 
####################################################### 
#                                                     # 
#                        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/T0058.inter 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0058.1akz.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0058.1udh.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 1784 atoms, MODEL 959 atoms, 937 common with TARGET 
           Number of atoms possible to evaluate: 856 
 
 
 CA-RMS TARGET<->PARENT(1akz)	 1.191923 
 
 CA-RMS TARGET<->PARENT(1udh)	 1.648171 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    36.45           91.9   422    94.2   448     ARMSMC  
     WELL ORDERED  . . . . .    35.19           92.6   419    94.2   445     ARMSMC  
     NO INTER CONTACTS . . .    36.13           92.7   302    95.9   315     ARMSMC  
     SHIFTED CHAIN . . . . .    55.80           79.5   117    87.3   134     ARMSMC  
     ALTERNATIVE PARENT  . .    88.26           50.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .     8.08           99.4   157    99.4   158     ARMSMC  
     LARGE SHIFTS/INSERTIONS   101.74           25.0    16    72.7    22     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    45.81           87.3   205    89.9   228     ARMSMC  
     BURIED  . . . . . . . .    24.52           96.3   217    98.6   220     ARMSMC  
     CORE  . . . . . . . . .    31.19           94.6   406    95.3   426     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   190     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0   176     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0   135     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   173     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    58     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    58     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    74     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    10     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    97     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    93     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0   180     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   148     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0   132     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0   102     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   102     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    74     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    57     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     6     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    80     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    68     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0   142     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    47     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    33     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    22     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    33     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    32     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    17     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    39     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     8     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    45     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    18     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    13     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     6     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 . . . . . . . .     0.00            0.0     0     0.0    15     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.40161     r(1,2) =   0.65280     r(1,3) =  -0.64231 
 r(2,1) =   0.91371     r(2,2) =   0.23810     r(2,3) =  -0.32931 
 r(3,1) =  -0.06204     r(3,2) =  -0.71914     r(3,3) =  -0.69209 
THE OFFSET VECTOR: 
 v(1) =  10.15283     v(2) =  14.52987     v(3) =  -8.92245 
 
 Number of iteration 32                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.87           (Number of atoms:  196) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.45        214    95.1   225     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0115                            CRMSCA  
     WELL ORDERED  . . . . .    2.45        213    95.1   224     CRMSCA  
     NO INTER CONTACTS . . .    2.20        153    96.8   158     CRMSCA  
     SHIFTED CHAIN . . . . .    4.27         60    88.2    68     CRMSCA  
     ALTERNATIVE PARENT  . .    6.33          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    0.73         79   100.0    79     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    8.68          9    75.0    12     CRMSCA  
     SURFACE . . . . . . . .    2.97        104    90.4   115     CRMSCA  
     BURIED  . . . . . . . .    1.83        110   100.0   110     CRMSCA  
     CORE  . . . . . . . . .    1.72        205    96.2   213     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.43        856    77.3  1107     CRMSMC  
     WELL ORDERED  . . . . .    2.42        848    77.4  1095     CRMSMC  
     NO INTER CONTACTS . . .    2.19        612    78.7   778     CRMSMC  
     SHIFTED CHAIN . . . . .    4.20        240    71.9   334     CRMSMC  
     ALTERNATIVE PARENT  . .    6.15          8    80.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    0.74        316    80.2   394     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    8.48         36    61.0    59     CRMSMC  
     SURFACE . . . . . . . .    2.92        416    73.5   566     CRMSMC  
     BURIED  . . . . . . . .    1.85        440    81.3   541     CRMSMC  
     CORE  . . . . . . . . .    1.73        820    78.2  1048     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   884     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   816     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   630     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   704     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   328     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   341     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    36     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   448     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   436     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   848     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.43        856    48.0  1784     CRMSALL 
     WELL ORDERED  . . . . .    2.42        848    49.6  1708     CRMSALL 
     NO INTER CONTACTS . . .    2.19        612    48.5  1262     CRMSALL 
     SHIFTED CHAIN . . . . .    4.20        240    45.3   530     CRMSALL 
     ALTERNATIVE PARENT  . .    6.15          8    61.5    13     CRMSALL 
     SECONDARY STRUCTURE . .    0.74        316    48.1   657     CRMSALL 
     LARGE SHIFTS/INSERTIONS    8.48         36    42.9    84     CRMSALL 
     SURFACE . . . . . . . .    2.92        416    45.8   908     CRMSALL 
     BURIED  . . . . . . . .    1.85        440    50.2   876     CRMSALL 
     CORE  . . . . . . . . .    1.73        820    48.2  1700     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    10.55      5    62.5     8     222-PVLPAESE-229  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    10.31     20    50.0    40     222-PVLPAESE-229  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    10.31     20    34.5    58     222-PVLPAESE-229  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.58      5    62.5     8     222-PVLPAESE-229  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.46     20    50.0    40     222-PVLPAESE-229  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.46     20    34.5    58     222-PVLPAESE-229  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.289      1.000       0.500    214    95.1   225     ERRCA  
     WELL ORDERED  . . . . .    1.278      1.000       0.500    213    95.1   224     ERRCA  
     NO INTER CONTACTS . . .    1.175      1.000       0.500    153    96.8   158     ERRCA  
     SHIFTED CHAIN . . . . .    2.865      1.000       0.500     60    88.2    68     ERRCA  
     ALTERNATIVE PARENT  . .    5.132      1.000       0.500      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    0.634      1.000       0.500     79   100.0    79     ERRCA  
     LARGE SHIFTS/INSERTIONS    7.920      1.000       0.500      9    75.0    12     ERRCA  
     SURFACE . . . . . . . .    1.682      1.000       0.500    104    90.4   115     ERRCA  
     BURIED  . . . . . . . .    0.917      1.000       0.500    110   100.0   110     ERRCA  
     CORE  . . . . . . . . .    0.998      1.000       0.500    205    96.2   213     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.288      1.000       0.500    856    77.3  1107     ERRMC  
     WELL ORDERED  . . . . .    1.274      1.000       0.500    848    77.4  1095     ERRMC  
     NO INTER CONTACTS . . .    1.180      1.000       0.500    612    78.7   778     ERRMC  
     SHIFTED CHAIN . . . . .    2.802      1.000       0.500    240    71.9   334     ERRMC  
     ALTERNATIVE PARENT  . .    4.827      1.000       0.500      8    80.0    10     ERRMC  
     SECONDARY STRUCTURE . .    0.640      1.000       0.500    316    80.2   394     ERRMC  
     LARGE SHIFTS/INSERTIONS    7.764      1.000       0.500     36    61.0    59     ERRMC  
     SURFACE . . . . . . . .    1.666      1.000       0.500    416    73.5   566     ERRMC  
     BURIED  . . . . . . . .    0.932      1.000       0.500    440    81.3   541     ERRMC  
     CORE  . . . . . . . . .    1.004      1.000       0.500    820    78.2  1048     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   884     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   816     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   630     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   704     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   328     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   258     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     5     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   341     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    36     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   448     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   436     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   848     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.288      1.000       0.500    856    48.0  1784     ERRALL 
     WELL ORDERED  . . . . .    1.274      1.000       0.500    848    49.6  1708     ERRALL 
     NO INTER CONTACTS . . .    1.180      1.000       0.500    612    48.5  1262     ERRALL 
     SHIFTED CHAIN . . . . .    2.802      1.000       0.500    240    45.3   530     ERRALL 
     ALTERNATIVE PARENT  . .    4.827      1.000       0.500      8    61.5    13     ERRALL 
     SECONDARY STRUCTURE . .    0.640      1.000       0.500    316    48.1   657     ERRALL 
     LARGE SHIFTS/INSERTIONS    7.764      1.000       0.500     36    42.9    84     ERRALL 
     SURFACE . . . . . . . .    1.666      1.000       0.500    416    45.8   908     ERRALL 
     BURIED  . . . . . . . .    0.932      1.000       0.500    440    50.2   876     ERRALL 
     CORE  . . . . . . . . .    1.004      1.000       0.500    820    48.2  1700     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)       151       192       199       204       209     214     225   DISTCA 
CA  (P)     67.11     85.33     88.44     90.67     92.89             225   DISTCA 
CA  (RMS)    0.60      0.81      0.93      1.09      1.83                   DISTCA 
 
ALL (N)       601       764       790       814       836     856    1784   DISTALL 
ALL (P)     33.69     42.83     44.28     45.63     46.86            1784   DISTALL 
ALL (RMS)    0.59      0.81      0.91      1.09      1.80                   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)         213           205             9          RMSLSI 
CA  (P)       94.67         91.11          4.00          RMSLSI 
CA  (RMS)      0.91          1.72          8.68          RMSLSI 
 
 
 
END of the results output 
