66.7     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .   107.31           14.3     7    77.8     9     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    60.19            0.0     1    33.3     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    94.75           12.5     8    80.0    10     ARMSSC4 
     BURIED  . . . . . . . .   138.53            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .   108.82           11.1     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.12230     r(1,2) =   0.97320     r(1,3) =  -0.19475 
 r(2,1) =  -0.32782     r(2,2) =  -0.14560     r(2,3) =  -0.93345 
 r(3,1) =  -0.93679     r(3,2) =   0.17801     r(3,3) =   0.30123 
THE OFFSET VECTOR: 
 v(1) =  18.78316     v(2) =  63.54432     v(3) =  32.04423 
 
 Number of iteration 22                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.79           (Number of atoms:   54) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.81         65    63.1   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0278                            CRMSCA  
     WELL ORDERED  . . . . .    1.57         57    67.1    85     CRMSCA  
     NO INTER CONTACTS . . .    1.80         43    79.6    54     CRMSCA  
     SHIFTED CHAIN . . . . .    2.41         35    47.9    73     CRMSCA  
     ALTERNATIVE PARENT  . .    4.11          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    1.24         37    56.9    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    4.13          9    19.1    47     CRMSCA  
     SURFACE . . . . . . . .    2.10         40    51.3    78     CRMSCA  
     BURIED  . . . . . . . .    1.20         25   100.0    25     CRMSCA  
     CORE  . . . . . . . . .    1.03         56   100.0    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.93        322    63.0   511     CRMSMC  
     WELL ORDERED  . . . . .    1.58        282    67.1   420     CRMSMC  
     NO INTER CONTACTS . . .    1.91        213    79.8   267     CRMSMC  
     SHIFTED CHAIN . . . . .    2.56        174    47.9   363     CRMSMC  
     ALTERNATIVE PARENT  . .    4.37         10   100.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    1.24        184    56.8   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    4.36         45    19.2   234     CRMSMC  
     SURFACE . . . . . . . .    2.27        198    51.2   387     CRMSMC  
     BURIED  . . . . . . . .    1.23        124   100.0   124     CRMSMC  
     CORE  . . . . . . . . .    1.12        277   100.0   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    3.41        255    58.9   433     CRMSSC  
     WELL ORDERED  . . . . .    2.65        156    62.9   248     CRMSSC  
     NO INTER CONTACTS . . .    3.22        156    74.3   210     CRMSSC  
     RELIABLE SIDE CHAINS  .    3.30        213    57.4   371     CRMSSC  
     CHANGED ANGLES  . . . .    4.13        140    49.8   281     CRMSSC  
     SECONDARY STRUCTURE . .    2.70        153    51.5   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS    5.88         35    16.4   213     CRMSSC  
     SURFACE . . . . . . . .    3.87        166    48.3   344     CRMSSC  
     BURIED  . . . . . . . .    2.32         89   100.0    89     CRMSSC  
     CORE  . . . . . . . . .    2.83        220   100.0   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.72        515    60.9   845     CRMSALL 
     WELL ORDERED  . . . . .    2.02        388    65.4   593     CRMSALL 
     NO INTER CONTACTS . . .    2.54        328    77.0   426     CRMSALL 
     SHIFTED CHAIN . . . . .    3.46        271    45.1   601     CRMSALL 
     ALTERNATIVE PARENT  . .    4.72         14   100.0    14     CRMSALL 
     SECONDARY STRUCTURE . .    2.07        301    54.0   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS    5.06         71    17.7   401     CRMSALL 
     SURFACE . . . . . . . .    3.13        326    49.7   656     CRMSALL 
     BURIED  . . . . . . . .    1.78        189   100.0   189     CRMSALL 
     CORE  . . . . . . . . .    2.11        444   100.0   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     4.11      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2     4.29      2     5.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     4.33     30   100.0    30      40-TNPSIQ-45   
 MC  LOOP  2     4.72     10     5.0   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.23     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2     4.87     18     5.2   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.31      6   100.0     6      40-TNPSIQ-45   
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.81     30   100.0    30      40-TNPSIQ-45   
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.25     45   100.0    45      40-TNPSIQ-45   
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.058      0.463       0.478     65    63.1   103     ERRCA  
     WELL ORDERED  . . . . .    2.119      0.485       0.503     57    67.1    85     ERRCA  
     NO INTER CONTACTS . . .    1.633      0.420       0.437     43    79.6    54     ERRCA  
     SHIFTED CHAIN . . . . .    1.796      0.336       0.336     35    47.9    73     ERRCA  
     ALTERNATIVE PARENT  . .    1.072      0.118       0.078      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    2.147      0.501       0.523     37    56.9    65     ERRCA  
     LARGE SHIFTS/INSERTIONS    0.959      0.135       0.074      9    19.1    47     ERRCA  
     SURFACE . . . . . . . .    2.246      0.462       0.473     40    51.3    78     ERRCA  
     BURIED  . . . . . . . .    1.758      0.465       0.486     25   100.0    25     ERRCA  
     CORE  . . . . . . . . .    2.234      0.516       0.543     56   100.0    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.101      0.466       0.484    322    63.0   511     ERRMC  
     WELL ORDERED  . . . . .    2.184      0.497       0.517    282    67.1   420     ERRMC  
     NO INTER CONTACTS . . .    1.692      0.424       0.442    213    79.8   267     ERRMC  
     SHIFTED CHAIN . . . . .    1.899      0.359       0.360    174    47.9   363     ERRMC  
     ALTERNATIVE PARENT  . .    1.092      0.131       0.110     10   100.0    10     ERRMC  
     SECONDARY STRUCTURE . .    2.176      0.508       0.533    184    56.8   324     ERRMC  
     LARGE SHIFTS/INSERTIONS    1.157      0.157       0.101     45    19.2   234     ERRMC  
     SURFACE . . . . . . . .    2.286      0.458       0.473    198    51.2   387     ERRMC  
     BURIED  . . . . . . . .    1.804      0.478       0.501    124   100.0   124     ERRMC  
     CORE  . . . . . . . . .    2.254      0.516       0.546    277   100.0   277     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.046      0.359       0.338    255    58.9   433     ERRSC  
     WELL ORDERED  . . . . .    2.030      0.384       0.387    156    62.9   248     ERRSC  
     NO INTER CONTACTS . . .    1.924      0.365       0.343    156    74.3   210     ERRSC  
     RELIABLE SIDE CHAINS  .    2.110      0.365       0.350    213    57.4   371     ERRSC  
     CHANGED ANGLES  . . . .    2.107      0.317       0.266    140    49.8   281     ERRSC  
     SHIFTED CHAIN . . . . .    2.050      0.299       0.256    131    42.4   309     ERRSC  
     ALTERNATIVE PARENT  . .    0.956      0.099       0.050      6   100.0     6     ERRSC  
     SECONDARY STRUCTURE . .    2.095      0.388       0.381    153    51.5   297     ERRSC  
     LARGE SHIFTS/INSERTIONS    2.018      0.216       0.109     35    16.4   213     ERRSC  
     SURFACE . . . . . . . .    2.204      0.347       0.320    166    48.3   344     ERRSC  
     BURIED  . . . . . . . .    1.750      0.382       0.371     89   100.0    89     ERRSC  
     CORE  . . . . . . . . .    2.050      0.382       0.374    220   100.0   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.071      0.417       0.416    515    60.9   845     ERRALL 
     WELL ORDERED  . . . . .    2.115      0.456       0.469    388    65.4   593     ERRALL 
     NO INTER CONTACTS . . .    1.790      0.399       0.400    328    77.0   426     ERRALL 
     SHIFTED CHAIN . . . . .    1.964      0.333       0.315    271    45.1   601     ERRALL 
     ALTERNATIVE PARENT  . .    1.038      0.120       0.092     14   100.0    14     ERRALL 
     SECONDARY STRUCTURE . .    2.139      0.452       0.462    301    54.0   557     ERRALL 
     LARGE SHIFTS/INSERTIONS    1.529      0.182       0.105     71    17.7   401     ERRALL 
     SURFACE . . . . . . . .    2.238      0.405       0.399    326    49.7   656     ERRALL 
     BURIED  . . . . . . . .    1.782      0.438       0.447    189   100.0   189     ERRALL 
     CORE  . . . . . . . . .    2.158      0.455       0.466    444   100.0   444     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)        47        54        54        64        65      65     103   DISTCA 
CA  (P)     45.63     52.43     52.43     62.14     63.11             103   DISTCA 
CA  (RMS)    0.64      0.79      0.79      1.71      1.81                   DISTCA 
 
ALL (N)       252       335       391       468       514     515     845   DISTALL 
ALL (P)     29.82     39.64     46.27     55.38     60.83             845   DISTALL 
ALL (RMS)    0.63      0.90      1.25      1.95      2.67                   DISTALL 
 
CA RMS: P<->T (parent <-> target), and T<->M (target <-> model) calculated using 
        CA positions for which there exists an alignment with principal parent, 
        and for which does not (LARGE SHIFTS/INSERTIONS): 
              P<->T         T<->M         T<->M (LSI) 
CA  (N)          56            56             9          RMSLSI 
CA  (P)       54.37         54.37          8.74          RMSLSI 
CA  (RMS)      1.04          1.03          4.13          RMSLSI 
 
 
 
END of the results output 
