MAKECIF - restrain maker.

Version 5.1.0 /27.06.2000/ - FEATURES


CONTENTS


Reference

    Author:    A.A.Vagin
                email: alexei@ysbl.york.ac.uk

    Reference:

    A. A. Vagin, G. N. Murshudov and B. V. Strokopytov
    BLANC: the program suite for protein crystallography 
    J. Appl. Cryst. (1998). 31, 98 - 102

Complete structure description

  Atomic model represents X-ray crystal structure solution.
  Complete description of this structure describes the crystall.

  Hierarchy

     First level of hierarchy of this description is the description of 
     the unit cell. It consists of the unit cell parameters and
     space group symmetry name. The contents of the unit cell is generated
     by the crystallographical symmetrical operators from the 
     contents of the asymmetrical part of unit cell.
     Cell parameters, the list and the description of the links between 
     symm.related chains, Space group id and the cryst.symm. operators 
     define the crystal.

     Second level describes the asymmetric part of unit cell.
     The asymmetric part of the unit cell consists of the unit 
     structural elements - chains. The list of the chains and list of 
     links between the chains define the asymmetrical part of the unit cell.
 
     Third level describes the chains. The description of chain is
     the list of monomer, list of modifications and the descriptions 
     of these modifications, the list of links inside chain and
     the descriptions of these links.      

     Fourth level describes the monomers. The description of monomer is
     the list of atoms, the list of bonds, the list of angles and so on.

     Fifth level describes the atoms. The atom's name, the atom's type,
     the coordinates, B-factor, occupancy, multyplicity define the atom.

  Definition

     Chain /group/ - is numbered set of "monomers". The list of "monomers",
     the links between monomers (for example: disulfide bridges, peptide bond),
     the description of some modification of monomers (for example: terminus
     of polypeptide chain) define the chain. The polymer (lenear or not as
     sugar) is covalet bonded set of monomers - chain. A set of water molecule
     is a chain. Chain may contain only one monomer. 

     Monomer /residue/ - is a set of atoms connected by bonds, or a single
     atom.

Representation in CIF

There are two part of description: constant and variable. The variable part is in the coordinate file, the constant part is in the dictionary.
  Coordinate file

	Coordinate file contains the information which dependent on the
	conformation of the molecule (coordinates, occupancy, B-factors)
        B-factors) and the list of modifications to and links between
        actual monomers. The information about the names of chains and 
        monomers, and  the serial numbers of monomers for the links must 
        be present in the CIFile. Link's ID, modification's ID, names of
        chains, monomers, atoms are the pointers to the chemical description
        in the dictionary.

  Dictionary

        Dictionary contains information about:

        1.  the chemical structure of the monomers (atom's types,
            bond's lengths, angles, chirality, planarity),
        2.  the tree like structure of each monomer, 
        3.  chemical structure of links between monomers (peptide bond,
            disulfide bridges,...), 
        4.  chemical details of the modifications of monomers (e.g. termini of
            polypeptide chains,...) 
        5.  energetic parameters.

        Some monomer has "minimal description : list of atom, atom's types
        and bonds. Complete description can be derived from minimal.

  Structure/Restraint files

    Coordinate file and Dictionary describe structure completely.
    But there are a lot of data in the dictionary which is not
    concern this particular structure. Makecif creates two files
    with necessary information from Dictionary:

    1. structure file with
  
       chemical atom's types, WDV and ion radii,
       tree like structure description

    2. restrain file with 
    
       description of bonds, angles, tortions, chiralities,
       planarities

What program doing

Program uses as input CIF or PDB file, check monomer's names and contents. If program can find the description of monomer in the dictionary, creates new one. Check structure description: chain's description, linkages, modifications. And finally program creates coordenate and structure files and (user choice) restraint file or generates coordinates for missing atoms.

  Read PDB file

    Reading PDB file Makecif uses from PDB file only folowing records:

    HEADER  COMPND  CRYST1  SCALE   HETATM  TER
    SSBOND  MODRES  LINK    CISPEP  ATOM    ANISOU


    a) atom name correction and element definition, if this is absent 
       in input file.

        Program changes PDB style of H atom's name to human style.
        For example : 1HN1 --> HN11
   
        Accoding PDB convention program change character ' (quota) to * (star)
        in atom's name of DNA/RNA.

        C-terminus atom O of polipeptide 'OT  ' --> 'OXT ',
        AND for DNA/RNA: 
           'OXT ' --> 'O3T '
           'O3G ' --> 'O3T ' 
           'O3P ' --> 'O3T '

        Atom O for water must has name 'O   '

        If there is character ' (quota) in atom's name program changes 
        it to , (comma)
        
    b) check and correction residue name,
       residue type definition.

        If there is character ' (quota) in residue's name program changes 
        it to , (comma)

        Program changes residue's name of DNA/RNA:
          CYT --> C
          ADE --> A
          THY --> T
          GUA --> G
          URI --> U

    c) chain correction,check chain connection
    
      

    d) read links and modification     


  Check monomers

   Program  checks a presence of description of monomers and defines
   type of monomers.

   There are following monomer's types:

      non-polymer
      peptide
      polymer         
      DNA/RNA
      pyranose
      solvent         

   Peptides (L and D peptides) are:
 
      'CYS','SER','THR','PRO','ALA','GLY','ASN','ASP' 
     ,'GLU','GLN','HIS','ARG','LYS','MET','ILE','LEU' 
     ,'VAL','PHE','TYR','TRP','TRY','PRZ','PR0','ILU' 
     ,'CYX','CSS','CSH','CYH','ASX','GLX','ACD','INI'
     ,'ABU','ALB','ALI','ARO','BAS','HYP','PCA','SAR' 
     ,'ABA','BMT','MLE','MVA','DVA','MSE','PTR','DAL' 
     ,'NLE','BLE','B1F','B2F','B2A','B2I','B2V','DPR'
     ,'DPN','DTR','DTH','TYS','CGU','ANT','ILG','OCS'
     ,'KCX','SAH','SAM','SEP','LLP','5HP','CSO','ORN'

   Polymers are: 

      'STA','DFO','FOR','BOC','IVA','NME','ACE','DAM'
     ,'ETA','ANI','ADD','ACB','TFA','DIP','MPR','CXM','BAL'

   DNA/RNA are: 

      'A  ','C  ','G  ','T  ','U  ','I  ','+A ','+C ' 
     ,'+G ','+T ','+U ','1MA','1MG','2MG','5MC','5MU'
     ,'7MG','H2U','M2G','OMC','OMG','OMU','PSU','YG '

   Pyranoses are: 

      'MAN','NAG','FUC','GAL','GLC','GCU','CEG','XYS' 
     ,'ARB','RIP','ABE','RAM','MAG','MMA','GSA'      


   Scheme of the check of the presence of description of monomers.
   Global search is an algorithm to matching two description.
   Make_new means to create new complete description.

         +------------------------------------+
         ! Look at the name in the dictionary !
         ! Is that in the dictionary ?        !
         +------------------------------------+
                !                     !
             no !                     ! yes
                v                     v
       +---------------+        +----------------------+
  +-->-! Global search !   yes  !  Minimal description !
  !    !   matching ?  !--->----!         ?            !
  !    +---------------+        +----------------------+
  !            !                   !           ! 
  !         no !                   ! yes       ! no
  !            !                   !           v
  !            v                   v  +----------------------+ 
  ^            !                   !  ! is this polipeptide, !
  !            !                   !  !  DNA/RNA, sugar ?    !
  !            !                   !  +----------------------+
  !            !                   !       !               !
  !            !                   !       ! no            ! yes
  !            !                   !       v               v
  !            !             no    !  +----------------+   !  
  +---<----------------<------------- ! Completeness ? !   !
               !                   !  +----------------+   !
               v                   v       !               !
               !                   !       ! yes           !
               !                   !       !               !
             +-----------------------+     v               v
             !       Make_new        !     !               !
             +-----------------------+     !               !
                        !                  !               !
                        !                  !               !
                        v                  v               v


  Check structure description
 
     1. check of atoms in special position.

     2. check of chain connectivity and definition of connection types.

       Only peptides, polymers , DNA/RNA and pyranos can form chain.

       There are following connection types, which can form chain:

         for peptides, polymers:

         'TRANS   '
         'CIS     '
         'PTRANS  '
         'PCIS    '
         'FOR_C-N '
         'FOR_C-C '
         'ACE_C-N '
         'DFO_C-N '
         'NME_N-C '
         'IVA_C-N '
         'BOC_C-N '
         'DFO_N-C '
         'STA_C-N '
         'STA_N-C '

         for DNA/RNA:

         'p       '

         for pyranoses:

         'BETA1-2 '
         'BETA1-3 '
         'BETA1-4 '
         'BETA1-6 '
         'ALPHA1-2'
         'ALPHA1-3'
         'ALPHA1-4'
         'ALPHA1-6'

     3. check of inter/intra chain links
        if description of link there is not in the dictionary, program
        can create it.

     4. check and create new list of chains and set type of terminus residues.

        Chain types:

        'non-polymer'
        'polypeptide'
        'DNA/RNA    '
        'saccharide'
        'water   '

        Terminus IDs:
 
        initial:

        'NH3     '
        'FOR-N   '
        'p5*END  '
        '5*END   '
        'NH3-COO '
        'TERMINUS'

        final:

        'COO     '
        'FOR-C   '
        'p3*END  '
        '3*END   '
        'NH3-COO '
        'TERMINUS'
        'CM-COO  '
      
     5. check completeness of atom's list of residue.


  Finally program create list of restraints or rebuilds missing atoms.

     Rebuilding
                
       Program rebuilds missing atoms used information from
       monomer's library.

     Restraints

       Program writes to output file ideal values of reatraints and
       its observed values. If output file is formatted file 
       ( keyword FORM = F ) it is possible to look at and check.       

Input files

Makecif uses as input CIF or PDB_file and libraries:
      mon_lib_com.cif   - description links and modifications
      mon_lib_prot.cif  - amino-acids
      mon_lib_na.cif    - DNA/RNA
      mon_lib_sug.cif   - sugars
      mon_lib_met.cif   - metals
      mon_lib_1.cif     - small molecules
      mon_lib_2.cif     -  - - - - -
       . . . . . . . . 
      ener_lib.cif,     - energetic parameters
Program can read additional library of monomers.

Output files

     1. with atomic coordinates, symmetry and unit cell
        parameters. / file extension "crd"/ 
     2. with chemical structure description and atomic
        scattering structure factors. / file extension "str"/
     3. with restraints: standard values of bonds, angles, 
        torsion angles, chirality centres, plan groups, its
        actual values in the structure. / file extension "rst"/
     4. with Van-der-Waals and H_bond restraints: standard values
        of distanceis and its actual values in the structure. /file
        extension "vdw"/

Dialogue and Keywords

Dialogue is a preferable way of running MAKECIF. Keywords with short explanations are printed by the program at the beginning of execution. However, the program automatically produces a batch command file during dialogue. This feature might be useful to repeate calculations.
   To get started with MAKECIF, you first have to answer two questions:

   1)  Do you want to have FILE-DOCUMENT /makecif.doc/ ? /<N>/Y/A :
       N - means without DOC-file
       Y - with new contents
       A - means to keep old contents and add new information
          with DOC-file program creates batch file: makecif.bat
    DOC  Y

   2) input-coord-file
     FILE_C  t.pdb

   After that you can use akeywords in any order, if you want to use.

  Keywords:

 
FILE_O   <new> - output_CIFiles /name without extention/
                  default name: 'new'

                        output files will be:  
 
                            new.crd
                            new.str
                            new.rst
                            new.vdw
                            new_XXX.ps
                            new.lib

FILE_L    < >  - additional library, " " means without this file

SPEC     <N>/Y - Y - check atoms in special position, N - not use it.

DMIN     <0.5> - minimal distance to recognize atom in special position

CONN   <N>/Y/D - N - only check chain"s connection between residues.
                  Y - use new chain"s connection between residues.
                  D - use new but ignore user"s definition

CIS     <N>/Y  - Y - check and change peptide link

SS     <Y>/N/D - N - only check SS-links
                  Y - use new SS-links between residues.
                  D - use new but ignore user"s definition

SUGAR  <N>/Y/D - N - only check links between residues.
                  Y - use new links between residues.
                  D - use new but ignore user"s definition

LINK   <N>/Y/D - N - only check links between residues.
                  Y - use new links between residues.
                  D - use new but ignore user"s definition

CHAIN   <N>/Y  - Y - check and change chain description

PEPT    <N>/Y  - Y - check and correct AA in PDB file (L or D)

SYMM   <N>/Y   - Y - use links between symmetry reated residues.

CHECK   <N>/Y  - Y - full check of all monomers

CUT      <0>   - distance cut_off, 0 - means without VDW and H-bond
                  restraints

HFLAG  <Y>/A/N - Y - hydrogen atoms where they are (not create new)
                  A - with all hydrogen atoms (rebuild all missing H atoms)
                  N - without hydrogen atoms (i.e. remove H)

RFLAG   <N>/Y  - Y - rebuild non-hydrogen atoms
                  restraints will not be created if HFLAG="A" or RFLAG="Y"

FORM    <F>/U  - format of restrain file, U - unformatted

NOSG    <0>    - Number of new space group

CELL    <0>    - new cell: A,B,C,Alpha,Beta,Gamma

LIST <M>/S/L   - S short output, L - long, M - medium

LOUT <new.lib> - output file of new dictionary
 

Make new ligands description

If the description of a monomer is absent in the library program will try to create library description and write it to special file for further inclusion to the library. Program creates PostScript files with the pictures of new monomers.

Libcheck

LIBCHECK
     - library manager.
            reads library of monomers, gives information about some
            monomer, creates PostScript file with picture and information
            about bonds, angles, ...
            can read additional library, add two libraries and write to
            a new library file ;
            can create description of new monomer reading coordinates
            from PDB file of CIFile.

Modcheck

MODCHECK
    - restrain checker.
            reads CIFiles of coordinates and restraints,
            gives information about restraints (to DOC_file),
            writes PDB_file or/and CIFile of coordinates.

Emin

EMIN
    - energy minimization / or B_factor regularization / 
            minimizes the energy of structure using the restraints files
            from program MAKECIF.
  
            E_total = E_bond + E_angle + E_tors + E_vdw + E_hb
                                  
                 E_bond  = Sum ( Kb * (Bobs     -Bidl)**2    )
                 E_angle = Sum ( Ka * (ANGLEobs -ANGLEidl)**2)
                 E_tors  = Sum ( Kt * (PHIobs   -PHIidl)**2  )
                 E_vdw   = Lennard-Jones 6-12 potential
                 E_bond  = 10-12 potential

Installation


   Copy file makecif.tar.gz

   and uncompress it (`gunzip makecif.tar.gz')  

   After untaring `makecif.tar' ( command: tar xvf makecif.tar ), 
   you will get a makecif directory with src, dic, and bin subdirectories
   and README file. 
   To build the executable, go in src subdirectory.
   Define compiler: setenv BLANC_FORT
   for example:

     for linux and mac:
   setenv BLANC_FORT "f77 -fno-globals -fno-automatic -O1 -w"
      for linux intel compiler:
   setenv BLANC_FORT "ifort -static -O1"
      for mac ibm compiler:
   setenv BLANC_FORT " xlf -qextname -qarch=auto -qtune=auto -qstrict -O3"
      else
   setenv BLANC_FORT "f77  -O1"

  1. `make makecif_all', the executable (makecif) will finish up in the bin
      directory; providing the full pathname (.../makecif/bin/makecif) one 
      can execute it from anywhere without having to define and environmental
      variable.

  2. `make libcheck_all' for libcheck program
  
  3. `make modcheck_all' for modcheck program
  
  4. `make emin_all' for emin program
  
  

PDB file format

CRYST1

  This record defines cell dimensions and space group symmetry
  corresponding to this crystal.

  Record Format

COLUMNS       DATA TYPE      FIELD         DEFINITION
-------------------------------------------------------------
 1 -  6       Record name    "CRYST1"
 7 - 15       Real(9.3)      a             a (Angstroms).
16 - 24       Real(9.3)      b             b (Angstroms).
25 - 33       Real(9.3)      c             c (Angstroms).
34 - 40       Real(7.2)      alpha         alpha (degrees).
41 - 47       Real(7.2)      beta          beta (degrees).
48 - 54       Real(7.2)      gamma         gamma (degrees).
56 - 66       LString        sGroup        Space group.

  Details

  The Hermann-Mauguin space group symbol is given without parentheses,e.g.
  P 43 21 2. Please note that the screw axis is described as a two 
  digit number.
  The full international Hermann-Mauguin symbol is used,e.g. P 1 21 1 instead
  of P 21.
  For a rhombohedral space group in the hexagonal setting, the lattice 
  type symbol used is H.

  Example:

         1         2         3         4         5         6         7       
1234567890123456789012345678901234567890123456789012345678901234567890123456789
CRYST1   76.560   55.400   84.650  90.00 116.53  90.00 P 1 21 1

SCALEn

 The SCALEn (n = 1, 2, or 3) records present the transformation from the
 orthogonal coordinates as contained in the entry to fractional 
 crystallographic coordinates.

 Record Format

COLUMNS       DATA TYPE      FIELD          DEFINITION
----------------------------------------------------------------
 1 -  6       Record name    "SCALEn"       n=1, 2, or 3
11 - 20       Real(10.6)     s[n][1]        Sn1
21 - 30       Real(10.6)     s[n][2]        Sn2
31 - 40       Real(10.6)     s[n][3]        Sn3
46 - 55       Real(10.5)     u[n]           Un

 Details


  The standard orthogonal Angstroms coordinate system used by the PDB is
  related to the axial system of the unit cell supplied (CRYST1 record) by the
  following definition:
  If vector a, vector b, vector c describe the crystallographic cell edges, and
  vector A, vector B, vector C are unit cell vectors in the default orthogonal
  Angstroms system, then vector A, vector B, vector C and vector a, vector b,
  vector c have the same origin; vector A is parallel to vector a, vector B is
  parallel to vector C times vector A, and vector C is parallel to vector a
  times vector b (i.e. vector c*).
  If the orthogonal Angstroms coordinates are X, Y, Z, and the fractional cell
  coordinates are xfrac, yfrac, zfrac, then:

   xfrac = S11X + S12Y + S13Z + U1
   yfrac = S21X + S22Y + S23Z + U2
   zfrac = S31X + S32Y + S33Z + U3

  For NMR, fiber diffraction - fiber sample, and theoretical model entries,
  SCALE is given as an identity matrix with no translation.


SSBOND

  The SSBOND record identifies each disulfide bond in protein and polypeptide
  structures by identifying the two residues involved in the bond.

  Record Format

  COLUMNS       DATA TYPE       FIELD          DEFINITION
----------------------------------------------------------------------------
 1 -  6       Record name     "SSBOND"
 8 - 10       Integer         serNum         Serial number.
12 - 14       LString(3)      "CYS"          Residue name.
16            Character       chainID1       Chain identifier.
18 - 21       Integer         seqNum1        Residue sequence number.
22            AChar           icode1         Insertion code.
26 - 28       LString(3)      "CYS"          Residue name.
30            Character       chainID2       Chain identifier.
32 - 35       Integer         seqNum2        Residue sequence number.
36            AChar           icode2         Insertion code.
60 - 65       SymOP           sym1           Symmetry operator for 1st residue.
67 - 72       SymOP           sym2           Symmetry operator for 2nd residue.

  Example:

         1         2         3         4         5         6         7       
1234567890123456789012345678901234567890123456789012345678901234567890123456789
SSBOND   1 CYS E   48    CYS E   51                          2555

  Details

  Bond distances between the sulfur atoms must be close to expected values.
  The cysteine closer to the N-terminal is listed first in each intra-chain
  pair.
  The cysteine which occurs first in the coordinate entry is listed first for
  inter-chain pairs.
  sym1 and sym2 are given as blank when the identity operator (and no cell
  translation) is to be applied to the residue.

LINK

  The LINK records specify connectivity between residues that is not implied by
  the primary structure. Connectivity is expressed in terms of the atom names.

  Record Format

  COLUMNS        DATA TYPE       FIELD       DEFINITION
-----------------------------------------------------------------------------
 1 -  6        Record name     "LINK  "
13 - 16        Atom            name1       Atom name.
17             Character       altLoc1     Alternate location indicator.
18 - 20        Residue name    resName1    Residue name.
22             Character       chainID1    Chain identifier.
23 - 26        Integer         resSeq1     Residue sequence number.
27             AChar           iCode1      Insertion code.
30 - 40        Real            Distance    Distance between atoms if 
                                           not defined in the dictionary
                                             (F10.5)
43 - 46        Atom            name2       Atom name.
47             Character       altLoc2     Alternate location indicator.
48 - 50        Residue name    resName2    Residue name.
52             Character       chainID2    Chain identifier.
53 - 56        Integer         resSeq2     Residue sequence number.
57             AChar           iCode2      Insertion code.
60 - 65        SymOP           sym1        Symmetry operator for 1st atom.
67 - 72        SymOP           sym2        Symmetry operator for 2nd atom.
73 - 80        LinkID          name1       Reference to link described
                                           in the dictionary
  Example:

         1         2         3         4         5         6         7       
1234567890123456789012345678901234567890123456789012345678901234567890123456789
LINK        MN    MN   391                 OE2 GLU   217            2565

   Details

   The atoms involved in bonds between HET groups or between a HET group
   and standard residue are listed.
   Interresidue linkages not implied by the primary structure are listed 
   e.g.reduced peptide bond).
   Non-standard linkages between residues, e.g.side-chain to side-chain, are
   listed.
   Each LINK record specifies one linkage.
   sym1 and sym2 are given as blank when the identity operator (and no cell
   translation) is to be applied to the atom.

   Note that Distance and LinkID columns are not in pdb definition. They are
   specific to refmac and makecif

CISPEP

   CISPEP records specify the prolines and other peptides found to be in the 
   cis conformation. 

   Record Format

COLUMNS       DATA TYPE       FIELD        DEFINITION
-------------------------------------------------------------------------
 1 -  6       Record name     "CISPEP"
 8 - 10       Integer         serNum       Record serial number.
12 - 14       LString(3)      pep1         Residue name.
16            Character       chainID1     Chain identifier.
18 - 21       Integer         seqNum1      Residue sequence number.
22            AChar           icode1       Insertion code.
26 - 28       LString(3)      pep2         Residue name.
30            Character       chainID2     Chain identifier.
32 - 35       Integer         seqNum2      Residue sequence number.
36            AChar           icode2       Insertion code.
44 - 46       Integer         modNum       Identifies the specific model.
54 - 59       Real(6.2)       measure      Measure of the angle in
                                           degrees.
  Example:

         1         2         3         4         5         6         7       
1234567890123456789012345678901234567890123456789012345678901234567890123456789
SSBOND   1 CYS E   48    CYS E   51                          2555

ATOM

   The ATOM records present the atomic coordinates for standard residues. They
   also present the occupancy and temperature factor for each atom. Heterogen
   coordinates use the HETATM record type. The element symbol is always
   present on each ATOM record; segment identifier and charge are optional.

   Record Format

COLUMNS        DATA TYPE       FIELD         DEFINITION
---------------------------------------------------------------------------
 1 -  6        Record name     "ATOM  "
 7 - 11        Integer         serial        Atom serial number.
13 - 16        Atom            name          Atom name.
17             Character       altLoc        Alternate location indicator.
18 - 20        Residue name    resName       Residue name.
22             Character       chainID       Chain identifier.
23 - 26        Integer         resSeq        Residue sequence number.
27             AChar           iCode         Code for insertion of residues.
31 - 38        Real(8.3)       x             Orthogonal coordinates for X in
                                             Angstroms.
39 - 46        Real(8.3)       y             Orthogonal coordinates for Y in
                                             Angstroms.
47 - 54        Real(8.3)       z             Orthogonal coordinates for Z in
                                             Angstroms.
55 - 60        Real(6.2)       occupancy     Occupancy.
61 - 66        Real(6.2)       tempFactor    Temperature factor.
73 - 76        LString(4)      segID         Segment identifier,left-justified.
77 - 78        LString(2)      element       Element symbol, right-justified.
79 - 80        LString(2)      charge        Charge on the atom.

   Details

   ATOM records for proteins are listed from amino to carboxyl terminus.
   Nucleic acid residues are listed from the 5' to the 3' terminus.
   No ordering is specified for polysaccharides.
   The list of ATOM records in a chain is terminated by a TER record.
   If more than one model is present in the entry, each model is delimited by
   MODEL and ENDMDL records.
   If an atom is provided in more than one position, then a non-blank alternate
   location indicator must be used as the alternate location indicator 
   for each of the positions. Within a residue all atoms that are associated
   with each other in a given conformation are assigned the same alternate
   position indicator.

ANISOU

 The ANISOU records present the anisotropic temperature factors.

 Record Format

COLUMNS        DATA TYPE       FIELD         DEFINITION
----------------------------------------------------------------------
 1 -  6        Record name     "ANISOU"
 7 - 11        Integer         serial        Atom serial number.
13 - 16        Atom            name          Atom name.
17             Character       altLoc        Alternate location
                                             indicator.
18 - 20        Residue name    resName       Residue name.
22             Character       chainID       Chain identifier.
23 - 26        Integer         resSeq        Residue sequence number.
27             AChar           iCode         Insertion code.
29 - 35        Integer         u[0][0]       U(1,1)
36 - 42        Integer         u[1][1]       U(2,2)
43 - 49        Integer         u[2][2]       U(3,3)
50 - 56        Integer         u[0][1]       U(1,2)
57 - 63        Integer         u[0][2]       U(1,3)
64 - 70        Integer         u[1][2]       U(2,3)
73 - 76        LString(4)      segID         Segment identifier,left-justified.
77 - 78        LString(2)      element       Element symbol,right-justified.
79 - 80        LString(2)      charge        Charge on the atom.

 Details

 Columns 7 - 27 and 73 - 80 are identical to the corresponding
 ATOM/HETATM record.
 The anisotropic temperature factors (columns 29 - 70) are scaled by a factor
 of 10**4 (Angstroms**2) and are presented as integers.
 The anisotropic temperature factors are stored in the same coordinate frame as
 the atomic coordinate records.

MODRES

  MODRES is mainly used to avoid 3 letter limitation of the pdb residue names. 
  Using this record one can change residue names for longer name (maximum 8 
  character) which is present in the dictionary file. It could also be used for
  any other modifications described in the dictionary.
  Example:
         1         2         3         4         5         6         7       
1234567890123456789012345678901234567890123456789012345678901234567890123456789
MODRES      DTT A  950  DTT_oxd                                         RENAME

  It means that residue number 950 of chain A is DTT in pdb but it should be
  interpreted as DTT_oxd which is present in dictionary (either supplied by us
  or created by user).
  Note that as all pdb records it is formatted also. Maximum length for 
  renamed residue is 8 characters.

TER
    termination record.

Example of Batch file

# --------------------------------
makecif <<stop
# --------------------------------
# first line :   "_DOC  <N>,Y,A "
#   N - means without DOC-file: "makecif.doc"
#   Y - create new file or rewrite if it is old file
#   A - means to keep old contents and add new information
#
_DOC  Y
#
#   input-coord-file
_FILE_C input.pdb
#
#      Keywords:
#
_spec Y
_END
stop

Example of input file

HEADER    HYDROLASE (ENDORIBONUCLEASE)            13-DEC-90   2SAR  
COMPND    RIBONUCLEASE SA (E.C.3.1.4.8) COMPLEX WITH 3*-*GUANYLIC ACID
LINK             LEU A   8     .               THR A  95                gap
SSBOND   1 CYS A    7    CYS A   96
CRYST1   64.900   78.320   38.790  90.00  90.00  90.00 P 21 21 21
SCALE1      0.015410  0.000000  0.000000        0.00000
SCALE2      0.000000  0.012770  0.000000        0.00000
SCALE3      0.000000  0.000000  0.025780        0.00000
ATOM      1  N   GLY A   4      49.878  12.391   1.471  1.00 22.84           N
ATOM      2  CA  GLY A   4      50.392  12.195   0.095  1.00 21.44           C
ATOM      3  C   GLY A   4      51.497  11.105   0.311  1.00 19.35           C
ATOM      4  O   GLY A   4      51.732  10.714   1.491  1.00 20.07           O
ATOM      5  N   THR A   5      51.943  10.633  -0.833  1.00 18.80           N
ATOM      6  CA  THR A   5      52.978   9.591  -1.068  1.00 18.48           C
ATOM      7  CB  THR A   5      52.579   8.524  -2.141  1.00 21.50           C
ATOM      8  OG1 THR A   5      51.306   7.990  -1.553  1.00 28.23           O
ATOM      9  CG2 THR A   5      53.417   7.313  -2.468  1.00 22.70           C
ATOM     10  C   THR A   5      54.245  10.338  -1.481  1.00 19.87           C
ATOM     11  O   THR A   5      54.107  11.414  -2.140  1.00 22.07           O
ATOM     12  N   VAL A   6      55.411   9.885  -1.065  1.00 14.29           N
ATOM     13  CA  VAL A   6      56.674  10.584  -1.455  1.00 11.27           C
ATOM     14  CB  VAL A   6      57.267  11.521  -0.387  1.00 14.08           C
ATOM     15  CG1 VAL A   6      57.506  10.835   0.953  1.00 13.75           C
ATOM     16  CG2 VAL A   6      58.601  12.152  -0.891  1.00 14.03           C
ATOM     17  C   VAL A   6      57.604   9.394  -1.863  1.00  9.96           C
ATOM     18  O   VAL A   6      57.589   8.352  -1.143  1.00 10.60           O
ATOM     19  N   CYS A   7      58.299   9.593  -2.933  1.00  9.43           N
ATOM     20  CA  CYS A   7      59.230   8.491  -3.295  1.00  8.16           C
ATOM     21  CB  CYS A   7      59.862   8.875  -4.600  1.00 11.22           C
ATOM     22  SG  CYS A   7      58.674   8.605  -5.948  1.00 13.06           S
ATOM     23  C   CYS A   7      60.328   8.445  -2.226  1.00  8.81           C
ATOM     24  O   CYS A   7      60.665   9.500  -1.695  1.00 12.60           O
ATOM     25  N   LEU A   8      60.830   7.282  -1.929  1.00 10.42           N
ATOM     26  CA  LEU A   8      61.948   7.038  -1.028  1.00  8.80           C
ATOM     27  CB  LEU A   8      62.273   5.519  -1.032  1.00  6.35           C
ATOM     31  C   LEU A   8      63.189   7.895  -1.465  1.00 12.21           C
ATOM     32  O   LEU A   8      63.958   8.546  -0.697  1.00 12.18           O
ATOM     33  N   THR A  95      59.269   2.156  -4.288  1.00 11.37           N
ATOM     34  CA  THR A  95      59.482   1.757  -5.679  1.00 11.20           C
ATOM     35  CB  THR A  95      58.110   1.160  -6.309  1.00 12.23           C
ATOM     36  OG1 THR A  95      57.309   2.337  -6.623  1.00 15.52           O
ATOM     37  CG2 THR A  95      57.400   0.169  -5.394  1.00  8.57           C
ATOM     38  C   THR A  95      60.088   2.925  -6.450  1.00 11.28           C
ATOM     39  O   THR A  95      60.392   2.774  -7.657  1.00 15.06           O
ATOM     40  N   CYS A  96      60.305   4.121  -5.923  1.00 10.25           N
ATOM     41  CA  CYS A  96      60.824   5.246  -6.657  1.00 12.91           C
ATOM     42  CB  CYS A  96      59.596   5.973  -7.309  1.00 12.80           C
ATOM     43  SG  CYS A  96      58.398   6.673  -6.122  1.00 11.60           S
ATOM     44  C   CYS A  96      61.741   6.176  -5.847  1.00 12.25           C
ATOM     45  O   CYS A  96      61.895   5.916  -4.665  1.00 11.30           O
ATOM     46  OXT CYS A  96      62.238   7.178  -6.423  1.00 12.45           O
ATOM     47  S   SO4 A  97      70.061  18.967  18.614  1.00 22.88           S
ATOM     48  O1  SO4 A  97      69.463  17.644  18.723  1.00 21.16           O
ATOM     49  O2  SO4 A  97      69.709  19.567  17.315  1.00 21.21           O
ATOM     50  O3  SO4 A  97      71.566  19.061  18.507  1.00 20.80           O
ATOM     51  O4  SO4 A  97      69.750  20.041  19.660  1.00 24.52           O
ATOM     52  O   HOH X 215      56.967   2.009   2.365  1.00 16.42           O
ATOM     53  O   HOH X 216      54.165   2.368   0.478  1.00 31.00           O
ATOM     54  O   HOH X 217      54.400   7.181  -5.723  1.00 35.24           O
ATOM     55  O   HOH X 218      63.721   0.084   0.107  1.00 24.55           O
ATOM     56  O   HOH X 219      56.259   2.010  -9.042  1.00 31.18           O
ATOM     57  O   HOH X 220      64.250   5.840  -8.328  1.00 42.84           O
ATOM     58  O   HOH X 221      60.213  10.112  24.687  1.00 28.17           O
ATOM     59  O   HOH X 222      62.790  13.500  20.557  1.00 28.93           O

Examples of output files

These output file was prepared for input file example.

Coordinate file: new.crd

data_structure_2SAR
_entry.id  2SAR
_database_2.code_PDB  2SAR
_struct_keywords.text  'HYDROLASE (ENDORIBONUCLEASE)'
_struct.title  'RIBONUCLEASE SA (E.C.3.1.4.8) COMPLEX WITH 3*-*GUANYLIC ACID '
_audit.creation_date  1990-12-13
_software.name  blanc
############
## ENTITY ##
############
loop_
_entity.id
_entity.type
AA    polypeptide
SO4   non-polymer
HOH   water
#####################
## ENTITY_POLY_SEQ ##
#####################
loop_
_entity_poly_seq.mon_id
_entity_poly_seq.ccp4_auth_seq_id
_entity_poly_seq.entity_id
_entity_poly_seq.ccp4_back_connect_type
_entity_poly_seq.ccp4_num_mon_back
_entity_poly_seq.ccp4_mod_id
#
 GLY         4  AA .        n/a   NH3
 THR         5  AA TRANS       4  .
 VAL         6  AA TRANS       5  .
 CYS         7  AA TRANS       6  .
 LEU         8  AA TRANS       7  .
 THR        95  AA gap         8  .
 CYS        96  AA TRANS      95  COO
#################
## ENTITY_LINK ##
#################
loop_
_entity_link.ccp4_link_id
_entity_link.ccp4_entity_id
_entity_link.ccp4_comp_id_1
_entity_link.ccp4_auth_seq_id_1
_entity_link.ccp4_atom_id_1
_entity_link.ccp4_comp_id_2
_entity_link.ccp4_auth_seq_id_2
_entity_link.ccp4_atom_id_2
_entity_link.dist
 SS       AA   CYS         7  SG    CYS        96  SG    .
##########
## CELL ##
##########
_cell.entry  2SAR
_cell.length_a       64.900
_cell.length_b       78.320
_cell.length_c       38.790
_cell.angle_alpha    90.000
_cell.angle_beta     90.000
_cell.angle_gamma    90.000
##############################
## FRACTIONALISATION MATRIX ##
##############################
_atom_sites.fract_transf_matrix[1][1]    0.015410
_atom_sites.fract_transf_matrix[1][2]    0.000000
_atom_sites.fract_transf_matrix[1][3]    0.000000
_atom_sites.fract_transf_matrix[2][1]    0.000000
_atom_sites.fract_transf_matrix[2][2]    0.012770
_atom_sites.fract_transf_matrix[2][3]    0.000000
_atom_sites.fract_transf_matrix[3][1]    0.000000
_atom_sites.fract_transf_matrix[3][2]    0.000000
_atom_sites.fract_transf_matrix[3][3]    0.025780
_atom_sites.fract_transf_vector[1]    0.000000
_atom_sites.fract_transf_vector[2]    0.000000
_atom_sites.fract_transf_vector[3]    0.000000
##############
## SYMMETRY ##
##############
_symmetry.entry.id  2SAR
_symmetry.space_group_name_H-M  'P 21 21 21'
_symmetry.Int_Tables_number     19
loop_
_symmetry_equiv.id
_symmetry_equiv.pos_as_xyz
  1  +X,+Y,+Z,
  2  1/2-X,-Y,1/2+Z,
  3  -X,1/2+Y,1/2-Z,
  4  1/2+X,1/2-Y,-Z,
#################
## STRUCT_ASYM ##
#################
loop_
_struct_asym.id
_struct_asym.entity_id
AA  AA
Aa  SO4
XX  HOH
###############
## ATOM_SITE ##
###############
loop_
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.auth_seq_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.type_symbol
_atom_site.calc_flag
     1 N    . GLY      AA    4    49.878   12.391    1.471  1.00  22.84 N    .
     2 CA   . GLY      AA    4    50.392   12.195    0.095  1.00  21.44 C    .
     3 C    . GLY      AA    4    51.497   11.105    0.311  1.00  19.35 C    .
     4 O    . GLY      AA    4    51.732   10.714    1.491  1.00  20.07 O    .
     5 N    . THR      AA    5    51.943   10.633   -0.833  1.00  18.80 N    .
     6 CA   . THR      AA    5    52.978    9.591   -1.068  1.00  18.48 C    .
     7 CB   . THR      AA    5    52.579    8.524   -2.141  1.00  21.50 C    .
     8 OG1  . THR      AA    5    51.306    7.990   -1.553  1.00  28.23 O    .
     9 CG2  . THR      AA    5    53.417    7.313   -2.468  1.00  22.70 C    .
    10 C    . THR      AA    5    54.245   10.338   -1.481  1.00  19.87 C    .
    11 O    . THR      AA    5    54.107   11.414   -2.140  1.00  22.07 O    .
    12 N    . VAL      AA    6    55.411    9.885   -1.065  1.00  14.29 N    .
    13 CA   . VAL      AA    6    56.674   10.584   -1.455  1.00  11.27 C    .
    14 CB   . VAL      AA    6    57.267   11.521   -0.387  1.00  14.08 C    .
    15 CG1  . VAL      AA    6    57.506   10.835    0.953  1.00  13.75 C    .
    16 CG2  . VAL      AA    6    58.601   12.152   -0.891  1.00  14.03 C    .
    17 C    . VAL      AA    6    57.604    9.394   -1.863  1.00   9.96 C    .
    18 O    . VAL      AA    6    57.589    8.352   -1.143  1.00  10.60 O    .
    19 N    . CYS      AA    7    58.299    9.593   -2.933  1.00   9.43 N    .
    20 CA   . CYS      AA    7    59.230    8.491   -3.295  1.00   8.16 C    .
    21 CB   . CYS      AA    7    59.862    8.875   -4.600  1.00  11.22 C    .
    22 SG   . CYS      AA    7    58.674    8.605   -5.948  1.00  13.06 S    .
    23 C    . CYS      AA    7    60.328    8.445   -2.226  1.00   8.81 C    .
    24 O    . CYS      AA    7    60.665    9.500   -1.695  1.00  12.60 O    .
    25 N    . LEU      AA    8    60.830    7.282   -1.929  1.00  10.42 N    .
    26 CA   . LEU      AA    8    61.948    7.038   -1.028  1.00   8.80 C    .
    27 CB   . LEU      AA    8    62.273    5.519   -1.032  1.00   6.35 C    .
    28 CG   . LEU      AA    8     0.000    0.000    0.000  0.00   0.00 C    M
    29 CD1  . LEU      AA    8     0.000    0.000    0.000  0.00   0.00 C    M
    30 CD2  . LEU      AA    8     0.000    0.000    0.000  0.00   0.00 C    M
    31 C    . LEU      AA    8    63.189    7.895   -1.465  1.00  12.21 C    .
    32 O    . LEU      AA    8    63.958    8.546   -0.697  1.00  12.18 O    .
    33 N    . THR      AA   95    59.269    2.156   -4.288  1.00  11.37 N    .
    34 CA   . THR      AA   95    59.482    1.757   -5.679  1.00  11.20 C    .
    35 CB   . THR      AA   95    58.110    1.160   -6.309  1.00  12.23 C    .
    36 OG1  . THR      AA   95    57.309    2.337   -6.623  1.00  15.52 O    .
    37 CG2  . THR      AA   95    57.400    0.169   -5.394  1.00   8.57 C    .
    38 C    . THR      AA   95    60.088    2.925   -6.450  1.00  11.28 C    .
    39 O    . THR      AA   95    60.392    2.774   -7.657  1.00  15.06 O    .
    40 N    . CYS      AA   96    60.305    4.121   -5.923  1.00  10.25 N    .
    41 CA   . CYS      AA   96    60.824    5.246   -6.657  1.00  12.91 C    .
    42 CB   . CYS      AA   96    59.596    5.973   -7.309  1.00  12.80 C    .
    43 SG   . CYS      AA   96    58.398    6.673   -6.122  1.00  11.60 S    .
    44 C    . CYS      AA   96    61.741    6.176   -5.847  1.00  12.25 C    .
    45 O    . CYS      AA   96    61.895    5.916   -4.665  1.00  11.30 O    .
    46 OXT  . CYS      AA   96    62.238    7.178   -6.423  1.00  12.45 O    .
    47 S    . SO4      Aa   97    70.061   18.967   18.614  1.00  22.88 S    .
    48 O1   . SO4      Aa   97    69.463   17.644   18.723  1.00  21.16 O    .
    49 O2   . SO4      Aa   97    69.709   19.567   17.315  1.00  21.21 O    .
    50 O3   . SO4      Aa   97    71.566   19.061   18.507  1.00  20.80 O    .
    51 O4   . SO4      Aa   97    69.750   20.041   19.660  1.00  24.52 O    .
    52 O    . HOH      XX  215    56.967    2.009    2.365  1.00  16.42 O    .
    53 O    . HOH      XX  216    54.165    2.368    0.478  1.00  31.00 O    .
    54 O    . HOH      XX  217    54.400    7.181   -5.723  1.00  35.24 O    .
    55 O    . HOH      XX  218    63.721    0.084    0.107  1.00  24.55 O    .
    56 O    . HOH      XX  219    56.259    2.010   -9.042  1.00  31.18 O    .
    57 O    . HOH      XX  220    64.250    5.840   -8.328  1.00  42.84 O    .
    58 O    . HOH      XX  221    60.213   10.112   24.687  1.00  28.17 O    .
    59 O    . HOH      XX  222    62.790   13.500   20.557  1.00  28.93 O    .
Chemical structure file: new.str
global_
_entry.id         2SAR
_audit.creation_date    13-DEC-90
_struct.title  'RIBONUCLEASE SA (E.C.3.1.4.8) COMPLEX WITH 3*-*GUANYLIC AC'
#
data_struct_list
loop_
_atom_type.symbol
_atom_type.scat_Cromer_Mann_a1
_atom_type.scat_Cromer_Mann_a2
_atom_type.scat_Cromer_Mann_a3
_atom_type.scat_Cromer_Mann_a4
_atom_type.scat_Cromer_Mann_b1
_atom_type.scat_Cromer_Mann_b2
_atom_type.scat_Cromer_Mann_b3
_atom_type.scat_Cromer_Mann_b4
_atom_type.scat_Cromer_Mann_c
_atom_type.scat_dispersion_real
_atom_type.scat_dispersion_imag
_atom_type.radius_contact
  N     12.21260   3.13220   2.01250   1.16630
         0.00570   9.89330  28.99750   0.58260
       -11.52900   0.02900   0.01800   0.00000
  C      2.31000   1.02000   1.58860   0.86500
        20.84390  10.20750   0.56870  51.65120
         0.21560   0.01700   0.00900   0.00000
  O      3.04850   2.28680   1.54630   0.86700
        13.27710   5.70110   0.32390  32.90890
         0.25080   0.04700   0.03200   0.00000
  S      6.29150   3.03530   1.98910   1.54100
         2.43860  32.33370   0.67850  81.69370
         1.14070   0.24400   0.33000   0.00000
loop_
_struct_atom.serial_number
_struct_atom.chem_type
_struct_atom.hydrogen_type
_struct_atom.PDB_res_id
_struct_atom.back
_struct_atom.forward
_struct_atom.extra
_struct_atom.psi_id
_struct_atom.distance
_struct_atom.theta
_struct_atom.psi
_struct_atom.radius
_struct_atom.ion_radius
    1 NT3  D    4     -1     2     0 .      -1.00   -1.00    0.00   1.60   1.32
    2 CH2  N    4      1     3     0 .       1.48   -1.00    0.00   1.92   0.00
    3 C    N    4      2     5     0 .       1.57  112.50    0.00   1.75   0.00
    4 O    A    4      3     0     0 cO5T    1.27  120.80 -173.09   1.52   1.28
    5 NH1  D    5      3     6     0 vl      1.32  111.64  170.14   1.60   1.32
    6 CH1  N    5      5    10     0 vll     1.49  128.66 -179.66   1.95   0.00
    7 CH1  N    5      6     9     0 Co1C    1.57  110.50 -122.63   1.95   0.00
    8 OH1  B    5      7     0     0 Co1C    1.50  109.60  117.40   1.52   1.28
    9 CH3  N    5      7     0     0 vv      1.51  110.50 -174.96   1.94   0.00
   10 C    N    5      6    12     0 vll     1.53  111.20 -102.91   1.75   0.00
   11 O    A    5     10     0     0 cO5T    1.27  120.80 -175.66   1.52   1.28
   12 NH1  D    6     10    13     0 vl      1.32  118.70  143.02   1.60   1.32
   13 CH1  N    6     12    17     0 vll     1.50  120.28  179.63   1.95   0.00
   14 CH1  N    6     13    16     0 Co1C    1.54  111.50 -125.07   1.95   0.00
   15 CH3  N    6     14     0     0 Co1C    1.52  110.50 -123.26   1.94   0.00
   16 CH3  N    6     14     0     0 vv      1.56  110.50  178.14   1.94   0.00
   17 C    N    6     13    19     0 vll     1.56  111.20 -135.03   1.75   0.00
   18 O    A    6     17     0     0 cO5T    1.27  120.80 -179.08   1.52   1.28
   19 NH1  D    7     17    20     0 vl      1.29  114.76  137.41   1.60   1.32
   20 CH1  N    7     19    23     0 vll     1.49  115.11  177.44   1.95   0.00
   21 CH2  N    7     20    22     0 Co1C    1.50  110.50 -115.85   1.92   0.00
   22 S    A    7     21     0     0 vv      1.82  114.40  -76.34   1.88   0.40
   23 C    N    7     20    25     0 vll     1.53  111.20  -67.93   1.75   0.00
   24 O    A    7     23     0     0 cO5T    1.23  120.80 -179.12   1.52   1.28
   25 NH1  D    8     23    26     0 vl      1.30  117.54  147.00   1.60   1.32
   26 CH1  N    8     25    31     0 vll     1.46  125.95  174.67   1.95   0.00
   27 CH2  N    8     26    28     0 Co1C    1.55  110.50 -122.56   1.92   0.00
   28 CH1  N    8     27    30     0 vv      1.53  116.30    0.00   1.95   0.00
   29 CH3  N    8     28     0     0 Co1C    1.52  110.70    0.00   1.94   0.00
   30 CH3  N    8     28     0     0 vv      1.52  110.70    0.00   1.94   0.00
   31 C    N    8     26    -1     0 vll     1.57  111.20  -53.91   1.75   0.00
   32 O    A    8     31     0     0 vf1     1.27  120.80  136.78   1.52   1.28
   33 NH1  D   95     -1    34     0 .      -1.00   -1.00    0.00   1.60   1.32
   34 CH1  N   95     33    38     0 .       1.46   -1.00    0.00   1.95   0.00
   35 CH1  N   95     34    37     0 Co1C    1.62  110.50 -127.20   1.95   0.00
   36 OH1  B   95     35     0     0 Co1C    1.46  109.60  124.19   1.52   1.28
   37 CH3  N   95     35     0     0 vv      1.52  110.50  -45.78   1.94   0.00
   38 C    N   95     34    40     0 .       1.53  111.20    0.00   1.75   0.00
   39 O    A   95     38     0     0 cO5T    1.25  120.80 -179.13   1.52   1.28
   40 NH1  D   96     38    41     0 vl      1.33  123.74   -3.31   1.60   1.32
   41 CH1  N   96     40    44     0 vll     1.44  124.17 -177.27   1.95   0.00
   42 CH2  N   96     41    43     0 Co1C    1.57  110.50 -127.44   1.92   0.00
   43 S    A   96     42     0     0 vv      1.83  114.40   63.21   1.88   0.40
   44 C    N   96     41    46     0 vll     1.54  111.20 -145.39   1.75   0.00
   45 OC   A   96     44     0     0 Co1P    1.22  121.00  180.00   1.52   1.28
   46 OC   A   96     44    -1     0 vv      1.26  121.00  179.67   1.52   1.28
   47 S    A   97     -1    51     0 .      -1.00   -1.00    0.00   1.88   0.40
   48 OS   A   97     47     0     0 CO7S    1.46  120.19  132.82   1.52   1.28
   49 OS   A   97     47     0     0 CO8S    1.47  105.54 -102.60   1.52   1.28
   50 OS   A   97     47     0     0 .       1.51  101.94    0.00   1.52   1.28
   51 OS   A   97     47    -1     0 .       1.53  101.94    0.00   1.52   1.28
   52 OH2  B  215     -1     0     0 .      -1.00   -1.00    0.00   1.52   1.28
   53 OH2  B  216     -1     0     0 .      -1.00   -1.00    0.00   1.52   1.28
   54 OH2  B  217     -1     0     0 .      -1.00   -1.00    0.00   1.52   1.28
   55 OH2  B  218     -1     0     0 .      -1.00   -1.00    0.00   1.52   1.28
   56 OH2  B  219     -1     0     0 .      -1.00   -1.00    0.00   1.52   1.28
   57 OH2  B  220     -1     0     0 .      -1.00   -1.00    0.00   1.52   1.28
   58 OH2  B  221     -1     0     0 .      -1.00   -1.00    0.00   1.52   1.28
   59 OH2  B  222     -1     0     0 .      -1.00   -1.00    0.00   1.52   1.28
Restrain file: new.rst
global_
_entry.id   2SAR
_struct.keywords   'HYDROLASE (ENDORIBONUCLEASE)'
_autid.creation_date   13-DEC-90
_struct.title     'RIBONUCLEASE SA (E.C.3.1.4.8) COMPLEX'
_lib.name     mon_lib
_lib.version  3.0
_lib.update   31/05/00
# ------------------------------------------------
data_restraints
#
loop_
#
_restr.record
_restr.number
_restr.label
_restr.period
_restr.atom_id_1
_restr.atom_id_2
_restr.atom_id_3
_restr.atom_id_4
_restr.value
_restr.dev
_restr.val_obs
_restr.dist
_restr.dist_dev
_restr.econst
# data_restr_GLY______0004-_AA
BOND      1 coval    .        1     2     .     .    1.491    0.021    1.482
    .        .     422.000 # N     CA
BOND      2 coval    .        2     3     .     .    1.516    0.018    1.567
    .        .     405.000 # CA    C
BOND      3 coval    .        3     4     .     .    1.231    0.020    1.265
    .        .     580.000 # C     O
ANGL      1 .        .        1     2     3     .  112.500    2.900  102.042
   2.500    0.042   70.000 # N     CA    C
ANGL      2 .        .        2     3     4     .  120.800    2.100  118.329
   2.393    0.025   85.000 # CA    C     O
# link_'TRANS   '_GLY______0004-_AA-THR______0005-_AA
BOND      4 coval    .        3     5     .     .    1.329    0.014    1.316
    .        .     471.000 # C     N
ANGL      3 .        .        4     3     5     .  123.000    1.600  129.584
   2.250    0.017   65.000 # O     C     N
ANGL      4 .        .        2     3     5     .  116.200    2.000  111.644
   2.417    0.026   20.000 # CA    C     N
ANGL      5 .        .        3     5     6     .  121.700    1.800  128.663
   2.435    0.021   80.000 # C     N     CA
TORS      1 psi      2        1     2     3     5  160.000   30.000  170.141
   3.645    0.076    0.000 # N     CA    C     N
TORS      2 omega    1        2     3     5     6  180.000   10.000 -179.661
   3.796    0.007   10.000 # CA    C     N     CA
TORS      3 phi      3        3     5     6    10   60.000   20.000 -102.910
   3.004    0.158    0.000 # C     N     CA    C
PLAN      1 plane1   .     2 . . .    0.020 .   -0.010 . . . # CA
PLAN      1 plane1   .     3 . . .    0.020 .    0.039 . . . # C
PLAN      1 plane1   .     4 . . .    0.020 .   -0.015 . . . # O
PLAN      1 plane1   .     5 . . .    0.020 .   -0.014 . . . # N
# data_restr_THR______0005-_AA
BOND      5 coval    .        5     6     .     .    1.458    0.019    1.488
    .        .     422.000 # N     CA
BOND      6 coval    .        6     7     .     .    1.540    0.027    1.565
    .        .     200.000 # CA    CB
BOND      7 coval    .        7     8     .     .    1.433    0.016    1.501
    .        .     320.000 # CB    OG1
BOND      8 coval    .        7     9     .     .    1.521    0.033    1.509
    .        .     200.000 # CB    CG2
BOND      9 coval    .        6    10     .     .    1.525    0.021    1.528
    .        .     405.000 # CA    C
BOND     10 coval    .       10    11     .     .    1.231    0.020    1.269
    .        .     580.000 # C     O
ANGL      6 .        .        7     6    10     .  110.100    1.900  111.073
   2.512    0.029   70.000 # CB    CA    C
ANGL      7 .        .        5     6     7     .  110.500    1.700  114.117
   2.464    0.025   65.000 # N     CA    CB
ANGL      8 .        .        8     7     9     .  103.300    2.000  105.694
   2.317    0.032   50.000 # OG1   CB    CG2
ANGL      9 .        .        6     7     8     .  109.600    1.500  100.973
   2.430    0.022   50.000 # CA    CB    OG1
ANGL     10 .        .        6     7     9     .  110.500    1.700  123.666
   2.515    0.026   45.000 # CA    CB    CG2
ANGL     11 .        .        5     6    10     .  111.200    2.800  106.095
   2.462    0.041   70.000 # N     CA    C
ANGL     12 .        .        6    10    11     .  120.800    1.700  117.691
   2.401    0.020   85.000 # CA    C     O
TORS      4 chi1     3        5     6     7     9  180.000   15.000 -174.956
   3.803    0.017    2.000 # N     CA    CB    CG2
CHIR      1 negativ  .        6     5     7    10    2.520    0.020   -2.627
    .        .     122.628 # CA    N     CB    C
CHIR      2 positiv  .        7     6     8     9    2.722    0.020    2.570
    .        .    -117.400 # CB    CA    OG1   CG2
# link_'TRANS   '_THR______0005-_AA-VAL______0006-_AA
BOND     11 coval    .       10    12     .     .    1.329    0.014    1.318
    .        .     471.000 # C     N
ANGL     13 .        .       11    10    12     .  123.000    1.600  123.456
   2.250    0.017   65.000 # O     C     N
ANGL     14 .        .        6    10    12     .  116.200    2.000  118.700
   2.425    0.026   20.000 # CA    C     N
ANGL     15 .        .       10    12    13     .  121.700    1.800  120.276
   2.435    0.021   80.000 # C     N     CA
TORS      5 psi      2        5     6    10    12  160.000   30.000  143.023
   3.644    0.077    0.000 # N     CA    C     N
TORS      6 omega    1        6    10    12    13  180.000   10.000  179.631
   3.804    0.007   10.000 # CA    C     N     CA
TORS      7 phi      3       10    12    13    17   60.000   20.000 -135.031
   3.004    0.158    0.000 # C     N     CA    C
PLAN      2 plane1   .     6 . . .    0.020 .   -0.007 . . . # CA
PLAN      2 plane1   .    10 . . .    0.020 .    0.023 . . . # C
PLAN      2 plane1   .    11 . . .    0.020 .   -0.008 . . . # O
PLAN      2 plane1   .    12 . . .    0.020 .   -0.008 . . . # N
# data_restr_VAL______0006-_AA
BOND     12 coval    .       12    13     .     .    1.458    0.019    1.495
    .        .     422.000 # N     CA
BOND     13 coval    .       13    14     .     .    1.540    0.027    1.540
    .        .     200.000 # CA    CB
BOND     14 coval    .       14    15     .     .    1.521    0.033    1.524
    .        .     200.000 # CB    CG1
BOND     15 coval    .       14    16     .     .    1.521    0.033    1.560
    .        .     200.000 # CB    CG2
BOND     16 coval    .       13    17     .     .    1.525    0.021    1.565
    .        .     405.000 # CA    C
BOND     17 coval    .       17    18     .     .    1.231    0.020    1.267
    .        .     580.000 # C     O
ANGL     16 .        .       14    13    17     .  109.100    2.200  114.513
   2.497    0.034   70.000 # CB    CA    C
ANGL     17 .        .       12    13    14     .  111.500    1.700  115.404
   2.479    0.025   65.000 # N     CA    CB
ANGL     18 .        .       15    14    16     .  110.800    2.200  109.396
   2.504    0.033   45.000 # CG1   CB    CG2
ANGL     19 .        .       13    14    15     .  110.500    1.700  113.343
   2.515    0.026   45.000 # CA    CB    CG1
ANGL     20 .        .       13    14    16     .  110.500    1.700  110.588
   2.515    0.026   45.000 # CA    CB    CG2
ANGL     21 .        .       12    13    17     .  111.200    2.800  102.387
   2.462    0.041   70.000 # N     CA    C
ANGL     22 .        .       13    17    18     .  120.800    1.700  118.069
   2.401    0.020   85.000 # CA    C     O
TORS      8 chi1     3       12    13    14    16  180.000   15.000  178.136
   3.812    0.017    2.000 # N     CA    CB    CG2
CHIR      3 negativ  .       13    12    14    17    2.519    0.020   -2.601
    .        .     125.069 # CA    N     CB    C
CHIR      4 negativ  .       14    13    15    16    2.622    0.020   -2.631
    .        .     123.263 # CB    CA    CG1   CG2
# link_'TRANS   '_VAL______0006-_AA-CYS______0007-_AA
BOND     18 coval    .       17    19     .     .    1.329    0.014    1.291
    .        .     471.000 # C     N
ANGL     23 .        .       18    17    19     .  123.000    1.600  127.165
   2.250    0.017   65.000 # O     C     N
ANGL     24 .        .       13    17    19     .  116.200    2.000  114.758
   2.425    0.026   20.000 # CA    C     N
ANGL     25 .        .       17    19    20     .  121.700    1.800  115.110
   2.435    0.021   80.000 # C     N     CA
TORS      9 psi      2       12    13    17    19  160.000   30.000  137.405
   3.644    0.077    0.000 # N     CA    C     N
TORS     10 omega    1       13    17    19    20  180.000   10.000  177.436
   3.804    0.007   10.000 # CA    C     N     CA
TORS     11 phi      3       17    19    20    23   60.000   20.000  -67.927
   3.004    0.158    0.000 # C     N     CA    C
PLAN      3 plane1   .    13 . . .    0.020 .   -0.001 . . . # CA
PLAN      3 plane1   .    17 . . .    0.020 .    0.005 . . . # C
PLAN      3 plane1   .    18 . . .    0.020 .   -0.002 . . . # O
PLAN      3 plane1   .    19 . . .    0.020 .   -0.002 . . . # N
# data_restr_CYS______0007-_AA
BOND     19 coval    .       19    20     .     .    1.458    0.019    1.488
    .        .     422.000 # N     CA
BOND     20 coval    .       20    21     .     .    1.530    0.020    1.500
    .        .     200.000 # CA    CB
BOND     21 coval    .       21    22     .     .    1.808    0.023    1.817
    .        .     450.000 # CB    SG
BOND     22 coval    .       20    23     .     .    1.525    0.021    1.533
    .        .     405.000 # CA    C
BOND     23 coval    .       23    24     .     .    1.231    0.020    1.228
    .        .     580.000 # C     O
ANGL     26 .        .       21    20    23     .  110.100    1.900  108.208
   2.504    0.029   70.000 # CB    CA    C
ANGL     27 .        .       19    20    21     .  110.500    1.700  106.605
   2.455    0.025   65.000 # N     CA    CB
ANGL     28 .        .       20    21    22     .  114.400    2.300  109.381
   2.810    0.036   50.000 # CA    CB    SG
ANGL     29 .        .       19    20    23     .  111.200    2.800  107.509
   2.462    0.041   70.000 # N     CA    C
ANGL     30 .        .       20    23    24     .  120.800    1.700  118.173
   2.401    0.020   85.000 # CA    C     O
TORS     12 chi1     3       19    20    21    22  180.000   15.000  -76.342
   4.104    0.019    2.000 # N     CA    CB    SG
CHIR      5 negativ  .       20    19    21    23    2.503    0.020   -2.814
    .        .     115.848 # CA    N     CB    C
# link_'TRANS   '_CYS______0007-_AA-LEU______0008-_AA
BOND     24 coval    .       23    25     .     .    1.329    0.014    1.301
    .        .     471.000 # C     N
ANGL     31 .        .       24    23    25     .  123.000    1.600  124.285
   2.250    0.017   65.000 # O     C     N
ANGL     32 .        .       20    23    25     .  116.200    2.000  117.536
   2.425    0.026   20.000 # CA    C     N
ANGL     33 .        .       23    25    26     .  121.700    1.800  125.954
   2.435    0.021   80.000 # C     N     CA
TORS     13 psi      2       19    20    23    25  160.000   30.000  146.996
   3.644    0.077    0.000 # N     CA    C     N
TORS     14 omega    1       20    23    25    26  180.000   10.000  174.674
   3.804    0.007   10.000 # CA    C     N     CA
TORS     15 phi      3       23    25    26    31   60.000   20.000  -53.906
   3.004    0.158    0.000 # C     N     CA    C
PLAN      4 plane1   .    20 . . .    0.020 .   -0.002 . . . # CA
PLAN      4 plane1   .    23 . . .    0.020 .    0.005 . . . # C
PLAN      4 plane1   .    24 . . .    0.020 .   -0.002 . . . # O
PLAN      4 plane1   .    25 . . .    0.020 .   -0.001 . . . # N
# data_restr_LEU______0008-_AA
BOND     25 coval    .       25    26     .     .    1.458    0.019    1.457
    .        .     422.000 # N     CA
BOND     26 coval    .       26    27     .     .    1.530    0.020    1.554
    .        .     200.000 # CA    CB
BOND     27 coval    .       26    31     .     .    1.525    0.021    1.570
    .        .     405.000 # CA    C
BOND     28 coval    .       31    32     .     .    1.231    0.020    1.267
    .        .     580.000 # C     O
ANGL     34 .        .       27    26    31     .  110.100    1.900  111.572
   2.504    0.029   70.000 # CB    CA    C
ANGL     35 .        .       25    26    27     .  110.500    1.700  108.835
   2.455    0.025   65.000 # N     CA    CB
ANGL     36 .        .       25    26    31     .  111.200    2.800  110.067
   2.462    0.041   70.000 # N     CA    C
ANGL     37 .        .       26    31    32     .  120.800    1.700  126.268
   2.401    0.020   85.000 # CA    C     O
CHIR      6 negativ  .       26    25    27    31    2.503    0.020   -2.663
    .        .     122.560 # CA    N     CB    C
# data_restr_THR______0095-_AA
BOND     29 coval    .       33    34     .     .    1.458    0.019    1.463
    .        .     422.000 # N     CA
BOND     30 coval    .       34    35     .     .    1.540    0.027    1.624
    .        .     200.000 # CA    CB
BOND     31 coval    .       35    36     .     .    1.433    0.016    1.458
    .        .     320.000 # CB    OG1
BOND     32 coval    .       35    37     .     .    1.521    0.033    1.524
    .        .     200.000 # CB    CG2
BOND     33 coval    .       34    38     .     .    1.525    0.021    1.525
    .        .     405.000 # CA    C
BOND     34 coval    .       38    39     .     .    1.231    0.020    1.254
    .        .     580.000 # C     O
ANGL     38 .        .       35    34    38     .  110.100    1.900  114.918
   2.512    0.029   70.000 # CB    CA    C
ANGL     39 .        .       33    34    35     .  110.500    1.700  110.258
   2.464    0.025   65.000 # N     CA    CB
ANGL     40 .        .       36    35    37     .  103.300    2.000  113.469
   2.317    0.032   50.000 # OG1   CB    CG2
ANGL     41 .        .       34    35    36     .  109.600    1.500  104.535
   2.430    0.022   50.000 # CA    CB    OG1
ANGL     42 .        .       34    35    37     .  110.500    1.700  113.569
   2.515    0.026   45.000 # CA    CB    CG2
ANGL     43 .        .       33    34    38     .  111.200    2.800  109.247
   2.462    0.041   70.000 # N     CA    C
ANGL     44 .        .       34    38    39     .  120.800    1.700  119.388
   2.401    0.020   85.000 # CA    C     O
TORS     16 chi1     3       33    34    35    37  180.000   15.000  -45.778
   3.803    0.017    2.000 # N     CA    CB    CG2
CHIR      7 negativ  .       34    33    35    38    2.520    0.020   -2.556
    .        .     127.196 # CA    N     CB    C
CHIR      8 positiv  .       35    34    36    37    2.722    0.020    2.649
    .        .    -124.193 # CB    CA    OG1   CG2
# link_'TRANS   '_THR______0095-_AA-CYS______0096-_AA
BOND     35 coval    .       38    40     .     .    1.329    0.014    1.325
    .        .     471.000 # C     N
ANGL     45 .        .       39    38    40     .  123.000    1.600  116.866
   2.250    0.017   65.000 # O     C     N
ANGL     46 .        .       34    38    40     .  116.200    2.000  123.741
   2.425    0.026   20.000 # CA    C     N
ANGL     47 .        .       38    40    41     .  121.700    1.800  124.167
   2.435    0.021   80.000 # C     N     CA
TORS     17 psi      2       33    34    38    40  160.000   30.000   -3.309
   3.644    0.077    0.000 # N     CA    C     N
TORS     18 omega    1       34    38    40    41  180.000   10.000 -177.268
   3.804    0.007   10.000 # CA    C     N     CA
TORS     19 phi      3       38    40    41    44   60.000   20.000 -145.385
   3.004    0.158    0.000 # C     N     CA    C
PLAN      5 plane1   .    34 . . .    0.020 .   -0.002 . . . # CA
PLAN      5 plane1   .    38 . . .    0.020 .    0.004 . . . # C
PLAN      5 plane1   .    39 . . .    0.020 .   -0.001 . . . # O
PLAN      5 plane1   .    40 . . .    0.020 .   -0.001 . . . # N
# data_restr_CYS______0096-_AA
BOND     36 coval    .       40    41     .     .    1.458    0.019    1.440
    .        .     422.000 # N     CA
BOND     37 coval    .       41    42     .     .    1.530    0.020    1.569
    .        .     200.000 # CA    CB
BOND     38 coval    .       42    43     .     .    1.808    0.023    1.826
    .        .     450.000 # CB    SG
BOND     39 coval    .       41    44     .     .    1.525    0.021    1.537
    .        .     405.000 # CA    C
BOND     40 coval    .       44    45     .     .    1.231    0.020    1.220
    .        .     580.000 # C     O
BOND     41 coval    .       44    46     .     .    1.231    0.020    1.258
    .        .     580.000 # C     OXT
ANGL     48 .        .       42    41    44     .  110.100    1.900  113.928
   2.504    0.029   70.000 # CB    CA    C
ANGL     49 .        .       40    41    42     .  110.500    1.700  106.960
   2.455    0.025   65.000 # N     CA    CB
ANGL     50 .        .       41    42    43     .  114.400    2.300  114.904
   2.810    0.036   50.000 # CA    CB    SG
ANGL     51 .        .       40    41    44     .  111.200    2.800  114.787
   2.462    0.041   70.000 # N     CA    C
ANGL     52 .        .       41    44    45     .  121.000    3.000  117.189
   2.403    0.035   85.000 # CA    C     O
ANGL     53 .        .       41    44    46     .  121.000    3.000  118.454
   2.403    0.035   85.000 # CA    C     OXT
TORS     20 chi1     3       40    41    42    43  180.000   15.000   63.207
   4.104    0.019    2.000 # N     CA    CB    SG
TORS     21 psi      2       40    41    44    46  160.000   30.000  179.673
   3.588    0.069    0.000 # N     CA    C     OXT
CHIR      9 negativ  .       41    40    42    44    2.503    0.020   -2.395
    .        .     127.437 # CA    N     CB    C
PLAN      6 oxt      .    44 . . .    0.020 .    0.015 . . . # C
PLAN      6 oxt      .    41 . . .    0.020 .   -0.004 . . . # CA
PLAN      6 oxt      .    45 . . .    0.020 .   -0.005 . . . # O
PLAN      6 oxt      .    46 . . .    0.020 .   -0.005 . . . # OXT
# data_restr_SO4______0097-_Aa
BOND     42 coval    .       47    48     .     .    1.460    0.020    1.456
    .        .     525.000 # S     O1
BOND     43 coval    .       47    49     .     .    1.460    0.020    1.474
    .        .     525.000 # S     O2
BOND     44 coval    .       47    50     .     .    1.460    0.020    1.512
    .        .     525.000 # S     O3
BOND     45 coval    .       47    51     .     .    1.460    0.020    1.531
    .        .     525.000 # S     O4
ANGL     54 .        .       49    47    50     .  109.470    3.000   98.634
   2.384    0.044  140.000 # O2    S     O3
ANGL     55 .        .       50    47    51     .  109.470    3.000  101.943
   2.384    0.044  140.000 # O3    S     O4
ANGL     56 .        .       49    47    51     .  109.470    3.000  105.544
   2.384    0.044  140.000 # O2    S     O4
ANGL     57 .        .       48    47    49     .  109.470    3.000  109.750
   2.384    0.044  140.000 # O1    S     O2
ANGL     58 .        .       48    47    50     .  109.470    3.000  118.079
   2.384    0.044  140.000 # O1    S     O3
ANGL     59 .        .       48    47    51     .  109.470    3.000  120.191
   2.384    0.044  140.000 # O1    S     O4
# link_'SS      '_CYS______0007-_AA-CYS______0096-_AA
BOND     46 disulf   .       22    43     .     .    2.031    0.020    1.960
    .        .     500.000 # SG    SG
ANGL     60 .        .       21    22    43     .  110.000    3.000  107.729
   3.147    0.057   50.000 # CB    SG    SG
ANGL     61 .        .       22    43    42     .  110.000    3.000  110.080
   3.147    0.057   50.000 # SG    SG    CB
TORS     22 ss       2       21    22    43    42   90.000   10.000  -90.361
   4.056    0.124    3.500 # CB    SG    SG    CB