 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
NUMBER-OF-PARENTS      4 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0076_1.1cfd.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0076_1.1ncx.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0076_1.1a2x_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0076_1.5icb.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 1087 atoms, MODEL 833 atoms, 297 common with TARGET 
           Number of atoms possible to evaluate: 264 
 
 
 CA-RMS TARGET<->PARENT(1cfd)	 2.655663 
 
 CA-RMS TARGET<->PARENT(1ncx)	 2.782501 
 
 CA-RMS TARGET<->PARENT(1a2x-A)	 3.224615 
 
 CA-RMS TARGET<->PARENT(5icb)	 2.843657 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    38.05           85.9   128    91.4   140     ARMSMC  
     WELL ORDERED  . . . . .    38.05           85.9   128    91.4   140     ARMSMC  
     NO INTER CONTACTS . . .    38.05           85.9   128    91.4   140     ARMSMC  
     SHIFTED CHAIN . . . . .    39.14           86.2   116    90.6   128     ARMSMC  
     ALTERNATIVE PARENT  . .    62.07           64.3    14    93.3    15     ARMSMC  
     SECONDARY STRUCTURE . .    11.10           98.4    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    48.41           72.2    36    75.0    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    35.06           84.8    99    90.0   110     ARMSMC  
     BURIED  . . . . . . . .    46.81           89.7    29    96.7    30     ARMSMC  
     CORE  . . . . . . . . .    33.12           91.3    92   100.0    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    60     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    38     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    57     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     6     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    49     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    13     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    48     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    48     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    37     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    38     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    37     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    11     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    16     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    16     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     1     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     3     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     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.20805     r(1,2) =   0.79715     r(1,3) =  -0.56681 
 r(2,1) =  -0.88463     r(2,2) =   0.40059     r(2,3) =   0.23867 
 r(3,1) =   0.41731     r(3,2) =   0.45176     r(3,3) =   0.78852 
THE OFFSET VECTOR: 
 v(1) = -30.35583     v(2) = -16.60942     v(3) = -53.06312 
 
 Number of iteration 59                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.17           (Number of atoms:   32) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    5.54         66    93.0    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0840                            CRMSCA  
     WELL ORDERED  . . . . .    5.54         66    93.0    71     CRMSCA  
     NO INTER CONTACTS . . .    5.54         66    93.0    71     CRMSCA  
     SHIFTED CHAIN . . . . .    5.60         60    92.3    65     CRMSCA  
     ALTERNATIVE PARENT  . .    3.56          7    87.5     8     CRMSCA  
     SECONDARY STRUCTURE . .    4.23         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .    4.74         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.50         20    80.0    25     CRMSCA  
     SURFACE . . . . . . . .    5.73         51    91.1    56     CRMSCA  
     BURIED  . . . . . . . .    4.85         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .    5.07         46   100.0    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    5.41        264    75.4   350     CRMSMC  
     WELL ORDERED  . . . . .    5.41        264    75.4   350     CRMSMC  
     NO INTER CONTACTS . . .    5.41        264    75.4   350     CRMSMC  
     SHIFTED CHAIN . . . . .    5.48        240    74.8   321     CRMSMC  
     ALTERNATIVE PARENT  . .    3.64         28    71.8    39     CRMSMC  
     SECONDARY STRUCTURE . .    4.23        128    80.5   159     CRMSMC  
     SHIFTED SS UNITS  . . .    4.83         64    80.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.34         80    65.0   123     CRMSMC  
     SURFACE . . . . . . . .    5.61        204    73.9   276     CRMSMC  
     BURIED  . . . . . . . .    4.69         60    81.1    74     CRMSMC  
     CORE  . . . . . . . . .    4.96        184    81.1   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   803     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   803     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   803     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   767     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   156     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0   234     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   624     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   179     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    5.41        264    24.3  1087     CRMSALL 
     WELL ORDERED  . . . . .    5.41        264    24.3  1087     CRMSALL 
     NO INTER CONTACTS . . .    5.41        264    24.3  1087     CRMSALL 
     SHIFTED CHAIN . . . . .    5.48        240    23.9  1003     CRMSALL 
     ALTERNATIVE PARENT  . .    3.64         28    25.7   109     CRMSALL 
     SECONDARY STRUCTURE . .    4.23        128    24.5   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.34         80    24.0   334     CRMSALL 
     SURFACE . . . . . . . .    5.61        204    24.1   848     CRMSALL 
     BURIED  . . . . . . . .    4.69         60    25.1   239     CRMSALL 
     CORE  . . . . . . . . .    4.96        184    24.4   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    13.60      2    40.0     5       1-STDDS-5    
 CA  LOOP  2     1.21     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3    10.27      4    66.7     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    12.91      8    32.0    25       1-STDDS-5    
 MC  LOOP  2     1.12     48    81.4    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3    10.03     16    55.2    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    12.91      8    12.9    62       1-STDDS-5    
 ALL LOOP  2     1.12     48    29.3   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3    10.03     16    19.0    84      66-PNGFDM-71   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     0.87     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     1.88      4    66.7     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     0.74     48    81.4    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     2.44     16    55.2    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     0.74     48    29.3   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     2.44     16    19.0    84      66-PNGFDM-71   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.096      1.000       0.500     66    93.0    71     ERRCA  
     WELL ORDERED  . . . . .    4.096      1.000       0.500     66    93.0    71     ERRCA  
     NO INTER CONTACTS . . .    4.096      1.000       0.500     66    93.0    71     ERRCA  
     SHIFTED CHAIN . . . . .    4.141      1.000       0.500     60    92.3    65     ERRCA  
     ALTERNATIVE PARENT  . .    2.734      1.000       0.500      7    87.5     8     ERRCA  
     SECONDARY STRUCTURE . .    3.164      1.000       0.500     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.329      1.000       0.500     20    80.0    25     ERRCA  
     SURFACE . . . . . . . .    4.330      1.000       0.500     51    91.1    56     ERRCA  
     BURIED  . . . . . . . .    3.300      1.000       0.500     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .    3.995      1.000       0.500     46   100.0    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.024      1.000       0.500    264    75.4   350     ERRMC  
     WELL ORDERED  . . . . .    4.024      1.000       0.500    264    75.4   350     ERRMC  
     NO INTER CONTACTS . . .    4.024      1.000       0.500    264    75.4   350     ERRMC  
     SHIFTED CHAIN . . . . .    4.073      1.000       0.500    240    74.8   321     ERRMC  
     ALTERNATIVE PARENT  . .    2.865      1.000       0.500     28    71.8    39     ERRMC  
     SECONDARY STRUCTURE . .    3.160      1.000       0.500    128    80.5   159     ERRMC  
     LARGE SHIFTS/INSERTIONS    4.229      1.000       0.500     80    65.0   123     ERRMC  
     SURFACE . . . . . . . .    4.234      1.000       0.500    204    73.9   276     ERRMC  
     BURIED  . . . . . . . .    3.308      1.000       0.500     60    81.1    74     ERRMC  
     CORE  . . . . . . . . .    3.934      1.000       0.500    184    81.1   227     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   803     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   803     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   803     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   767     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   156     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   743     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   394     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0   234     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   624     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   179     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.024      1.000       0.500    264    24.3  1087     ERRALL 
     WELL ORDERED  . . . . .    4.024      1.000       0.500    264    24.3  1087     ERRALL 
     NO INTER CONTACTS . . .    4.024      1.000       0.500    264    24.3  1087     ERRALL 
     SHIFTED CHAIN . . . . .    4.073      1.000       0.500    240    23.9  1003     ERRALL 
     ALTERNATIVE PARENT  . .    2.865      1.000       0.500     28    25.7   109     ERRALL 
     SECONDARY STRUCTURE . .    3.160      1.000       0.500    128    24.5   522     ERRALL 
     LARGE SHIFTS/INSERTIONS    4.229      1.000       0.500     80    24.0   334     ERRALL 
     SURFACE . . . . . . . .    4.234      1.000       0.500    204    24.1   848     ERRALL 
     BURIED  . . . . . . . .    3.308      1.000       0.500     60    25.1   239     ERRALL 
     CORE  . . . . . . . . .    3.934      1.000       0.500    184    24.4   753     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)        19        30        34        41        60      66      71   DISTCA 
CA  (P)     26.76     42.25     47.89     57.75     84.51              71   DISTCA 
CA  (RMS)    0.70      1.02      1.31      2.08      4.23                   DISTCA 
 
ALL (N)        74       117       134       170       241     264    1087   DISTALL 
ALL (P)      6.81     10.76     12.33     15.64     22.17            1087   DISTALL 
ALL (RMS)    0.67      1.01      1.29      2.19      4.21                   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)          46            46            20          RMSLSI 
CA  (P)       64.79         64.79         28.17          RMSLSI 
CA  (RMS)      1.65          5.07          6.50          RMSLSI 
 
 
 
END of the results output 
