 
####################################################### 
#                                                     # 
#                        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/T0001.inter 
CONANA-PAIR            ../CONANA/T0001.pair 
# 
NUMBER-OF-PARENTS      5 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0001.4dfr_B.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp2.T0001.3dfr.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp2.T0001.8dfr.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp2.T0001.1drf.rot 
ALIGNMENT-DALI(5)      ../PARENTS/casp2.T0001.1dyr.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 1211 atoms, MODEL 162 atoms, 157 common with TARGET 
           Number of atoms possible to evaluate: 157 
 
 
 CA-RMS TARGET<->PARENT(4dfr_B)	 1.747068 
 
 CA-RMS TARGET<->PARENT(3dfr)	 1.763903 
 
 CA-RMS TARGET<->PARENT(8dfr)	 1.949174 
 
 CA-RMS TARGET<->PARENT(1drf)	 2.143564 
 
 CA-RMS TARGET<->PARENT(1dyr)	 1.942374 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   312     ARMSMC  
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0   199     ARMSMC  
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0   248     ARMSMC  
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0   192     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0    44     ARMSMC  
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0   174     ARMSMC  
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    52     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   176     ARMSMC  
     BURIED  . . . . . . . .     0.00            0.0     0     0.0   136     ARMSMC  
     CORE  . . . . . . . . .     0.00            0.0     0     0.0   260     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   125     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    65     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    98     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   112     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    69     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    72     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0    17     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    70     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    72     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    53     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0   104     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    92     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    44     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    67     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    77     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    57     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    55     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0    13     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    49     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    15     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    55     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    37     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    77     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    33     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    11     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    21     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    29     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    30     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     5     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    21     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     5     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    25     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     8     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    28     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    13     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     8     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    13     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    13     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     8     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     3     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     9     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     1     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.40441     r(1,2) =   0.80158     r(1,3) =   0.44037 
 r(2,1) =   0.78361     r(2,2) =   0.05541     r(2,3) =   0.61877 
 r(3,1) =   0.47160     r(3,2) =   0.59532     r(3,3) =  -0.65053 
THE OFFSET VECTOR: 
 v(1) =  14.58888     v(2) =  -0.40179     v(3) =  28.16919 
 
 Number of iteration 57                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.61           (Number of atoms:  100) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.85        157   100.0   157     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0182                            CRMSCA  
     WELL ORDERED  . . . . .    2.58        105   100.0   105     CRMSCA  
     NO INTER CONTACTS . . .    2.64        125   100.0   125     CRMSCA  
     SHIFTED CHAIN . . . . .    3.29         96   100.0    96     CRMSCA  
     ALTERNATIVE PARENT  . .    4.09         22   100.0    22     CRMSCA  
     SECONDARY STRUCTURE . .    2.14         87   100.0    87     CRMSCA  
     SHIFTED SS UNITS  . . .    2.20         28   100.0    28     CRMSCA  
     LARGE SHIFTS/INSERTIONS    4.46         26   100.0    26     CRMSCA  
     SURFACE . . . . . . . .    3.16         89   100.0    89     CRMSCA  
     BURIED  . . . . . . . .    2.38         68   100.0    68     CRMSCA  
     CORE  . . . . . . . . .    2.41        131   100.0   131     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.85        157    20.3   773     CRMSMC  
     WELL ORDERED  . . . . .    2.58        105    21.0   499     CRMSMC  
     NO INTER CONTACTS . . .    2.64        125    20.4   614     CRMSMC  
     SHIFTED CHAIN . . . . .    3.29         96    20.4   470     CRMSMC  
     ALTERNATIVE PARENT  . .    4.09         22    20.6   107     CRMSMC  
     SECONDARY STRUCTURE . .    2.14         87    20.2   431     CRMSMC  
     SHIFTED SS UNITS  . . .    2.20         28    20.3   138     CRMSMC  
     LARGE SHIFTS/INSERTIONS    4.46         26    20.5   127     CRMSMC  
     SURFACE . . . . . . . .    3.16         89    20.3   439     CRMSMC  
     BURIED  . . . . . . . .    2.38         68    20.4   334     CRMSMC  
     CORE  . . . . . . . . .    2.41        131    20.3   646     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   583     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   328     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   430     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   513     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   307     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   328     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    89     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   327     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   256     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   494     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.85        157    13.0  1211     CRMSALL 
     WELL ORDERED  . . . . .    2.58        105    14.2   737     CRMSALL 
     NO INTER CONTACTS . . .    2.64        125    13.4   930     CRMSALL 
     SHIFTED CHAIN . . . . .    3.29         96    13.3   720     CRMSALL 
     ALTERNATIVE PARENT  . .    4.09         22    13.3   165     CRMSALL 
     SECONDARY STRUCTURE . .    2.14         87    12.9   676     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.46         26    13.5   193     CRMSALL 
     SURFACE . . . . . . . .    3.16         89    13.0   683     CRMSALL 
     BURIED  . . . . . . . .    2.38         68    12.9   528     CRMSALL 
     CORE  . . . . . . . . .    2.41        131    12.9  1018     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.79      9   100.0     9      50-ESMRDDLPG-58   
 CA  LOOP  2     5.94      8   100.0     8      68-ERSFSVDT-75   
 CA  LOOP  3     2.04      3   100.0     3      91-SLD-93   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.79      9    20.9    43      50-ESMRDDLPG-58   
 MC  LOOP  2     5.94      8    20.0    40      68-ERSFSVDT-75   
 MC  LOOP  3     2.04      3    20.0    15      91-SLD-93   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.79      9    14.5    62      50-ESMRDDLPG-58   
 ALL LOOP  2     5.94      8    12.3    65      68-ERSFSVDT-75   
 ALL LOOP  3     2.04      3    13.6    22      91-SLD-93   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.56      9   100.0     9      50-ESMRDDLPG-58   
 CA  LOOP  2     2.18      8   100.0     8      68-ERSFSVDT-75   
 CA  LOOP  3     0.13      3   100.0     3      91-SLD-93   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.56      9    20.9    43      50-ESMRDDLPG-58   
 MC  LOOP  2     2.18      8    20.0    40      68-ERSFSVDT-75   
 MC  LOOP  3     0.13      3    20.0    15      91-SLD-93   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.56      9    14.5    62      50-ESMRDDLPG-58   
 ALL LOOP  2     2.18      8    12.3    65      68-ERSFSVDT-75   
 ALL LOOP  3     0.13      3    13.6    22      91-SLD-93   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.214      0.809       0.404    157   100.0   157     ERRCA  
     WELL ORDERED  . . . . .    2.011      0.828       0.414    105   100.0   105     ERRCA  
     NO INTER CONTACTS . . .    2.106      0.815       0.408    125   100.0   125     ERRCA  
     SHIFTED CHAIN . . . . .    2.616      0.818       0.409     96   100.0    96     ERRCA  
     ALTERNATIVE PARENT  . .    3.311      0.787       0.393     22   100.0    22     ERRCA  
     SECONDARY STRUCTURE . .    1.760      0.811       0.406     87   100.0    87     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.679      0.799       0.400     26   100.0    26     ERRCA  
     SURFACE . . . . . . . .    2.430      0.800       0.400     89   100.0    89     ERRCA  
     BURIED  . . . . . . . .    1.932      0.820       0.410     68   100.0    68     ERRCA  
     CORE  . . . . . . . . .    1.923      0.810       0.405    131   100.0   131     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.214      0.809       0.404    157    20.3   773     ERRMC  
     WELL ORDERED  . . . . .    2.011      0.828       0.414    105    21.0   499     ERRMC  
     NO INTER CONTACTS . . .    2.106      0.815       0.408    125    20.4   614     ERRMC  
     SHIFTED CHAIN . . . . .    2.616      0.818       0.409     96    20.4   470     ERRMC  
     ALTERNATIVE PARENT  . .    3.311      0.787       0.393     22    20.6   107     ERRMC  
     SECONDARY STRUCTURE . .    1.760      0.811       0.406     87    20.2   431     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.679      0.799       0.400     26    20.5   127     ERRMC  
     SURFACE . . . . . . . .    2.430      0.800       0.400     89    20.3   439     ERRMC  
     BURIED  . . . . . . . .    1.932      0.820       0.410     68    20.4   334     ERRMC  
     CORE  . . . . . . . . .    1.923      0.810       0.405    131    20.3   646     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   583     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   328     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   430     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   513     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   307     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   336     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0    77     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   328     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    89     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   327     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   256     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   494     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.214      0.809       0.404    157    13.0  1211     ERRALL 
     WELL ORDERED  . . . . .    2.011      0.828       0.414    105    14.2   737     ERRALL 
     NO INTER CONTACTS . . .    2.106      0.815       0.408    125    13.4   930     ERRALL 
     SHIFTED CHAIN . . . . .    2.616      0.818       0.409     96    13.3   720     ERRALL 
     ALTERNATIVE PARENT  . .    3.311      0.787       0.393     22    13.3   165     ERRALL 
     SECONDARY STRUCTURE . .    1.760      0.811       0.406     87    12.9   676     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.679      0.799       0.400     26    13.5   193     ERRALL 
     SURFACE . . . . . . . .    2.430      0.800       0.400     89    13.0   683     ERRALL 
     BURIED  . . . . . . . .    1.932      0.820       0.410     68    12.9   528     ERRALL 
     CORE  . . . . . . . . .    1.923      0.810       0.405    131    12.9  1018     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)        18        81       112       148       157     157     157   DISTCA 
CA  (P)     11.46     51.59     71.34     94.27    100.00             157   DISTCA 
CA  (RMS)    0.66      1.42      1.77      2.44      2.85                   DISTCA 
 
ALL (N)        18        81       112       148       157     157    1211   DISTALL 
ALL (P)      1.49      6.69      9.25     12.22     12.96            1211   DISTALL 
ALL (RMS)    0.66      1.42      1.77      2.44      2.85                   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)         131           131            26          RMSLSI 
CA  (P)       83.44         83.44         16.56          RMSLSI 
CA  (RMS)      1.26          2.41          4.46          RMSLSI 
 
 
 
END of the results output 
