(- suse linux 8.1
- modeller6v2
- file pdb is pdb1f4a.ent
)
with file modelo1.top the process to run correctly
INCLUDE
SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE = 'archivo.ali'
SET KNOWNS = '1f4aC'
SET SEQUENCE = 'sec1'
SET STARTING_MODEL= 1
SET ENDING_MODEL = 1
CALL ROUTINE = 'model'
----------------------------------------------------------------------------------------------------- BUT
with file modelo2.top the process not run
INCLUDE
SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE = 'archivo.ali'
SET KNOWNS = '1f4aC'
SET SEQUENCE = 'sec1'
SET STARTING_MODEL= 1
SET ENDING_MODEL = 1
CALL ROUTINE = 'model'
and log file is:
MODELLER 6v2, 17 Feb 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF
SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej
Sali
All Rights
Reserved
Written by A.
Sali
with help from A.
Fiser, R. Sanchez, M.A. Marti-Renom,
B. Jerkovic, A. Badretdinov, F.
Melo,
J.P. Overington & E.
Feyfant
Rockefeller University, New York,
USA
Harvard University, Cambridge,
USA
Imperial Cancer Research Fund, London,
UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux bioinf4 2.4.19-4GB
i686
Date and time of
compilation : 07/16/2002
11:42:16
Job starting time (YY/MM/DD HH:MM:SS): 2003/04/23
11:53:47.784
TOP_________> 105 705 SET ALNFILE =
'archivo.ali'
TOP_________> 106 706 SET KNOWNS =
'1f4aC'
TOP_________> 107 707 SET SEQUENCE = 'sec1'
TOP_________> 108 708 SET STARTING_MODEL = 1
TOP_________> 109 709 SET ENDING_MODEL = 1
Dynamically allocated memory
at finish
[B,kB,MB]: 2200483
2148.909 2.099
Starting
time
: 2003/04/23 11:53:47.784
Closing
time
: 2003/04/23 11:53:50.734
Total CPU time
[seconds]
: 2.88
----------------------------------------------------------------------------------------
which is a problem?
which is a difference between the files modelo1.top and modelo2.top?
is a bug the modeller?
the files top to contain the same information but with file model2.top
the process not run.
thanks..
INCLUDE
SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE = 'archivo.ali'
SET KNOWNS = '1f4aC'
SET SEQUENCE = 'sec1'
SET STARTING_MODEL= 1
SET ENDING_MODEL = 1
CALL ROUTINE = 'model'
INCLUDE
SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE = 'archivo.ali'
SET KNOWNS = '1f4aC'
SET SEQUENCE = 'sec1'
SET STARTING_MODEL= 1
SET ENDING_MODEL = 1
CALL ROUTINE = 'model'
MODELLER 6v2, 17 Feb 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from A. Fiser, R. Sanchez, M.A. Marti-Renom,
B. Jerkovic, A. Badretdinov, F. Melo,
J.P. Overington & E. Feyfant
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux bioinf4 2.4.19-4GB i686
Date and time of compilation : 07/16/2002 11:42:16
Job starting time (YY/MM/DD HH:MM:SS): 2003/04/23 11:53:47.784
TOP_________> 105 705 SET ALNFILE = 'archivo.ali'
TOP_________> 106 706 SET KNOWNS = '1f4aC'
TOP_________> 107 707 SET SEQUENCE = 'sec1'
TOP_________> 108 708 SET STARTING_MODEL = 1
TOP_________> 109 709 SET ENDING_MODEL = 1
Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099
Starting time : 2003/04/23 11:53:47.784
Closing time : 2003/04/23 11:53:50.734
Total CPU time [seconds] : 2.88
MODELLER 6v2, 17 Feb 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from A. Fiser, R. Sanchez, M.A. Marti-Renom,
B. Jerkovic, A. Badretdinov, F. Melo,
J.P. Overington & E. Feyfant
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux bioinf4 2.4.19-4GB i686
Date and time of compilation : 07/16/2002 11:42:16
Job starting time (YY/MM/DD HH:MM:SS): 2003/04/23 11:48:58.409
TOP_________> 105 705 SET ALNFILE = 'archivo.ali'
TOP_________> 106 706 SET KNOWNS = '1f4aC'
TOP_________> 107 707 SET SEQUENCE = 'sec1'
TOP_________> 108 708 SET STARTING_MODEL = 1
TOP_________> 109 709 SET ENDING_MODEL = 1
TOP_________> 110 710 CALL ROUTINE = 'model'
TOP_________> 111 399 CALL ROUTINE = 'getnames'
TOP_________> 112 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION;
= 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA;
TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
TOP_________> 113 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI;
ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE;
NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE;
'
TOP_________> 114 511 STRING_OPERATE OPERATION = 'CONCATENATE', ;
STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE
TOP_________> 115 512 STRING_OPERATE OPERATION = 'CONCATENATE', ;
STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI;
LE
TOP_________> 116 513 SET ROOT_NAME = SEQUENCE
TOP_________> 117 514 RETURN
TOP_________> 118 400 CALL ROUTINE = 'homcsr'
TOP_________> 119 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;
NCE
Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
Dynamically allocated memory at amaxbnd [B,kB,MB]: 3908769 3817.157 3.728
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
Read the alignment from file : archivo.ali
Total number of alignment positions: 108
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1f4aC 108 1 1f4a
2 sec1 108 1 sec1
TOP_________> 120 107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open 11 OLD SEQUENTIAL ./pdb1f4a.ent
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
check_a_344_> << END OF COMMAND
TOP_________> 121 108 CALL ROUTINE = GENERATE_METHOD
TOP_________> 122 77 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
Dynamically allocated memory at amaxseq [B,kB,MB]: 3799237 3710.192 3.623
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
Read the alignment from file : archivo.ali
Total number of alignment positions: 108
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1f4aC 108 1 1f4a
TOP_________> 123 78 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
Read the alignment from file : archivo.ali
Total number of alignment positions: 108
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1f4aC 108 1 1f4a
TOP_________> 124 79 IF ARGUMENTS = INITIAL_MALIGN3D 0, OPERATION = 'EQ', THEN;
= 'GO_TO NO_INITIAL_MALIGN3D'
TOP_________> 125 82 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;
NCE
Dynamically allocated memory at amaxseq [B,kB,MB]: 3908769 3817.157 3.728
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
Read the alignment from file : archivo.ali
Total number of alignment positions: 108
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1f4aC 108 1 1f4a
2 sec1 108 1 sec1
TOP_________> 126 83 READ_TOPOLOGY FILE = TOPLIB
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//top_heav.lib
openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL6v2}/modlib/models.lib
TOP_________> 127 84 READ_PARAMETERS FILE = PARLIB
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//par.lib
Dynamically allocated memory at amattacns [B,kB,MB]: 3909165 3817.544 3.728
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//par.lib
rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MRFP MODE
227 561 661 112 0 0
TOP_________> 128 85 CALL ROUTINE = 'create_topology'
TOP_________> 129 100 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 12 108
atom names : C +N
atom indices : 878 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 12 108
atom names : C CA +N O
atom indices : 878 873 0 879
mkilst______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 108 879 910 0 0 396
patch_______> segment topology patched using RTF: 1 ; LYS ; NTER
segments residues atoms bonds angles dihedrals impropers:
1 108 879 910 1249 1506 396
iatmcls_286W> MODEL atom not classified: ASN:OT1 ASN
iatmcls_286W> MODEL atom not classified: ASN:OT2 ASN
patch_______> segment topology patched using RTF: 108 ; ASN ; CTER
segments residues atoms bonds angles dihedrals impropers:
1 108 880 911 1251 1508 397
genseg______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 108 880 911 1251 1508 397
TOP_________> 130 101 CALL ROUTINE = 'default_patches'
TOP_________> 131 504 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;
NCE
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
Read the alignment from file : archivo.ali
Total number of alignment positions: 108
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1f4aC 108 1 1f4a
2 sec1 108 1 sec1
TOP_________> 132 505 PATCH_SS_TEMPLATES
TOP_________> 133 506 RETURN
TOP_________> 134 102 CALL ROUTINE = 'special_patches'
TOP_________> 135 501 RETURN
TOP_________> 136 103 RETURN
TOP_________> 137 86 TRANSFER_XYZ CLUSTER_CUT = -1.0
transfe_506_> MODEL is an average of all templates.
transfe_511_> Number of templates for coordinate transfer: 1
After transfering coordinates of the equivalent template atoms,
there are defined, undefined atoms in MODEL: 843 37
TOP_________> 138 87 BUILD_MODEL INITIALIZE_XYZ = OFF
TOP_________> 139 88 WRITE_MODEL FILE = MODEL
openf5__224_> Open 14 UNKNOWN SEQUENTIAL sec1.ini
wrpdb2__568_> Residues, atoms, selected atoms: 108 880 880
TOP_________> 140 89 RETURN
TOP_________> 141 109 IF ARGUMENTS = EXIT_STAGE 2, OPERATION = 'EQ', THEN = 'RE;
TURN'
TOP_________> 142 110 IF ARGUMENTS = CREATE_RESTRAINTS 0, OPERATION = 'EQ', THE;
N ='GO_TO __SKIP_RSRS'
TOP_________> 143 111 CALL ROUTINE = 'mkhomcsr'
TOP_________> 144 116 MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS;
= OFF
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: stereo
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.
Added bond,angle,dihedral,improper restraints : 911 1251 1472 387
Total number of restraints before, now : 0 4021
make_re_422_> Number of previous, current restraints : 0 4021
make_re_423_> Number of previous, current selected restraints: 0 4021
TOP_________> 145 117 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;
NCE
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
openf5__224_> Open 11 OLD SEQUENTIAL archivo.ali
Read the alignment from file : archivo.ali
Total number of alignment positions: 108
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1f4aC 108 1 1f4a
2 sec1 108 1 sec1
TOP_________> 146 118 MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_;
RESTRAINTS = ON
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: phi-psi_binormal
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mnch1.bin
initmdt_400_> Distance function type: 1
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mnch1.mdt
irddata_401_> USER SYMMETRY, SYMMETRY: 1 T
SYMMETRIC = .T. ==> NALN*NALN/2
SYMMETRIC = .F. ==> NALN*NALN
All protein pairs always generated.
getdata_643_> Protein accepted: 1f4aC
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4021 4127
make_re_423_> Number of previous, current selected restraints: 4021 4127
TOP_________> 147 119 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.3, SPLINE_MIN_POINT;
S = 5
TOP_________> 148 120 MAKE_RESTRAINTS RESTRAINT_TYPE = 'omega_dihedral', ADD_RE;
STRAINTS = ON
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: omega_dihedral
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/omega.bin
initmdt_400_> Distance function type: 1
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/omega.mdt
irddata_401_> USER SYMMETRY, SYMMETRY: 1 T
SYMMETRIC = .T. ==> NALN*NALN/2
SYMMETRIC = .F. ==> NALN*NALN
All protein pairs always generated.
getdata_643_> Protein accepted: 1f4aC
getdata_289_> Proteins (all/accepted): 1 1
omgdel__425W> Unselected all O C +N +CA dihedrals: 117
make_re_422_> Number of previous, current restraints : 4127 4234
make_re_423_> Number of previous, current selected restraints: 4127 4117
TOP_________> 149 121 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RES;
TRAINTS = ON
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: chi1_dihedral
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin
initmdt_400_> Distance function type: 1
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1.mdt
irddata_401_> USER SYMMETRY, SYMMETRY: 1 T
SYMMETRIC = .T. ==> NALN*NALN/2
SYMMETRIC = .F. ==> NALN*NALN
All protein pairs always generated.
getdata_643_> Protein accepted: 1f4aC
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4234 4328
make_re_423_> Number of previous, current selected restraints: 4117 4211
TOP_________> 150 122 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RES;
TRAINTS = ON
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: chi2_dihedral
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin
initmdt_400_> Distance function type: 1
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi2.mdt
irddata_401_> USER SYMMETRY, SYMMETRY: 1 T
SYMMETRIC = .T. ==> NALN*NALN/2
SYMMETRIC = .F. ==> NALN*NALN
All protein pairs always generated.
getdata_643_> Protein accepted: 1f4aC
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4328 4400
make_re_423_> Number of previous, current selected restraints: 4211 4283
TOP_________> 151 123 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RES;
TRAINTS = ON
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: chi3_dihedral
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin
initmdt_400_> Distance function type: 1
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi3.mdt
irddata_401_> USER SYMMETRY, SYMMETRY: 1 T
SYMMETRIC = .T. ==> NALN*NALN/2
SYMMETRIC = .F. ==> NALN*NALN
All protein pairs always generated.
getdata_643_> Protein accepted: 1f4aC
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4400 4431
make_re_423_> Number of previous, current selected restraints: 4283 4314
TOP_________> 152 124 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RES;
TRAINTS = ON
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: chi4_dihedral
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin
initmdt_400_> Distance function type: 1
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi4.mdt
irddata_401_> USER SYMMETRY, SYMMETRY: 1 T
SYMMETRIC = .T. ==> NALN*NALN/2
SYMMETRIC = .F. ==> NALN*NALN
All protein pairs always generated.
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
getdata_643_> Protein accepted: 1f4aC
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4431 4441
make_re_423_> Number of previous, current selected restraints: 4314 4324
TOP_________> 153 125 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.7, SPLINE_MIN_POINT;
S = 5
TOP_________> 154 126 SET RES_TYPES = 'STD'
TOP_________> 155 127 SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_;
DISTANCE
TOP_________> 156 128 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON
TOP_________> 157 129 SET RESTRAINT_GROUP = 9
TOP_________> 158 130 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : CA
Residue types to be searched for (RES_TYPES) : STD
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 108
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
1 1 : LYS --- 108 : ASN 108
TOP_________> 159 131 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : CA
Residue types to be searched for (RES_TYPES) : STD
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 108
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
1 1 : LYS --- 108 : ASN 108
TOP_________> 160 132 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN;
TS = 'ON'
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: distance
make_re_422_> Number of previous, current restraints : 4441 5369
make_re_423_> Number of previous, current selected restraints: 4324 5252
TOP_________> 161 133 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_N-O_DI;
STANCE
TOP_________> 162 134 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = OFF
TOP_________> 163 135 SET RESTRAINT_GROUP = 10
TOP_________> 164 136 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'N'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : N
Residue types to be searched for (RES_TYPES) : STD
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 108
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
1 1 : LYS --- 108 : ASN 108
TOP_________> 165 137 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : O
Residue types to be searched for (RES_TYPES) : STD
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 108
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
1 1 : LYS --- 108 : ASN 108
TOP_________> 166 138 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN;
TS = 'ON'
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: distance
make_re_422_> Number of previous, current restraints : 5369 6479
make_re_423_> Number of previous, current selected restraints: 5252 6362
TOP_________> 167 139 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-MC_;
DISTANCE
TOP_________> 168 140 SET RESIDUE_SPAN_RANGE = 1 2, RESIDUE_SPAN_SIGN = OFF
TOP_________> 169 141 SET RESTRAINT_GROUP = 23, RESTRAINT_STDEV = 0.5 1.5
TOP_________> 170 142 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : SDCH
Residue types to be searched for (RES_TYPES) : STD
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 447
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
1 1 : LYS --- 7 : VAL 7
2 9 : LEU --- 17 : LEU 9
3 19 : LEU --- 39 : LYS 21
4 41 : ARG --- 53 : ASN 13
5 55 : GLU --- 91 : HSD 37
6 93 : TYR --- 108 : ASN 16
TOP_________> 171 143 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : MNCH
Residue types to be searched for (RES_TYPES) : STD
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 433
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
1 1 : LYS --- 108 : ASN 108
TOP_________> 172 144 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN;
TS = 'ON'
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: distance
make_re_422_> Number of previous, current restraints : 6479 8525
make_re_423_> Number of previous, current selected restraints: 6362 8408
TOP_________> 173 145 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-SC_;
DISTANCE
TOP_________> 174 146 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON
TOP_________> 175 147 SET RESTRAINT_GROUP = 26, RESTRAINT_STDEV = 0.5 2.0
TOP_________> 176 148 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : SDCH
Residue types to be searched for (RES_TYPES) : STD
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 447
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
1 1 : LYS --- 7 : VAL 7
2 9 : LEU --- 17 : LEU 9
3 19 : LEU --- 39 : LYS 21
4 41 : ARG --- 53 : ASN 13
5 55 : GLU --- 91 : HSD 37
6 93 : TYR --- 108 : ASN 16
TOP_________> 177 149 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : SDCH
Residue types to be searched for (RES_TYPES) : STD
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 447
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
1 1 : LYS --- 7 : VAL 7
2 9 : LEU --- 17 : LEU 9
3 19 : LEU --- 39 : LYS 21
4 41 : ARG --- 53 : ASN 13
5 55 : GLU --- 91 : HSD 37
6 93 : TYR --- 108 : ASN 16
TOP_________> 178 150 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN;
TS = 'ON'
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: distance
make_re_422_> Number of previous, current restraints : 8525 9158
make_re_423_> Number of previous, current selected restraints: 8408 9041
TOP_________> 179 151 CALL ROUTINE = 'hetatm_restraints'
TOP_________> 180 160 SET RESTRAINT_TYPE = 'distance'
TOP_________> 181 161 SET DISTANCE_RSR_MODEL = 7
TOP_________> 182 162 SET MAXIMAL_DISTANCE = 7.0
TOP_________> 183 163 SET ADD_RESTRAINTS = ON
TOP_________> 184 164 SET RESTRAINT_GROUP = 27
TOP_________> 185 165 SET RESTRAINT_STDEV = 0.2 0.0
TOP_________> 186 166 SET RESIDUE_SPAN_RANGE = 0 99999, RESIDUE_SPAN_SIGN = OFF
TOP_________> 187 167 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_TY;
PES = 'ALL'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : ALL
Residue types to be searched for (RES_TYPES) : ALL
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 880
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
1 1 : LYS --- 108 : ASN 108
TOP_________> 188 168 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY;
PES = 'HET'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : ALL
Residue types to be searched for (RES_TYPES) : HET
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 0
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
TOP_________> 189 169 MAKE_RESTRAINTS
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: distance
make_re_422_> Number of previous, current restraints : 9158 9158
make_re_423_> Number of previous, current selected restraints: 9041 9041
TOP_________> 190 170 RETURN
TOP_________> 191 152 CALL ROUTINE = 'blk_restraints'
TOP_________> 192 173 SET RESTRAINT_TYPE = 'distance'
TOP_________> 193 174 SET DISTANCE_RSR_MODEL = 7
TOP_________> 194 175 SET MAXIMAL_DISTANCE = 10.0
TOP_________> 195 176 SET ADD_RESTRAINTS = ON
TOP_________> 196 177 SET RESTRAINT_GROUP = 27
TOP_________> 197 178 SET RESTRAINT_STDEV = 0.05 0.0
TOP_________> 198 179 SET RESIDUE_SPAN_RANGE = 0 0, RESIDUE_SPAN_SIGN = ON
TOP_________> 199 180 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_T;
YPES = 'BLK'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : ALL
Residue types to be searched for (RES_TYPES) : BLK
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 0
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
TOP_________> 200 181 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_T;
YPES = 'BLK'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : ALL
Residue types to be searched for (RES_TYPES) : BLK
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 0
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
TOP_________> 201 182 MAKE_RESTRAINTS
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: distance
make_re_422_> Number of previous, current restraints : 9158 9158
make_re_423_> Number of previous, current selected restraints: 9041 9041
TOP_________> 202 183 SET RESTRAINT_STDEV = 0.2 0.0
TOP_________> 203 184 SET RESIDUE_SPAN_RANGE = 1 99999, RESIDUE_SPAN_SIGN = OFF
TOP_________> 204 185 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA', RES_TY;
PES = 'ALL'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : CA
Residue types to be searched for (RES_TYPES) : ALL
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 108
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
1 1 : LYS --- 108 : ASN 108
TOP_________> 205 186 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY;
PES = 'BLK'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : ALL
Residue types to be searched for (RES_TYPES) : BLK
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): INITIALIZE
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 0
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
TOP_________> 206 187 MAKE_RESTRAINTS
Dynamically allocated memory at amprmcns [B,kB,MB]: 8280957 8086.872 7.897
make_re_417_> Restraint type to be calculated: distance
make_re_422_> Number of previous, current restraints : 9158 9158
make_re_423_> Number of previous, current selected restraints: 9041 9041
TOP_________> 207 188 DELETE_ALIGNMENT
TOP_________> 208 189 RETURN
Dynamically allocated memory at amaxseq [B,kB,MB]: 8171425 7979.907 7.793
TOP_________> 209 153 CALL ROUTINE = 'special_restraints'
TOP_________> 210 498 RETURN
TOP_________> 211 154 CONDENSE_RESTRAINTS
delete__443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 9158 8362
TOP_________> 212 155 WRITE_RESTRAINTS FILE = CSRFILE
openf5__224_> Open 14 UNKNOWN SEQUENTIAL sec1.rsr
TOP_________> 213 156 SET RESIDUE_SPAN_RANGE = -999 -999, RESIDUE_SPAN_SIGN = O;
N
TOP_________> 214 157 RETURN
TOP_________> 215 112 LABEL __SKIP_RSRS
TOP_________> 216 113 RETURN
TOP_________> 217 401 IF ARGUMENTS = EXIT_STAGE 1, OPERATION = 'GE', THEN = 'RE;
TURN'
TOP_________> 218 402 CALL ROUTINE = 'rd_restraints'
TOP_________> 219 255 READ_RESTRAINTS FILE = CSRFILE, ADD_RESTRAINTS = 'off'
openf5__224_> Open 11 OLD SEQUENTIAL sec1.rsr
openf5__224_> Open 11 OLD SEQUENTIAL sec1.rsr
rdcsr2__307_> Number of restraints read : 0
Number of excluded pairs read: 0
Number of pseudo atoms read : 0
Dynamically allocated memory at amprmcns [B,kB,MB]: 8171425 7979.907 7.793
openf5__224_> Open 11 OLD SEQUENTIAL sec1.rsr
openf5__224_> Open 11 OLD SEQUENTIAL sec1.rsr
rdcsr2__307_> Number of restraints read : 0
Number of excluded pairs read: 0
Number of pseudo atoms read : 0
rdcsrs__304_> Restraints in memory, selected restraints: 8362 8362
Explicitly excluded atom pairs in memory : 0
Pseudo atoms in memory : 0
TOP_________> 220 256 RETURN
TOP_________> 221 403 CALL ROUTINE = 'multiple_models'
TOP_________> 222 192 DO ID2 = STARTING_MODEL ENDING_MODEL 1
TOP_________> 223 193 SET FINAL_MODEL = 'default'
TOP_________> 224 194 CALL ROUTINE = 'single_model'
TOP_________> 225 205 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS
TOP_________> 226 206 SET ID1 = 0
TOP_________> 227 207 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = ';
.D'
openf5__224_> Open 18 UNKNOWN SEQUENTIAL sec1.D00000001
TOP_________> 228 208 READ_MODEL FILE = MODEL
openf5__224_> Open 11 OLD SEQUENTIAL sec1.ini
openf5__224_> Open 11 OLD SEQUENTIAL sec1.ini
rdatm___297_> Segments, residues, atoms: 1 108 880
rdatm___298_> Segment: 1 1 1 880
iatmcls_286W> MODEL atom not classified: ASN:OT1 ASN
iatmcls_286W> MODEL atom not classified: ASN:OT2 ASN
TOP_________> 229 209 CALL ROUTINE = 'select_atoms'
TOP_________> 230 267 PICK_ATOMS SELECTION_SEGMENT ='@:@' 'X:X', SELECTION_SEAR;
CH ='segment', PICK_ATOMS_SET =1, RES_TYPES =;
'all', ATOM_TYPES ='all', SELECTION_FROM ='a;
ll', SELECTION_STATUS ='initialize'
Number of atoms to choose from, total : 880 880
Atom types to be searched for (ATOM_TYPES) : all
Residue types to be searched for (RES_TYPES) : all
Selection mode (SELECTION_MODE) : ATOM
What to do with atoms & sets (SELECTION_STATUS): initialize
SEGMENT search; residue range (2i5,2a5) : 1 108 1: 108:
selatm__462_> Number of selected atoms : 880
List of segments of contiguous residues with at least one selected atom:
SEGMENT RESNUM AA --- RESNUM AA LEN
1 1 : LYS --- 108 : ASN 108
TOP_________> 231 268 RETURN
TOP_________> 232 210 CALL ROUTINE = RAND_METHOD
TOP_________> 233 251 RANDOMIZE_XYZ
randomi_498_> Atoms,selected atoms,random_seed,amplitude: 880 880 1 4.0000
randomi_496_> Amplitude is > 0; randomization is done.
TOP_________> 234 252 RETURN
TOP_________> 235 211 MAKE_SCHEDULE
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/sched.lib
TOP_________> 236 212 WRITE_SCHEDULE FILE = SCHFILE
openf5__224_> Open 14 UNKNOWN SEQUENTIAL sec1.sch
TOP_________> 237 213 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ;
THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E;
XT', FILE_ID = '.B'
TOP_________> 238 214 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1
TOP_________> 239 215 CALL ROUTINE = 'single_model_pass'
TOP_________> 240 231 DO SCHEDULE_STEP = 1 N_SCHEDULE 1
TOP_________> 241 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID;
1
TOP_________> 242 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
pick_re_612_> Number of MODEL atoms, selected restraints; 880 6147
TOP_________> 243 234 OPTIMIZE
Dynamically allocated memory at ampairs [B,kB,MB]: 8301657 8107.087 7.917
TOP_________> 244 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ;
THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P;
DB_EXT, FILE_ID = .B'
TOP_________> 245 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 246 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 247 238 END_DO
TOP_________> 248 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID;
1
TOP_________> 249 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
pick_re_612_> Number of MODEL atoms, selected restraints; 880 6814
TOP_________> 250 234 OPTIMIZE
TOP_________> 251 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ;
THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P;
DB_EXT, FILE_ID = .B'
TOP_________> 252 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 253 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 254 238 END_DO
TOP_________> 255 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID;
1
TOP_________> 256 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
pick_re_612_> Number of MODEL atoms, selected restraints; 880 7223
TOP_________> 257 234 OPTIMIZE
TOP_________> 258 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ;
THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P;
DB_EXT, FILE_ID = .B'
TOP_________> 259 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 260 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 261 238 END_DO
TOP_________> 262 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID;
1
TOP_________> 263 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
pick_re_612_> Number of MODEL atoms, selected restraints; 880 7508
TOP_________> 264 234 OPTIMIZE
TOP_________> 265 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ;
THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P;
DB_EXT, FILE_ID = .B'
TOP_________> 266 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 267 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 268 238 END_DO
TOP_________> 269 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID;
1
TOP_________> 270 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
pick_re_612_> Number of MODEL atoms, selected restraints; 880 7763
TOP_________> 271 234 OPTIMIZE
TOP_________> 272 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ;
THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P;
DB_EXT, FILE_ID = .B'
TOP_________> 273 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 274 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 275 238 END_DO
TOP_________> 276 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID;
1
TOP_________> 277 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
pick_re_612_> Number of MODEL atoms, selected restraints; 880 7983
TOP_________> 278 234 OPTIMIZE
TOP_________> 279 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ;
THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P;
DB_EXT, FILE_ID = .B'
TOP_________> 280 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 281 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 282 238 END_DO
TOP_________> 283 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID;
1
TOP_________> 284 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
pick_re_612_> Number of MODEL atoms, selected restraints; 880 8137
TOP_________> 285 234 OPTIMIZE
TOP_________> 286 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ;
THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P;
DB_EXT, FILE_ID = .B'
TOP_________> 287 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 288 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 289 238 END_DO
TOP_________> 290 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID;
1
TOP_________> 291 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
pick_re_612_> Number of MODEL atoms, selected restraints; 880 8351
TOP_________> 292 234 OPTIMIZE
TOP_________> 293 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ;
THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P;
DB_EXT, FILE_ID = .B'
TOP_________> 294 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 295 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 296 238 END_DO
TOP_________> 297 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID;
1
TOP_________> 298 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
pick_re_612_> Number of MODEL atoms, selected restraints; 880 8362
TOP_________> 299 234 OPTIMIZE
TOP_________> 300 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ;
THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P;
DB_EXT, FILE_ID = .B'
TOP_________> 301 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 302 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 303 238 END_DO
TOP_________> 304 239 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE
TOP_________> 305 271 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =;
'EQ', THEN = RETURN
TOP_________> 306 272 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER;
ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN;
ED.TMP'
TOP_________> 307 273 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS
TOP_________> 308 274 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ;
'GO_TO __BEGIN_MD'
TOP_________> 309 285 CALL ROUTINE = MD_LEVEL
TOP_________> 310 310 SET UPDATE_DYNAMIC = 0.39
TOP_________> 311 311 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0
TOP_________> 312 312 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M;
ETHOD = 3
TOP_________> 313 313 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V;
ELOCITIES = ON
TOP_________> 314 314 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V;
ELOCITIES = OFF
TOP_________> 315 315 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL'
TOP_________> 316 316 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300
TOP_________> 317 317 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL'
TOP_________> 318 318 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL'
TOP_________> 319 319 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL'
TOP_________> 320 320 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL'
TOP_________> 321 321 RETURN
TOP_________> 322 286 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ;
'GO_TO __AFTER_MD'
TOP_________> 323 291 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200
TOP_________> 324 292 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER;
ATION = 'INDEX', THEN = 'GO_TO __NO_FIT'
TOP_________> 325 306 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE
TOP_________> 326 307 RETURN
TOP_________> 327 240 LABEL __ABORT
TOP_________> 328 241 SET ERROR_STATUS = 0
TOP_________> 329 242 RETURN
TOP_________> 330 216 END_DO
TOP_________> 331 217 IUPAC_MODEL
iupac_m_487_> NH1/2 swapped: 177.9643 11 11
iupac_m_487_> NH1/2 swapped: 175.3387 12 12
iupac_m_486_> OE1/2 swapped: -135.8989 15 15
iupac_m_487_> NH1/2 swapped: 176.8704 24 24
iupac_m_483_> CD1/2 CE1/2 swapped: 112.8727 31 31
iupac_m_487_> NH1/2 swapped: -177.5065 44 44
iupac_m_485_> OD1/2 swapped: -174.8288 80 80
TOP_________> 332 218 SET ID1 = 9999
TOP_________> 333 219 SET OUTPUT2 = OUTPUT
TOP_________> 334 220 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul;
t', FILE_ID = '.V', FILE_EXT = ''
>> ENERGY; Differences between the model's features and restraints:
ID1, ID2 : 9999 1
Number of all residues in MODEL : 108
Number of all, selected real atoms : 880 880
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 8362 8362
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1470
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 120
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SCHEDULE_STEP, N_SCHEDULE : 9 9
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 658.5682
Symmetry term within energy : 0.0000
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 911 0 0 0.004 0.004 4.7334 1.000
2 Bond angle potential : 1251 0 0 2.016 2.016 96.283 1.000
3 Stereochemical cosine torsion poten: 676 0 20 46.641 46.641 213.87 1.000
4 Stereochemical improper torsion pot: 387 0 0 1.113 1.113 10.430 1.000
5 Soft-sphere overlap restraints : 1470 0 0 0.002 0.002 0.55332 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.00000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.00000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.00000 1.000
9 Distance restraints 1 (CA-CA) : 928 0 1 0.252 0.252 44.439 1.000
10 Distance restraints 2 (N-O) : 1110 0 1 0.284 0.284 68.056 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.00000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.00000 1.000
13 Mainchain Omega dihedral restraints: 107 0 0 3.537 3.537 14.948 1.000
14 Sidechain Chi_1 dihedral restraints: 94 0 0 58.670 58.670 14.422 1.000
15 Sidechain Chi_2 dihedral restraints: 72 0 0 63.006 63.006 22.940 1.000
16 Sidechain Chi_3 dihedral restraints: 31 0 0 42.911 42.911 15.224 1.000
17 Sidechain Chi_4 dihedral restraints: 10 0 0 80.110 80.110 7.6834 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.00000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.00000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.00000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.00000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.00000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 2046 0 0 0.469 0.469 74.586 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.00000 1.000
25 Phi/Psi pair of dihedral restraints: 106 5 5 29.326 43.894 18.548 1.000
26 Distance restraints 4 (SDCH-SDCH) : 633 0 0 0.794 0.794 51.850 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.00000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.00000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.00000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.00000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.00000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.00000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.00000 1.000
openf5__224_> Open 17 UNKNOWN SEQUENTIAL sec1.V99990001
# Heavy relative violation of each residue is written to: sec1.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3254 29P 30P C N 234 236 -53.69 -58.70 8.97 0.54 -64.50 175.19 13.65
1 30P 30P N CA 236 237 -37.94 -30.50 147.20
2 3320 95A 96P C N 773 775 -69.26 -58.70 11.40 1.60 -64.50 178.05 13.04
2 96P 96P N CA 775 776 -34.81 -30.50 147.20
3 3321 96P 97I C N 780 782 49.60 -97.30 147.36 6.38 -120.60 170.84 11.37
3 97I 97I N CA 782 783 115.64 127.20 130.30
4 3324 99T 100N C N 807 809 -99.19 -63.20 75.76 11.49 -63.20 75.76 11.49
4 100N 100N N CA 809 810 -107.76 -41.10 -41.10
5 3330 105I 106T C N 856 858 -54.70 -63.20 19.84 2.12 -78.10 151.98 7.29
5 106T 106T N CA 858 859 -60.03 -42.10 149.80
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 6 13 27 61 56 84 84 102 111 111
<< end of ENERGY.
TOP_________> 335 221 SET OUTPUT = OUTPUT2
TOP_________> 336 222 CALL ROUTINE = 'user_after_single_model'
TOP_________> 337 228 RETURN
TOP_________> 338 223 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ;
= PDB_EXT
openf5__224_> Open 14 UNKNOWN SEQUENTIAL sec1.B99990001
wrpdb2__568_> Residues, atoms, selected atoms: 108 880 880
TOP_________> 339 224 SET FINAL_MODEL = FILE
TOP_________> 340 225 RETURN
TOP_________> 341 195 END_DO
TOP_________> 342 196 IF ARGUMENTS = DO_LOOPS 1, OPERATION = 'NE', THEN = 'GO_T;
O NO_LOOPS'
TOP_________> 343 202 RETURN
TOP_________> 344 404 IF ARGUMENTS =FINAL_MALIGN3D 1, OPERATION ='NE', THEN ='G;
O_TO NO_MALIGN3D'
TOP_________> 345 411 RETURN
Dynamically allocated memory at finish [B,kB,MB]: 8301657 8107.087 7.917
Starting time : 2003/04/23 11:48:58.409
Closing time : 2003/04/23 11:49:53.150
Total CPU time [seconds] : 54.51