Hi,

I have a problem creating a model for a small protein with two zinc atoms. I use the ADD_RESTRAINT commands to create distance restrictions between the zincs and the residues attached to them. Looking at the log file, it looks that the restrictions are read without problems but at the end some ini file is read and I get an Atom index is out of bounds message. I am attaching the top, alignment and log file. I would appreciate any help.

Thanks

Alfredo Cardenas

Top file:

# Homology modelling by the MODELLER TOP routine 'model'.

INCLUDE # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file

SET ALNFILE = 'alignment1.txt' # alignment filename

SET KNOWNS = '1PTQ' # codes of the templates

SET SEQUENCE = 'pkci' # code of the target

#SET TOPOLOGY_MODEL = 1

SET HETATM_IO = on

SET TOPLIB = '$(LIB)/top.lib'

SET PARLIB = '$(LIB)/par.lib'

#SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files

SET STARTING_MODEL= 1 # index of the first model

SET ENDING_MODEL = 1 # index of the last model

# (determines how many models to calculate)

CALL ROUTINE = 'model' # do homology modelling

SUBROUTINE ROUTINE = 'special_restraints'

ADD_RESTRAINT ATOM_IDS = 'SG:14' 'ZN:55', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'SG:17' 'ZN:55', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'NE2:39' 'ZN:55', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'SG:42' 'ZN:55', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'SG:31' 'ZN:54', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'SG:34' 'ZN:54', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'SG:50' 'ZN:54', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

ADD_RESTRAINT ATOM_IDS = 'NE2:53' 'ZN:54', ;

RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1

RETURN

END_SUBROUTINE

Align file:

C; alignment of catalytic domain ok PKCiota and PKCtheta

>P1;1PTQ

structureX:1PTQ::::::::

HRFKVYNYMSPTFCDHCGSLLWGLVKQGLKCEDCGMNVHHKCREKVANLC---/--*

>P1;pkci

sequence:pkci::::::::

HTFQAKRFNRRAHCAICTDRIWGLGRQGYKCINCKLLVHKKCHKLVTIECGRH/zz*

Log file:

MODELLER 7v7, Sep 12, 2004 09:15pm

PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

Written by A. Sali

with help from

B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,

N. Eswar, F. Alber, B. Oliva, A. Fiser,

R. Sanchez, B. Yerkovich, A. Badretdinov,

F. Melo, J.P. Overington, E. Feyfant

University of California, San Francisco, USA

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, Win2000 build 2195 Service Pack 4, C000826, uni, x86 Family 15 Model 2 Stepping 7

Date and time of compilation : 09/13/2004 17:17:22

Job starting time (YY/MM/DD HH:MM:SS): 2005/01/28 14:19:34.867

getprog_531W> ROUTINE redefined: special_restraints

TOP_________> 108 746 SET ALNFILE = 'alignment1.txt'

TOP_________> 109 747 SET KNOWNS = '1PTQ'

TOP_________> 110 748 SET SEQUENCE = 'pkci'

TOP_________> 111 749 SET HETATM_IO = ON

TOP_________> 112 750 SET TOPLIB = '$(LIB)/top.lib'

TOP_________> 113 751 SET PARLIB = '$(LIB)/par.lib'

TOP_________> 114 752 SET STARTING_MODEL = 1

TOP_________> 115 753 SET ENDING_MODEL = 1

TOP_________> 116 754 CALL ROUTINE = 'model'

TOP_________> 117 419 CALL ROUTINE = 'getnames'

TOP_________> 118 531 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION;

= 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA;

TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'

TOP_________> 119 532 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI;

ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE;

NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE;

TOP_________> 120 533 STRING_OPERATE OPERATION = 'CONCATENATE', ;

STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE

TOP_________> 121 534 STRING_OPERATE OPERATION = 'CONCATENATE', ;

STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI;

TOP_________> 122 535 SET ROOT_NAME = SEQUENCE

TOP_________> 123 536 RETURN

TOP_________> 124 420 CALL ROUTINE = 'homcsr'

TOP_________> 125 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;

NCE

Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

Dynamically allocated memory at amaxbnd [B,kB,MB]: 1516107 1480.573 1.446

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

read_al_374_> Non-standard residue type,position,sequence: z 54 2

read_al_374_> Non-standard residue type,position,sequence: z 55 2

Read the alignment from file : alignment1.txt

Total number of alignment positions: 55

# Code #_Res #_Segm PDB_code Name

-------------------------------------------------------------------------------

1 1PTQ 50 1 1PTQ

2 pkci 55 2 pkci

TOP_________> 126 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER;

ATION = 'ne', THEN = 'GO_TO __ACCELRYS1'

TOP_________> 127 117 CHECK_ALIGNMENT

check_a_343_> >> BEGINNING OF COMMAND

openf5__224_> Open 11 OLD SEQUENTIAL ./\1PTQ.atm

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_________> 128 118 CALL ROUTINE = GENERATE_METHOD

TOP_________> 129 83 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

Read the alignment from file : alignment1.txt

Total number of alignment positions: 50

# Code #_Res #_Segm PDB_code Name

-------------------------------------------------------------------------------

1 1PTQ 50 1 1PTQ

TOP_________> 130 84 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

Read the alignment from file : alignment1.txt

Total number of alignment positions: 50

# Code #_Res #_Segm PDB_code Name

-------------------------------------------------------------------------------

1 1PTQ 50 1 1PTQ

TOP_________> 131 85 IF ARGUMENTS = INITIAL_MALIGN3D 0, OPERATION = 'EQ', THEN;

= 'GO_TO NO_INITIAL_MALIGN3D'

TOP_________> 132 88 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;

NCE

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

read_al_374_> Non-standard residue type,position,sequence: z 54 2

read_al_374_> Non-standard residue type,position,sequence: z 55 2

Read the alignment from file : alignment1.txt

Total number of alignment positions: 55

# Code #_Res #_Segm PDB_code Name

-------------------------------------------------------------------------------

1 1PTQ 50 1 1PTQ

2 pkci 55 2 pkci

TOP_________> 133 89 READ_TOPOLOGY FILE = TOPLIB

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib\/top.lib

read_to_238_> Reading CHARMM residue topology file version: 22 1

openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL7v7}/modlib/models.lib

TOP_________> 134 90 READ_PARAMETERS FILE = PARLIB

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib\/par.lib

Dynamically allocated memory at amattacns [B,kB,MB]: 1516657 1481.110 1.446

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib\/par.lib

rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MRFP MODE

227 561 661 112 0 0

TOP_________> 135 91 CALL ROUTINE = 'create_topology'

TOP_________> 136 106 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF

getf_______W> RTF restraint not found in the atoms list:

residue type, indices: 7 53

atom names : C +N

atom indices : 884 0

getf_______W> RTF restraint not found in the atoms list:

residue type, indices: 7 1

atom names : N -C CA H

atom indices : 1 0 3 2

getf_______W> RTF restraint not found in the atoms list:

residue type, indices: 7 53

atom names : C CA +N O

atom indices : 884 871 0 885

mkilst______> segment topology constructed from sequence and RTF:

segments residues atoms bonds angles dihedrals impropers:

1 53 885 894 0 0 284

patch_______> segment topology patched using RTF: 1 ; HIS ; NTER

segments residues atoms bonds angles dihedrals impropers:

1 53 887 896 1609 2350 284

patch_______> segment topology patched using RTF: 53 ; HIS ; CTER

segments residues atoms bonds angles dihedrals impropers:

1 53 888 897 1611 2353 285

genseg______> segment topology constructed from sequence and RTF:

segments residues atoms bonds angles dihedrals impropers:

1 53 888 897 1611 2353 285

mkilst______> segment topology constructed from sequence and RTF:

segments residues atoms bonds angles dihedrals impropers:

2 55 890 897 1611 2353 285

genseg______> segment topology constructed from sequence and RTF:

segments residues atoms bonds angles dihedrals impropers:

2 55 890 897 1611 2353 285

TOP_________> 137 107 CALL ROUTINE = 'default_patches'

TOP_________> 138 526 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;

NCE

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

read_al_374_> Non-standard residue type,position,sequence: z 54 2

read_al_374_> Non-standard residue type,position,sequence: z 55 2

Read the alignment from file : alignment1.txt

Total number of alignment positions: 55

# Code #_Res #_Segm PDB_code Name

-------------------------------------------------------------------------------

1 1PTQ 50 1 1PTQ

2 pkci 55 2 pkci

TOP_________> 139 527 PATCH_SS_TEMPLATES

TOP_________> 140 528 RETURN

TOP_________> 141 108 CALL ROUTINE = 'special_patches'

TOP_________> 142 523 RETURN

TOP_________> 143 109 RETURN

TOP_________> 144 92 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: 328 562

TOP_________> 145 93 BUILD_MODEL INITIALIZE_XYZ = OFF

build___467W> All coordinates in MODEL have been assigned.

build___468W> Some coordinates in MODEL are still undefined.

build___464W> Inventing the MODEL coordinates.

TOP_________> 146 94 WRITE_MODEL FILE = MODEL

openf5__224_> Open 14 UNKNOWN SEQUENTIAL pkci.ini

wrpdb2__568_> Residues, atoms, selected atoms: 55 890 890

TOP_________> 147 95 RETURN

TOP_________> 148 119 IF ARGUMENTS = EXIT_STAGE 2, OPERATION = 'EQ', THEN = 'RE;

TURN'

TOP_________> 149 120 IF ARGUMENTS = CREATE_RESTRAINTS 0, OPERATION = 'EQ', THE;

N ='GO_TO __SKIP_RSRS'

TOP_________> 150 121 CALL ROUTINE = 'mkhomcsr'

TOP_________> 151 126 MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS;

= OFF

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: stereo

r_stere_607W> Cannot find params in params file:

CHARMM atoms : NY CA CPT H

IUPAC atoms : NE1 CD1 CE2 HE1

Atom indices : 367 365 369 368

Residues : TRP TRP TRP TRP

addprm__440W> Adding params (mean,force,period): 1.0268 60.0000 0

For atoms: NY CA CPT H

r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.

Added bond,angle,dihedral,improper restraints : 897 1611 1936 285

Total number of restraints before, now : 0 4729

make_re_422_> Number of previous, current restraints : 0 4729

make_re_423_> Number of previous, current selected restraints: 0 4729

TOP_________> 152 127 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;

NCE

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

openf5__224_> Open 20 OLD SEQUENTIAL alignment1.txt

openf5__224_> Open 13 OLD SEQUENTIAL ./\1PTQ.atm

read_al_374_> Non-standard residue type,position,sequence: z 54 2

read_al_374_> Non-standard residue type,position,sequence: z 55 2

Read the alignment from file : alignment1.txt

Total number of alignment positions: 55

# Code #_Res #_Segm PDB_code Name

-------------------------------------------------------------------------------

1 1PTQ 50 1 1PTQ

2 pkci 55 2 pkci

TOP_________> 153 128 MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_;

RESTRAINTS = ON

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: phi-psi_binormal

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mnch1.bin

initmdt_400_> Distance function type: 1

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 1PTQ

getdata_289_> Proteins (all/accepted): 1 1

make_re_422_> Number of previous, current restraints : 4729 4780

make_re_423_> Number of previous, current selected restraints: 4729 4780

TOP_________> 154 129 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.3, SPLINE_MIN_POINT;

S = 5

TOP_________> 155 130 MAKE_RESTRAINTS RESTRAINT_TYPE = 'omega_dihedral', ADD_RE;

STRAINTS = ON

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: omega_dihedral

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/omega.bin

initmdt_400_> Distance function type: 1

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 1PTQ

getdata_289_> Proteins (all/accepted): 1 1

delete__442E> One or more atoms absent from MODEL: O: 53: C: 53: N: 54: CA: 54:

delete__442E> One or more atoms absent from MODEL: O: 54: C: 54: N: 55: CA: 55:

omgdel__425W> Unselected all O C +N +CA dihedrals: 52

make_re_422_> Number of previous, current restraints : 4780 4832

make_re_423_> Number of previous, current selected restraints: 4780 4780

TOP_________> 156 131 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RES;

TRAINTS = ON

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: chi1_dihedral

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin

initmdt_400_> Distance function type: 1

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 1PTQ

getdata_289_> Proteins (all/accepted): 1 1

make_re_422_> Number of previous, current restraints : 4832 4878

make_re_423_> Number of previous, current selected restraints: 4780 4826

TOP_________> 157 132 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RES;

TRAINTS = ON

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: chi2_dihedral

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin

initmdt_400_> Distance function type: 1

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 1PTQ

getdata_289_> Proteins (all/accepted): 1 1

make_re_422_> Number of previous, current restraints : 4878 4913

make_re_423_> Number of previous, current selected restraints: 4826 4861

TOP_________> 158 133 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RES;

TRAINTS = ON

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: chi3_dihedral

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin

initmdt_400_> Distance function type: 1

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 1PTQ

getdata_289_> Proteins (all/accepted): 1 1

make_re_422_> Number of previous, current restraints : 4913 4928

make_re_423_> Number of previous, current selected restraints: 4861 4876

TOP_________> 159 134 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RES;

TRAINTS = ON

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: chi4_dihedral

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin

initmdt_400_> Distance function type: 1

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 1PTQ

getdata_289_> Proteins (all/accepted): 1 1

make_re_422_> Number of previous, current restraints : 4928 4940

make_re_423_> Number of previous, current selected restraints: 4876 4888

TOP_________> 160 135 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.7, SPLINE_MIN_POINT;

S = 5

TOP_________> 161 136 SET RES_TYPES = 'STD'

TOP_________> 162 137 SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_;

DISTANCE

TOP_________> 163 138 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON

TOP_________> 164 139 SET RESTRAINT_GROUP = 9

TOP_________> 165 140 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

selatm__462_> Number of selected atoms : 53

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 1 : HIS --- 53 : HIS 53

TOP_________> 166 141 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

selatm__462_> Number of selected atoms : 53

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 1 : HIS --- 53 : HIS 53

TOP_________> 167 142 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN;

TS = 'ON'

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: distance

make_re_422_> Number of previous, current restraints : 4940 5639

make_re_423_> Number of previous, current selected restraints: 4888 5587

TOP_________> 168 143 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_N-O_DI;

STANCE

TOP_________> 169 144 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = OFF

TOP_________> 170 145 SET RESTRAINT_GROUP = 10

TOP_________> 171 146 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'N'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

selatm__462_> Number of selected atoms : 53

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 1 : HIS --- 53 : HIS 53

TOP_________> 172 147 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

selatm__462_> Number of selected atoms : 53

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 1 : HIS --- 53 : HIS 53

TOP_________> 173 148 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN;

TS = 'ON'

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: distance

make_re_422_> Number of previous, current restraints : 5639 6463

make_re_423_> Number of previous, current selected restraints: 5587 6411

TOP_________> 174 149 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-MC_;

DISTANCE

TOP_________> 175 150 SET RESIDUE_SPAN_RANGE = 1 2, RESIDUE_SPAN_SIGN = OFF

TOP_________> 176 151 SET RESTRAINT_GROUP = 23, RESTRAINT_STDEV = 0.5 1.5

TOP_________> 177 152 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

selatm__462_> Number of selected atoms : 676

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 1 : HIS --- 53 : HIS 53

TOP_________> 178 153 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

selatm__462_> Number of selected atoms : 212

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 1 : HIS --- 53 : HIS 53

TOP_________> 179 154 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN;

TS = 'ON'

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: distance

make_re_422_> Number of previous, current restraints : 6463 7008

make_re_423_> Number of previous, current selected restraints: 6411 6956

TOP_________> 180 155 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-SC_;

DISTANCE

TOP_________> 181 156 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON

TOP_________> 182 157 SET RESTRAINT_GROUP = 26, RESTRAINT_STDEV = 0.5 2.0

TOP_________> 183 158 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

selatm__462_> Number of selected atoms : 676

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 1 : HIS --- 53 : HIS 53

TOP_________> 184 159 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

selatm__462_> Number of selected atoms : 676

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 1 : HIS --- 53 : HIS 53

TOP_________> 185 160 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN;

TS = 'ON'

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: distance

make_re_422_> Number of previous, current restraints : 7008 7226

make_re_423_> Number of previous, current selected restraints: 6956 7174

TOP_________> 186 161 CALL ROUTINE = 'hetatm_restraints'

TOP_________> 187 170 SET RESTRAINT_TYPE = 'distance'

TOP_________> 188 171 SET DISTANCE_RSR_MODEL = 7

TOP_________> 189 172 SET MAXIMAL_DISTANCE = 7.0

TOP_________> 190 173 SET ADD_RESTRAINTS = ON

TOP_________> 191 174 SET RESTRAINT_GROUP = 27

TOP_________> 192 175 SET RESTRAINT_STDEV = 0.2 0.0

TOP_________> 193 176 SET RESIDUE_SPAN_RANGE = 0 99999, RESIDUE_SPAN_SIGN = OFF

TOP_________> 194 177 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_TY;

PES = 'ALL'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

selatm__462_> Number of selected atoms : 890

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 1 : HIS --- 55 : ZN2 55

TOP_________> 195 178 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY;

PES = 'HET'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

selatm__462_> Number of selected atoms : 2

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 54 : ZN2 --- 55 : ZN2 2

TOP_________> 196 179 MAKE_RESTRAINTS

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: distance

make_re_422_> Number of previous, current restraints : 7226 7226

make_re_423_> Number of previous, current selected restraints: 7174 7174

TOP_________> 197 180 RETURN

TOP_________> 198 162 CALL ROUTINE = 'blk_restraints'

TOP_________> 199 183 SET RESTRAINT_TYPE = 'distance'

TOP_________> 200 184 SET DISTANCE_RSR_MODEL = 7

TOP_________> 201 185 SET MAXIMAL_DISTANCE = 10.0

TOP_________> 202 186 SET ADD_RESTRAINTS = ON

TOP_________> 203 187 SET RESTRAINT_GROUP = 27

TOP_________> 204 188 SET RESTRAINT_STDEV = 0.05 0.0

TOP_________> 205 189 SET RESIDUE_SPAN_RANGE = 0 0, RESIDUE_SPAN_SIGN = ON

TOP_________> 206 190 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_T;

YPES = 'BLK'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

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_________> 207 191 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_T;

YPES = 'BLK'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

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_________> 208 192 MAKE_RESTRAINTS

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: distance

make_re_422_> Number of previous, current restraints : 7226 7226

make_re_423_> Number of previous, current selected restraints: 7174 7174

TOP_________> 209 193 SET RESTRAINT_STDEV = 0.2 0.0

TOP_________> 210 194 SET RESIDUE_SPAN_RANGE = 1 99999, RESIDUE_SPAN_SIGN = OFF

TOP_________> 211 195 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA', RES_TY;

PES = 'ALL'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

selatm__462_> Number of selected atoms : 53

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 1 : HIS --- 53 : HIS 53

TOP_________> 212 196 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY;

PES = 'BLK'

Number of atoms to choose from, total : 890 890

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 55 1: 55:

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_________> 213 197 MAKE_RESTRAINTS

Dynamically allocated memory at amprmcns [B,kB,MB]: 5191489 5069.813 4.951

make_re_417_> Restraint type to be calculated: distance

make_re_422_> Number of previous, current restraints : 7226 7226

make_re_423_> Number of previous, current selected restraints: 7174 7174

TOP_________> 214 198 DELETE_ALIGNMENT

TOP_________> 215 199 RETURN

Dynamically allocated memory at amaxseq [B,kB,MB]: 5097041 4977.579 4.861

TOP_________> 216 163 CALL ROUTINE = 'special_restraints'

TOP_________> 217 756 ADD_RESTRAINT ATOM_IDS = 'SG:14' 'ZN:55', RESTRAINT_PARAM;

ETERS = 3 1 1 27 2 2 0 3.0 0.1

Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861

TOP_________> 218 757 ADD_RESTRAINT ATOM_IDS = 'SG:17' 'ZN:55', RESTRAINT_PARAM;

ETERS = 3 1 1 27 2 2 0 3.0 0.1

Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861

TOP_________> 219 758 ADD_RESTRAINT ATOM_IDS = 'NE2:39' 'ZN:55', RESTRAINT_PARA;

METERS = 3 1 1 27 2 2 0 3.0 0.1

Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861

TOP_________> 220 759 ADD_RESTRAINT ATOM_IDS = 'SG:42' 'ZN:55', RESTRAINT_PARAM;

ETERS = 3 1 1 27 2 2 0 3.0 0.1

Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861

TOP_________> 221 760 ADD_RESTRAINT ATOM_IDS = 'SG:31' 'ZN:54', RESTRAINT_PARAM;

ETERS = 3 1 1 27 2 2 0 3.0 0.1

Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861

TOP_________> 222 761 ADD_RESTRAINT ATOM_IDS = 'SG:34' 'ZN:54', RESTRAINT_PARAM;

ETERS = 3 1 1 27 2 2 0 3.0 0.1

Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861

TOP_________> 223 762 ADD_RESTRAINT ATOM_IDS = 'SG:50' 'ZN:54', RESTRAINT_PARAM;

ETERS = 3 1 1 27 2 2 0 3.0 0.1

Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861

TOP_________> 224 763 ADD_RESTRAINT ATOM_IDS = 'NE2:53' 'ZN:54', RESTRAINT_PARA;

METERS = 3 1 1 27 2 2 0 3.0 0.1

Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861

TOP_________> 225 764 RETURN

TOP_________> 226 164 CONDENSE_RESTRAINTS

delete__443_> Restraints marked for deletion were removed.

Total number of restraints before, now: 7234 6845

TOP_________> 227 165 WRITE_RESTRAINTS FILE = CSRFILE

openf5__224_> Open 14 UNKNOWN SEQUENTIAL pkci.rsr

TOP_________> 228 166 SET RESIDUE_SPAN_RANGE = -999 -999, RESIDUE_SPAN_SIGN = O;

top_mod_451W> Requested schedule step not available: 0

SCHEDULE_STEP set to N_SCHEDULE.

TOP_________> 229 167 RETURN

TOP_________> 230 122 LABEL __SKIP_RSRS

TOP_________> 231 123 RETURN

TOP_________> 232 421 IF ARGUMENTS = EXIT_STAGE 1, OPERATION = 'GE', THEN = 'RE;

TURN'

TOP_________> 233 422 CALL ROUTINE = 'rd_restraints'

TOP_________> 234 276 READ_RESTRAINTS FILE = CSRFILE, ADD_RESTRAINTS = 'off'

openf5__224_> Open 11 OLD SEQUENTIAL pkci.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]: 5097191 4977.726 4.861

openf5__224_> Open 11 OLD SEQUENTIAL pkci.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: 6845 6845

Explicitly excluded atom pairs in memory : 0

Pseudo atoms in memory : 0

TOP_________> 235 277 RETURN

TOP_________> 236 423 CALL ROUTINE = 'multiple_models'

TOP_________> 237 202 DO ID2 = STARTING_MODEL ENDING_MODEL 1

TOP_________> 238 203 SET FINAL_MODEL = 'default'

TOP_________> 239 204 CALL ROUTINE = 'single_model'

TOP_________> 240 215 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS

TOP_________> 241 216 SET ID1 = 0

TOP_________> 242 217 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = ';

.D'

openf5__224_> Open 18 UNKNOWN SEQUENTIAL pkci.D00000001

TOP_________> 243 218 READ_MODEL FILE = MODEL

openf5__224_> Open 11 OLD SEQUENTIAL pkci.ini

rdatm___297_> Segments, residues, atoms: 2 55 438

rdatm___298_> Segment: 1 1 53 436

rdatm___298_> Segment: 2 54 55 2

TOP_________> 244 219 CALL ROUTINE = 'select_atoms'

TOP_________> 245 288 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 : 438 438

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 55 1: 55:

selatm__462_> Number of selected atoms : 438

List of segments of contiguous residues with at least one selected atom:

SEGMENT RESNUM AA --- RESNUM AA LEN

1 1 : HIS --- 55 : ZN2 55

TOP_________> 246 289 RETURN

TOP_________> 247 220 CALL ROUTINE = RAND_METHOD

TOP_________> 248 272 RANDOMIZE_XYZ

randomi_498_> Atoms,selected atoms,random_seed,amplitude: 438 438 1 4.0000

randomi_496_> Amplitude is > 0; randomization is done.

TOP_________> 249 273 RETURN

TOP_________> 250 221 MAKE_SCHEDULE

openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/sched.lib

TOP_________> 251 222 WRITE_SCHEDULE FILE = SCHFILE

openf5__224_> Open 14 UNKNOWN SEQUENTIAL pkci.sch

TOP_________> 252 223 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ;

THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E;

XT', FILE_ID = '.B'

TOP_________> 253 224 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1

TOP_________> 254 225 CALL ROUTINE = 'single_model_pass'

TOP_________> 255 252 DO SCHEDULE_STEP = 1 N_SCHEDULE 1

TOP_________> 256 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID;

TOP_________> 257 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF

csrrng__299E> Atom index is out of bounds: 441 438

recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

Dynamically allocated memory at finish [B,kB,MB]: 5094825 4975.415 4.859

Starting time : 2005/01/28 14:19:34.867

Closing time : 2005/01/28 14:19:42.305

Total CPU time [seconds] : 5.45

************************************************************

Alfredo Cardenas

Assistant Professor

Department of Chemistry

University of South Florida

4202 E. Fowler Ave, SCA 400

Tampa, FL 33620-5250

Phone: (813) 974-1591

Fax: (813) 974-1733

************************************************************