 
####################################################### 
#                                                     # 
#                        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/T0017.inter 
CONANA-LIGAND          ../CONANA/T0017.ligand 
# 
NUMBER-OF-PARENTS      6 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0017.2gst_A.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp2.T0017.1hna.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp2.T0017.1gta.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp2.T0017.2gsr_A.rot 
ALIGNMENT-DALI(5)      ../PARENTS/casp2.T0017.1glq_A.rot 
ALIGNMENT-DALI(6)      ../PARENTS/casp2.T0017.1gss_A.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) 
 
           TARGET 1812 atoms, MODEL 1812 atoms, 1812 common with TARGET 
           Number of atoms possible to evaluate: 1623 
 
 
 CA-RMS TARGET<->PARENT(2gst_A)	 0.470591 
 
 CA-RMS TARGET<->PARENT(1hna)	 1.015151 
 
 CA-RMS TARGET<->PARENT(1gta)	 1.552161 
 
 CA-RMS TARGET<->PARENT(2gsr_A)	 1.882936 
 
 CA-RMS TARGET<->PARENT(1glq_A)	 1.983916 
 
 CA-RMS TARGET<->PARENT(1gss_A)	 2.076905 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    40.82           77.7   386    89.4   432     ARMSMC  
     WELL ORDERED  . . . . .    38.49           81.3   342    92.2   371     ARMSMC  
     NO INTER CONTACTS . . .    41.15           75.9   320    87.4   366     ARMSMC  
     SHIFTED CHAIN . . . . .    49.69           70.0    10    76.9    13     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    24.56           87.4   254    97.7   260     ARMSMC  
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSMC  
     LIGAND CONTACTS . . . .    45.13           91.7    12    92.3    13     ARMSMC  
     SURFACE . . . . . . . .    46.66           72.9   199    87.3   228     ARMSMC  
     BURIED  . . . . . . . .    33.52           82.9   187    91.7   204     ARMSMC  
     CORE  . . . . . . . . .    40.82           77.7   386    89.4   432     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    74.78           48.6   175    89.7   195     ARMSSC1 
     WELL ORDERED  . . . . .    75.38           49.3   148    92.5   160     ARMSSC1 
     NO INTER CONTACTS . . .    75.97           47.2   144    87.8   164     ARMSSC1 
     RELIABLE SIDE CHAINS  .    74.48           48.5   167    89.3   187     ARMSSC1 
     CHANGED ANGLES  . . . .    90.31           35.5    31    81.6    38     ARMSSC1 
     SHIFTED CHAIN . . . . .    83.38           33.3     3    60.0     5     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    74.23           52.1   121    98.4   123     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC1 
     LIGAND CONTACTS . . . .    11.95          100.0     2   100.0     2     ARMSSC1 
     SURFACE . . . . . . . .    77.90           42.2    90    86.5   104     ARMSSC1 
     BURIED  . . . . . . . .    71.32           55.3    85    93.4    91     ARMSSC1 
     CORE  . . . . . . . . .    74.78           48.6   175    89.7   195     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.94           39.3   150    89.3   168     ARMSSC2 
     WELL ORDERED  . . . . .    76.38           43.3   120    93.0   129     ARMSSC2 
     NO INTER CONTACTS . . .    77.58           39.3   122    87.1   140     ARMSSC2 
     RELIABLE SIDE CHAINS  .    70.86           37.4   115    87.8   131     ARMSSC2 
     CHANGED ANGLES  . . . .    90.94           24.3    37    80.4    46     ARMSSC2 
     SHIFTED CHAIN . . . . .    74.08            0.0     3    60.0     5     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    76.44           41.1   107    98.2   109     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC2 
     LIGAND CONTACTS . . . .   119.95            0.0     1    50.0     2     ARMSSC2 
     SURFACE . . . . . . . .    80.01           34.1    82    87.2    94     ARMSSC2 
     BURIED  . . . . . . . .    75.38           45.6    68    91.9    74     ARMSSC2 
     CORE  . . . . . . . . .    77.94           39.3   150    89.3   168     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    85.43           19.6    56    88.9    63     ARMSSC3 
     WELL ORDERED  . . . . .    89.24           13.5    37    94.9    39     ARMSSC3 
     NO INTER CONTACTS . . .    86.49           22.2    45    86.5    52     ARMSSC3 
     RELIABLE SIDE CHAINS  .    82.68           22.0    50    87.7    57     ARMSSC3 
     CHANGED ANGLES  . . . .    83.04           21.4    28    84.8    33     ARMSSC3 
     SHIFTED CHAIN . . . . .   132.30            0.0     3    75.0     4     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    85.85           20.0    45    97.8    46     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC3 
     LIGAND CONTACTS . . . .    89.25            0.0     1   100.0     1     ARMSSC3 
     SURFACE . . . . . . . .    83.12           17.1    41    87.2    47     ARMSSC3 
     BURIED  . . . . . . . .    91.47           26.7    15    93.8    16     ARMSSC3 
     CORE  . . . . . . . . .    85.43           19.6    56    88.9    63     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    94.78           14.3    28    84.8    33     ARMSSC4 
     WELL ORDERED  . . . . .    87.25            6.2    16    94.1    17     ARMSSC4 
     NO INTER CONTACTS . . .    89.93           14.3    21    80.8    26     ARMSSC4 
     RELIABLE SIDE CHAINS  .    94.78           14.3    28    84.8    33     ARMSSC4 
     CHANGED ANGLES  . . . .    96.13           11.8    17    81.0    21     ARMSSC4 
     SHIFTED CHAIN . . . . .    65.84           33.3     3    75.0     4     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    97.08           13.6    22   100.0    22     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .   100.12           18.2    22    81.5    27     ARMSSC4 
     BURIED  . . . . . . . .    71.88            0.0     6   100.0     6     ARMSSC4 
     CORE  . . . . . . . . .    94.78           14.3    28    84.8    33     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.51453     r(1,2) =  -0.24243     r(1,3) =  -0.82249 
 r(2,1) =  -0.55049     r(2,2) =  -0.82882     r(2,3) =  -0.10008 
 r(3,1) =  -0.65743     r(3,2) =   0.50427     r(3,3) =  -0.55991 
THE OFFSET VECTOR: 
 v(1) =  63.99198     v(2) =  71.24752     v(3) =  35.82433 
 
 Number of iteration 40                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.35           (Number of atoms:  157) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.73        194    89.4   217     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0141                            CRMSCA  
     WELL ORDERED  . . . . .    2.60        173    92.5   187     CRMSCA  
     NO INTER CONTACTS . . .    2.70        161    87.5   184     CRMSCA  
     SHIFTED CHAIN . . . . .    2.93          5    71.4     7     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    1.61        128    98.5   130     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0     0     CRMSCA  
     LIGAND CONTACTS . . . .    1.12          8    80.0    10     CRMSCA  
     SURFACE . . . . . . . .    2.73        100    87.0   115     CRMSCA  
     BURIED  . . . . . . . .    2.73         94    92.2   102     CRMSCA  
     CORE  . . . . . . . . .    2.73        194    89.4   217     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.78        960    89.4  1074     CRMSMC  
     WELL ORDERED  . . . . .    2.66        851    92.4   921     CRMSMC  
     NO INTER CONTACTS . . .    2.75        796    87.5   910     CRMSMC  
     SHIFTED CHAIN . . . . .    3.17         24    70.6    34     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    1.65        638    98.5   648     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0     0     CRMSMC  
     LIGAND CONTACTS . . . .    1.20         37    88.1    42     CRMSMC  
     SURFACE . . . . . . . .    2.84        495    87.0   569     CRMSMC  
     BURIED  . . . . . . . .    2.71        465    92.1   505     CRMSMC  
     CORE  . . . . . . . . .    2.78        960    89.4  1074     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    4.30        847    89.7   944     CRMSSC  
     WELL ORDERED  . . . . .    4.09        701    93.3   751     CRMSSC  
     NO INTER CONTACTS . . .    4.24        693    87.7   790     CRMSSC  
     RELIABLE SIDE CHAINS  .    4.42        741    88.8   834     CRMSSC  
     CHANGED ANGLES  . . . .    4.75        184    86.4   213     CRMSSC  
     SECONDARY STRUCTURE . .    3.42        610    98.7   618     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0     0     CRMSSC  
     LIGAND CONTACTS . . . .    4.20         47    87.0    54     CRMSSC  
     SURFACE . . . . . . . .    4.12        426    87.1   489     CRMSSC  
     BURIED  . . . . . . . .    4.47        421    92.5   455     CRMSSC  
     CORE  . . . . . . . . .    4.30        847    89.7   944     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.62       1623    89.6  1812     CRMSALL 
     WELL ORDERED  . . . . .    3.43       1392    92.9  1499     CRMSALL 
     NO INTER CONTACTS . . .    3.57       1337    87.6  1526     CRMSALL 
     SHIFTED CHAIN . . . . .    3.73         38    70.4    54     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    2.74       1122    98.6  1138     CRMSALL 
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0     0     CRMSALL 
     LIGAND CONTACTS . . . .    3.32         79    88.8    89     CRMSALL 
     SURFACE . . . . . . . .    3.53        826    87.0   949     CRMSALL 
     BURIED  . . . . . . . .    3.72        797    92.4   863     CRMSALL 
     CORE  . . . . . . . . .    3.62       1623    89.6  1812     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOPS 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 . . . . . . . . . .    1.936      1.000       0.500    194    89.4   217     ERRCA  
     WELL ORDERED  . . . . .    1.835      1.000       0.500    173    92.5   187     ERRCA  
     NO INTER CONTACTS . . .    1.897      1.000       0.500    161    87.5   184     ERRCA  
     SHIFTED CHAIN . . . . .    2.700      1.000       0.500      5    71.4     7     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    1.424      1.000       0.500    128    98.5   130     ERRCA  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0     0     ERRCA  
     LIGAND CONTACTS . . . .    1.042      1.000       0.500      8    80.0    10     ERRCA  
     SURFACE . . . . . . . .    2.029      1.000       0.500    100    87.0   115     ERRCA  
     BURIED  . . . . . . . .    1.838      1.000       0.500     94    92.2   102     ERRCA  
     CORE  . . . . . . . . .    1.936      1.000       0.500    194    89.4   217     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.973      1.000       0.500    960    89.4  1074     ERRMC  
     WELL ORDERED  . . . . .    1.878      1.000       0.500    851    92.4   921     ERRMC  
     NO INTER CONTACTS . . .    1.928      1.000       0.500    796    87.5   910     ERRMC  
     SHIFTED CHAIN . . . . .    2.877      1.000       0.500     24    70.6    34     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    1.450      1.000       0.500    638    98.5   648     ERRMC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0     0     ERRMC  
     LIGAND CONTACTS . . . .    1.092      1.000       0.500     37    88.1    42     ERRMC  
     SURFACE . . . . . . . .    2.113      1.000       0.500    495    87.0   569     ERRMC  
     BURIED  . . . . . . . .    1.824      1.000       0.500    465    92.1   505     ERRMC  
     CORE  . . . . . . . . .    1.973      1.000       0.500    960    89.4  1074     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.257      1.000       0.500    847    89.7   944     ERRSC  
     WELL ORDERED  . . . . .    3.062      1.000       0.500    701    93.3   751     ERRSC  
     NO INTER CONTACTS . . .    3.130      1.000       0.500    693    87.7   790     ERRSC  
     RELIABLE SIDE CHAINS  .    3.304      1.000       0.500    741    88.8   834     ERRSC  
     CHANGED ANGLES  . . . .    3.972      1.000       0.500    184    86.4   213     ERRSC  
     SHIFTED CHAIN . . . . .    3.694      1.000       0.500     18    69.2    26     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    2.820      1.000       0.500    610    98.7   618     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0     0     ERRSC  
     LIGAND CONTACTS . . . .    3.149      1.000       0.500     47    87.0    54     ERRSC  
     SURFACE . . . . . . . .    3.372      1.000       0.500    426    87.1   489     ERRSC  
     BURIED  . . . . . . . .    3.141      1.000       0.500    421    92.5   455     ERRSC  
     CORE  . . . . . . . . .    3.257      1.000       0.500    847    89.7   944     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.622      1.000       0.500   1623    89.6  1812     ERRALL 
     WELL ORDERED  . . . . .    2.454      1.000       0.500   1392    92.9  1499     ERRALL 
     NO INTER CONTACTS . . .    2.532      1.000       0.500   1337    87.6  1526     ERRALL 
     SHIFTED CHAIN . . . . .    3.321      1.000       0.500     38    70.4    54     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    2.176      1.000       0.500   1122    98.6  1138     ERRALL 
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0     0     ERRALL 
     LIGAND CONTACTS . . . .    2.289      1.000       0.500     79    88.8    89     ERRALL 
     SURFACE . . . . . . . .    2.734      1.000       0.500    826    87.0   949     ERRALL 
     BURIED  . . . . . . . .    2.506      1.000       0.500    797    92.4   863     ERRALL 
     CORE  . . . . . . . . .    2.622      1.000       0.500   1623    89.6  1812     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)        52       139       169       183       190     194     217   DISTCA 
CA  (P)     23.96     64.06     77.88     84.33     87.56             217   DISTCA 
CA  (RMS)    0.71      1.20      1.49      1.82      2.19                   DISTCA 
 
ALL (N)       313       918      1183      1428      1575    1623    1812   DISTALL 
ALL (P)     17.27     50.66     65.29     78.81     86.92            1812   DISTALL 
ALL (RMS)    0.72      1.27      1.61      2.19      2.92                   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)         217           194             0          RMSLSI 
CA  (P)      100.00         89.40          0.00          RMSLSI 
CA  (RMS)      0.47          2.73          0.00          RMSLSI 
 
 
 
END of the results output 
