REFMAC (CCP4: Supported Program)

User's manual for the program REFMAC, version 5.*

Input and output files - Coordinate files

For a complete description of the PDB file see the PDB guide - Format Description Version 2.3. Here only short descriptions of the records used by REFMAC are given. REFMAC will use MODRES, SSBOND, LINK and CISPEP records to define restraints used in refinement; this is dependent on the MAKE_restraints keyword input. There are some CCP4-specific extensions to the standard definitions, which are shown in red below.

Note that PDB is a formatted file, so care should be taken when edited manually. Both the order of the records, and the placing of characters in the correct column within a record, is important. The easiest way to enter restraints or review and edit the restraints in a file, is using the CCP4I task 'Edit Restraints in PDB File'.

PDB records recognised by REFMAC

When the program reads a PDB file, it uses the following records from PDB:

ANISOU
ATOM
CISPEP
CRYST1
LINK
MODRES
SCALE
SSBOND
TER

Summary of CCP4-specific features

The standard residue name field in the MODRES record is expanded to 6 characters (the extension is into columns normally used for comment).
An additional ID field in the MODRES record to cross-reference to the list of modifications in the CCP4 libraries.
An additional ID field in the LINK record to cross-reference to the list of links in the CCP4 libraries.
REFMAC will always check the input symmetry operations for SSBOND and LINK records. If both the input operations are 1555 (i.e. the identity operator) or are missing, then REFMAC will treat the bond as being within the same asymmetric unit but if the input suggests the bond is between asymmetric units (e.g. input 1555 and 2555), it will perform a search of all the neighbouring asymmetric units to find the correct bond. REFMAC will output the correct symmetry operations to the PDB file.

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:

CRYST1   76.560   55.400   84.650  90.00 116.53  90.00 P 1 21 1

MODRES

MODRES is mainly used to avoid the 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:

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.

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. Non-standard coordinate systems should be explained in the remarks.

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.

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.
The SSBOND record does not have fields for alternate location indicators. The solution to this is to use a LINK record to define a disulphide bridge between atoms which have alternate conformations and to give the LINK ID 'SS'.

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. This record supplements information given in CONECT records and is provided here for convenience in searching.

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.

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          linkid      Cross-reference to LINK definition in CCP4 libraries

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.
These records do not specify connectivity within a HET group (see CONECT), hydrogen bonds (see HYDBND), or disulfide bridges (see SSBOND).
Hydrogen bonds and salt bridges are described on HYDBND and SLTBRG records, respectively.
sym1 and sym2 are given as blank when the identity operator (and no cell translation) is to be applied to the atom.
For NMR entries only one set (or model) of LINK records will be supplied

CISPEP

CISPEP records specify the prolines and other peptides found to be in the cis conformation. This record replaces the use of footnote records to list cis peptides.

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.

Details

Cis peptides are those with omega angles of 0°±30°. Deviations larger than 30° are listed in REMARK 500.
Each cis peptide is listed on a separate line, with an incrementally ascending sequence number.

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.
For more information on atom naming conventions, see Appendix 3, and for residue names, see Appendix 4 and the HET section of this document.
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.
For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/HETATM list uses the following general rules:

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.
ANISOU values are listed only if they have been provided by the depositor.

TER

termination record. More information to follow.