 
####################################################### 
#                                                     # 
#                        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 2466 atoms, 1211 common with TARGET 
           Number of atoms possible to evaluate: 1211 
 
 
 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 . . . . . . . . . .    55.10           63.8   312   100.0   312     ARMSMC  
     WELL ORDERED  . . . . .    40.28           75.4   199   100.0   199     ARMSMC  
     NO INTER CONTACTS . . .    55.95           64.9   248   100.0   248     ARMSMC  
     SHIFTED CHAIN . . . . .    59.15           59.4   192   100.0   192     ARMSMC  
     ALTERNATIVE PARENT  . .    60.59           43.2    44   100.0    44     ARMSMC  
     SECONDARY STRUCTURE . .    33.07           78.2   174   100.0   174     ARMSMC  
     LARGE SHIFTS/INSERTIONS    72.32           32.7    52   100.0    52     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    59.32           56.8   176   100.0   176     ARMSMC  
     BURIED  . . . . . . . .    49.10           72.8   136   100.0   136     ARMSMC  
     CORE  . . . . . . . . .    50.97           70.0   260   100.0   260     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.49           43.2   125   100.0   125     ARMSSC1 
     WELL ORDERED  . . . . .    75.20           50.8    65   100.0    65     ARMSSC1 
     NO INTER CONTACTS . . .    87.83           40.8    98   100.0    98     ARMSSC1 
     RELIABLE SIDE CHAINS  .    81.18           46.4   112   100.0   112     ARMSSC1 
     CHANGED ANGLES  . . . .   103.24           17.4    69   100.0    69     ARMSSC1 
     SHIFTED CHAIN . . . . .    82.21           47.2    72   100.0    72     ARMSSC1 
     ALTERNATIVE PARENT  . .    82.29           41.2    17   100.0    17     ARMSSC1 
     SECONDARY STRUCTURE . .    81.42           45.7    70   100.0    70     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    85.90           42.9    21   100.0    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    89.13           40.3    72   100.0    72     ARMSSC1 
     BURIED  . . . . . . . .    77.74           47.2    53   100.0    53     ARMSSC1 
     CORE  . . . . . . . . .    84.21           43.3   104   100.0   104     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    75.57           43.5    92   100.0    92     ARMSSC2 
     WELL ORDERED  . . . . .    74.11           54.5    44   100.0    44     ARMSSC2 
     NO INTER CONTACTS . . .    76.12           44.8    67   100.0    67     ARMSSC2 
     RELIABLE SIDE CHAINS  .    74.33           44.2    77   100.0    77     ARMSSC2 
     CHANGED ANGLES  . . . .    85.76           33.3    57   100.0    57     ARMSSC2 
     SHIFTED CHAIN . . . . .    73.29           43.6    55   100.0    55     ARMSSC2 
     ALTERNATIVE PARENT  . .    81.23           30.8    13   100.0    13     ARMSSC2 
     SECONDARY STRUCTURE . .    80.03           46.9    49   100.0    49     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    85.61           33.3    15   100.0    15     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    78.12           34.5    55   100.0    55     ARMSSC2 
     BURIED  . . . . . . . .    71.61           56.8    37   100.0    37     ARMSSC2 
     CORE  . . . . . . . . .    73.45           45.5    77   100.0    77     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    80.03           18.2    33   100.0    33     ARMSSC3 
     WELL ORDERED  . . . . .    85.77           27.3    11   100.0    11     ARMSSC3 
     NO INTER CONTACTS . . .    75.72           19.0    21   100.0    21     ARMSSC3 
     RELIABLE SIDE CHAINS  .    82.84           17.2    29   100.0    29     ARMSSC3 
     CHANGED ANGLES  . . . .    79.65           16.7    30   100.0    30     ARMSSC3 
     SHIFTED CHAIN . . . . .    68.36           25.0    20   100.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .    65.37           40.0     5   100.0     5     ARMSSC3 
     SECONDARY STRUCTURE . .    78.89           23.8    21   100.0    21     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    68.03           20.0     5   100.0     5     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    83.04           16.0    25   100.0    25     ARMSSC3 
     BURIED  . . . . . . . .    69.81           25.0     8   100.0     8     ARMSSC3 
     CORE  . . . . . . . . .    81.99           17.9    28   100.0    28     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   118.21           23.1    13   100.0    13     ARMSSC4 
     WELL ORDERED  . . . . .   106.89           40.0     5   100.0     5     ARMSSC4 
     NO INTER CONTACTS . . .   112.20           25.0     8   100.0     8     ARMSSC4 
     RELIABLE SIDE CHAINS  .   118.21           23.1    13   100.0    13     ARMSSC4 
     CHANGED ANGLES  . . . .   118.21           23.1    13   100.0    13     ARMSSC4 
     SHIFTED CHAIN . . . . .   126.67           12.5     8   100.0     8     ARMSSC4 
     ALTERNATIVE PARENT  . .   155.63            0.0     3   100.0     3     ARMSSC4 
     SECONDARY STRUCTURE . .   116.28           22.2     9   100.0     9     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   174.06            0.0     1   100.0     1     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .   112.53           27.3    11   100.0    11     ARMSSC4 
     BURIED  . . . . . . . .   145.55            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .   112.31           25.0    12   100.0    12     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.26551     r(1,2) =  -0.76468     r(1,3) =  -0.58717 
 r(2,1) =  -0.69922     r(2,2) =   0.26658     r(2,3) =  -0.66335 
 r(3,1) =   0.66378     r(3,2) =   0.58668     r(3,3) =  -0.46390 
THE OFFSET VECTOR: 
 v(1) =  46.12049     v(2) =  22.36085     v(3) =   6.35822 
 
 Number of iteration 56                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.30           (Number of atoms:  113) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    4.34        157   100.0   157     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0276                            CRMSCA  
     WELL ORDERED  . . . . .    4.03        105   100.0   105     CRMSCA  
     NO INTER CONTACTS . . .    4.35        125   100.0   125     CRMSCA  
     SHIFTED CHAIN . . . . .    2.79         96   100.0    96     CRMSCA  
     ALTERNATIVE PARENT  . .    4.07         22   100.0    22     CRMSCA  
     SECONDARY STRUCTURE . .    4.82         87   100.0    87     CRMSCA  
     SHIFTED SS UNITS  . . .    1.82         28   100.0    28     CRMSCA  
     LARGE SHIFTS/INSERTIONS    4.20         26   100.0    26     CRMSCA  
     SURFACE . . . . . . . .    4.39         89   100.0    89     CRMSCA  
     BURIED  . . . . . . . .    4.27         68   100.0    68     CRMSCA  
     CORE  . . . . . . . . .    4.36        131   100.0   131     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    4.44        773   100.0   773     CRMSMC  
     WELL ORDERED  . . . . .    4.05        499   100.0   499     CRMSMC  
     NO INTER CONTACTS . . .    4.46        614   100.0   614     CRMSMC  
     SHIFTED CHAIN . . . . .    2.90        470   100.0   470     CRMSMC  
     ALTERNATIVE PARENT  . .    4.15        107   100.0   107     CRMSMC  
     SECONDARY STRUCTURE . .    4.89        431   100.0   431     CRMSMC  
     SHIFTED SS UNITS  . . .    1.88        138   100.0   138     CRMSMC  
     LARGE SHIFTS/INSERTIONS    4.25        127   100.0   127     CRMSMC  
     SURFACE . . . . . . . .    4.49        439   100.0   439     CRMSMC  
     BURIED  . . . . . . . .    4.37        334   100.0   334     CRMSMC  
     CORE  . . . . . . . . .    4.48        646   100.0   646     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    5.67        583   100.0   583     CRMSSC  
     WELL ORDERED  . . . . .    5.55        328   100.0   328     CRMSSC  
     NO INTER CONTACTS . . .    5.61        430   100.0   430     CRMSSC  
     RELIABLE SIDE CHAINS  .    5.63        513   100.0   513     CRMSSC  
     CHANGED ANGLES  . . . .    6.47        307   100.0   307     CRMSSC  
     SECONDARY STRUCTURE . .    6.16        328   100.0   328     CRMSSC  
     LARGE SHIFTS/INSERTIONS    6.05         89   100.0    89     CRMSSC  
     SURFACE . . . . . . . .    5.77        327   100.0   327     CRMSSC  
     BURIED  . . . . . . . .    5.54        256   100.0   256     CRMSSC  
     CORE  . . . . . . . . .    5.60        494   100.0   494     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    5.03       1211   100.0  1211     CRMSALL 
     WELL ORDERED  . . . . .    4.73        737   100.0   737     CRMSALL 
     NO INTER CONTACTS . . .    4.99        930   100.0   930     CRMSALL 
     SHIFTED CHAIN . . . . .    3.53        720   100.0   720     CRMSALL 
     ALTERNATIVE PARENT  . .    4.80        165   100.0   165     CRMSALL 
     SECONDARY STRUCTURE . .    5.53        676   100.0   676     CRMSALL 
     LARGE SHIFTS/INSERTIONS    5.03        193   100.0   193     CRMSALL 
     SURFACE . . . . . . . .    5.09        683   100.0   683     CRMSALL 
     BURIED  . . . . . . . .    4.96        528   100.0   528     CRMSALL 
     CORE  . . . . . . . . .    5.03       1018   100.0  1018     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.81      9   100.0     9      50-ESMRDDLPG-58   
 CA  LOOP  2     5.20      8   100.0     8      68-ERSFSVDT-75   
 CA  LOOP  3     4.42      3   100.0     3      91-SLD-93   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.84     43   100.0    43      50-ESMRDDLPG-58   
 MC  LOOP  2     5.21     40   100.0    40      68-ERSFSVDT-75   
 MC  LOOP  3     4.59     15   100.0    15      91-SLD-93   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.49     62   100.0    62      50-ESMRDDLPG-58   
 ALL LOOP  2     6.35     65   100.0    65      68-ERSFSVDT-75   
 ALL LOOP  3     5.38     22   100.0    22      91-SLD-93   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.53      9   100.0     9      50-ESMRDDLPG-58   
 CA  LOOP  2     3.11      8   100.0     8      68-ERSFSVDT-75   
 CA  LOOP  3     0.05      3   100.0     3      91-SLD-93   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.81     43   100.0    43      50-ESMRDDLPG-58   
 MC  LOOP  2     3.39     40   100.0    40      68-ERSFSVDT-75   
 MC  LOOP  3     1.54     15   100.0    15      91-SLD-93   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.64     62   100.0    62      50-ESMRDDLPG-58   
 ALL LOOP  2     4.98     65   100.0    65      68-ERSFSVDT-75   
 ALL LOOP  3     2.35     22   100.0    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 . . . . . . . . . .    8.007      0.684       0.713    157   100.0   157     ERRCA  
     WELL ORDERED  . . . . .    8.383      0.735       0.756    105   100.0   105     ERRCA  
     NO INTER CONTACTS . . .    8.188      0.708       0.731    125   100.0   125     ERRCA  
     SHIFTED CHAIN . . . . .    7.627      0.637       0.687     96   100.0    96     ERRCA  
     ALTERNATIVE PARENT  . .    6.279      0.478       0.549     22   100.0    22     ERRCA  
     SECONDARY STRUCTURE . .    8.470      0.734       0.750     87   100.0    87     ERRCA  
     LARGE SHIFTS/INSERTIONS    6.122      0.460       0.536     26   100.0    26     ERRCA  
     SURFACE . . . . . . . .    7.651      0.634       0.673     89   100.0    89     ERRCA  
     BURIED  . . . . . . . .    8.472      0.751       0.766     68   100.0    68     ERRCA  
     CORE  . . . . . . . . .    8.381      0.729       0.748    131   100.0   131     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.944      0.675       0.706    773   100.0   773     ERRMC  
     WELL ORDERED  . . . . .    8.356      0.730       0.752    499   100.0   499     ERRMC  
     NO INTER CONTACTS . . .    8.134      0.699       0.724    614   100.0   614     ERRMC  
     SHIFTED CHAIN . . . . .    7.567      0.631       0.683    470   100.0   470     ERRMC  
     ALTERNATIVE PARENT  . .    6.275      0.479       0.557    107   100.0   107     ERRMC  
     SECONDARY STRUCTURE . .    8.421      0.726       0.742    431   100.0   431     ERRMC  
     LARGE SHIFTS/INSERTIONS    6.139      0.464       0.544    127   100.0   127     ERRMC  
     SURFACE . . . . . . . .    7.564      0.624       0.665    439   100.0   439     ERRMC  
     BURIED  . . . . . . . .    8.443      0.743       0.759    334   100.0   334     ERRMC  
     CORE  . . . . . . . . .    8.298      0.717       0.737    646   100.0   646     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.151      0.577       0.609    583   100.0   583     ERRSC  
     WELL ORDERED  . . . . .    7.747      0.644       0.668    328   100.0   328     ERRSC  
     NO INTER CONTACTS . . .    7.370      0.602       0.631    430   100.0   430     ERRSC  
     RELIABLE SIDE CHAINS  .    7.123      0.578       0.609    513   100.0   513     ERRSC  
     CHANGED ANGLES  . . . .    6.430      0.484       0.522    307   100.0   307     ERRSC  
     SHIFTED CHAIN . . . . .    6.600      0.531       0.579    336   100.0   336     ERRSC  
     ALTERNATIVE PARENT  . .    5.239      0.386       0.436     77   100.0    77     ERRSC  
     SECONDARY STRUCTURE . .    7.686      0.618       0.644    328   100.0   328     ERRSC  
     LARGE SHIFTS/INSERTIONS    4.926      0.365       0.402     89   100.0    89     ERRSC  
     SURFACE . . . . . . . .    6.557      0.508       0.550    327   100.0   327     ERRSC  
     BURIED  . . . . . . . .    7.911      0.665       0.684    256   100.0   256     ERRSC  
     CORE  . . . . . . . . .    7.552      0.615       0.646    494   100.0   494     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.584      0.631       0.662   1211   100.0  1211     ERRALL 
     WELL ORDERED  . . . . .    8.105      0.695       0.718    737   100.0   737     ERRALL 
     NO INTER CONTACTS . . .    7.804      0.657       0.684    930   100.0   930     ERRALL 
     SHIFTED CHAIN . . . . .    7.150      0.588       0.638    720   100.0   720     ERRALL 
     ALTERNATIVE PARENT  . .    5.899      0.445       0.511    165   100.0   165     ERRALL 
     SECONDARY STRUCTURE . .    8.075      0.676       0.696    676   100.0   676     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.686      0.427       0.490    193   100.0   193     ERRALL 
     SURFACE . . . . . . . .    7.114      0.572       0.614    683   100.0   683     ERRALL 
     BURIED  . . . . . . . .    8.193      0.706       0.724    528   100.0   528     ERRALL 
     CORE  . . . . . . . . .    7.944      0.669       0.694   1018   100.0  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)        48       100       125       139       148     157     157   DISTCA 
CA  (P)     30.57     63.69     79.62     88.54     94.27             157   DISTCA 
CA  (RMS)    0.63      1.12      1.51      1.88      2.35                   DISTCA 
 
ALL (N)       314       643       854      1015      1123    1211    1211   DISTALL 
ALL (P)     25.93     53.10     70.52     83.82     92.73            1211   DISTALL 
ALL (RMS)    0.70      1.16      1.59      2.12      2.88                   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          4.36          4.20          RMSLSI 
 
 
 
END of the results output 
