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[ccp4bb]: REFMAC5 and heme



hi,

i am trying to use the latest version of REFMAC5 for a protein which
contains a heme. i used residue name "HEM", and even corrected the atom
names of "FE  ", " N_A", " N_B", " N_C" and " N_D" to match the PDB
standard,  but refmac tells me that it
does not recognise my ligand.  it says my ligand resembles existing entry
"MHM" (file mon_lib_10.cif) and that it will create a new dictionary entry
for me based on that.  i don't know why it doesn't recognise my heme,
which is surely a commonly used ligand, except perhaps that the dictionary
entry (defined in file mon_lib_1.cif) contains hydrogens while my
coordinates do not.

i took a look at the documentation and there was a lot about creating new
dictionary entries by various means (sketcher, etc) but i didn't notice
anything about using existing dictionary entries, so that i guessed it
should happen automatically.(?)


i would like to know 
a) why REFMAC does not recognise my ligand as "HEM"
b) should i try to force it to recognise my heme and
c) how would i go about that?

attached are my REFMAC output, my HEM coordinates, and my script.

thank you,
 
=======================================================================
"Politicians can survive sex scandals or fiscal mismanagement,
but they cannot survive being laughed at."  - Robert Park
=======================================================================
                        David J. Schuller
                        modern man in a post-modern world
                        University of California-Irvine
                        schuller@uci.edu
<!--SUMMARY_BEGIN-->




1##########################################################
 ##########################################################
 ##########################################################
 ### CCP PROGRAM SUITE: Refmac_5.0  VERSION 4.0: 14/07/00##
 ##########################################################
 User: schuller  Run date: 26/10/00  Run time:18:26:55


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.

 as well as any specific reference in the program write-up.


<!--SUMMARY_END-->
 $TEXT:Reference1: $$ comment $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 Comment line--- #
 Data line--- LABIN FP=FP11 SIGFP=SIGFP11  FREE=FreeR_flag
 Data line--- LABO FC=FC PHIC=PHIC    FWT=2FOFCWT PHWT=PH2FOFCWT                      DELFWT=FOFCWT  PHDELWT=PHFOFCWT
 Data line--- MAKE HYDR Y
 Data line--- REFI TYPE REST
 Data line--- REFI RESI MLKF
 Data line--- REFI BREF MIXED
 Comment line--- #
 Comment line--- #
 Data line--- SCAL TYPE BULK
 Data line--- NCYC 5
 Data line--- MONI FEW
 Data line--- end
<!--SUMMARY_BEGIN-->
  (Q)QOPEN allocated #  1
 User:   schuller             Logical Name: HKLIN
 Status: READONLY   Filename: ../../mtz/gn11_free.mtz
<!--SUMMARY_END-->
 * Input Program Labels :
 
 H K L FP SIGFP FREE FPART1 PHIP1 FPART2 PHIP2 FPART3 PHIP3 HLA HLB HLC HLD FOM
 PHIB
 
 * Input File Labels :
 
 H K L FP11 SIGFP11 dum2 FreeR_flag
 
 * Lookup Table : the number indicates the input column no.
 * Array element n corresponds to the nth program label
 
     1    2    3    4    5    7    0    0    0    0    0    0    0    0    0
     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
     0    0    0    0
 
 
    ****           Input and Default parameters#            ****
 
 
Input coordinate file.  Logical name - XYZIN actual file name  - start.pdb
Output coordinate file. Logical name - XYZOUT actual file name - refm01.pdb
Input reflection file.  Logical name - HKLIN actual file name  - ../../mtz/gn11_free.mtz
Output reflection file. Logical name - HKLOUT actual file name - refm01.mtz
 
Cell from mtz :    63.167    63.167   100.378    90.000    90.000    90.000
Space group from mtz: number -   96; name - P43212
 
  Refinement type                        : Restrained
 
 
    ****                 Makecif parameters                 ****
 
Dictionary files for restraints : /usr/share/local/ccp4_master/refmac5/dic/mon*cif
Parameters for new entry and VDW: /usr/share/local/ccp4_master/refmac5/dic/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    hydrogens in input coordinate file will be kept
    Symmetry related links be analysed and used
    Cis peptides will be found and used automatically
 
 
  Residual                               : Rice Maximum Likelihood for Fs
 
    ****          Least-square scaling parameters           ****
 
Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Bulk solvent based on Babinet"s principle
Constant bulk solvent in non protein region
Probe radii for non-ions     1.400
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800
 
  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0222
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    53.4522  1.4997
  Estimated number of reflections :      39642
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.5000
  Refinement cycles       :     5
  Scaling type                           :
          Bulk solvent using using Babinet principle
  using working set of reflns but not experimental sigmas
 
  Estimation of SigmaA Using 2 Gaussians:
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas
 
  Scaling and SigmaA resln:    53.4522  1.4997
 
  Damping factors:     1.0000  1.0000
 
 
    ****          Geometry restraints and weights           ****
 
 
                                              Sigma:
 Bonding distances
          Weight =  1.00
 
 Bond angles
          Weight =  1.00
 
 Planar groups
          WEIGHT= 1.00
 
 Chiral centers
          Weight= 1.00
 
 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.30
          Sigma for VDW trhough torsion angle     =  0.50
          Sigma for HBOND                         =  0.50
          Sigma for metal-ion                     =  0.50
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+vdw2+( 0.20)
          VDW distance through torsion = vdw1+vdw2+(-0.75)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)
 
 TORSION ANGLES
          Weight= 1.00
 
 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)         1.50A**2
     Main chain angle (1-3 neighbour)        2.00A**2
     Side chain bond                         3.00A**2
     Side chain angle                        4.50A**2
 
 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.03A
     Thermal parameters                      0.03A
     Occupancy parameters                    0.20A
 
Monitoring style is "FEW". Minimum information will be printed out
---------------------------------------------------------------
 
 Input file : start.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      3.1
 _lib_update       16/07/00
  ------------------------------
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      3.1
 _lib_update       16/07/00
  ------------------------------
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      3.1
 _lib_update       16/07/00
  ------------------------------
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      3.1
 _lib_update       16/07/00
  ------------------------------
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      3.1
 _lib_update       16/07/00
  ------------------------------
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      3.1
 _lib_update       16/07/00
  ------------------------------
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      3.1
 _lib_update       16/07/00
  ------------------------------
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      3.1
 _lib_update       16/07/00
  ------------------------------
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      3.1
 _lib_update       16/07/00
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          :  2406
                with complete description    :   335
  NUMBER OF MODIFICATIONS                    :    37
  NUMBER OF LINKS                            :    62
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

 FORMATTED      OLD     file opened on unit  45
 Logical name: ATOMSF, Full name: /usr/share/local/ccp4_master/ccp4/lib/data/atomsf.lib


 FORMATTED      OLD     file opened on unit   8
 Logical name: SYMOP, Full name: /usr/share/local/ccp4_master/ccp4/lib/data/symop.lib

  WARNING: Chain_list is not correct. Program changed it.
  Number of atoms    :    1812
  Number of residues :     391
  Number of chaines  :       3
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : monomer looks like MHM     program will use this one
  WARNING : monomer has the minimal description
                          program will create complete description
  WARNING : MHM      : default angle value will used
                  chem_type : C   -O   -H     120.000 (CGD -O2D -DHO2)
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -O       0.890 (DHO2-O2D )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -H     120.000 (C4D -CHA -HHA )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -CR5   120.000 (C4D -CHA -C1A )
  WARNING : MHM      : default angle value will used
                  chem_type : H   -C   -CR5   120.000 (HHA -CHA -C1A )
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -C       1.015 (HHA -CHA )
  WARNING : MHM      : default angle value will used
                  chem_type : C   -O   -H     120.000 (CGA -O1A -AHO1)
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -O       0.890 (AHO1-O1A )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -NR5 -CR5   108.000 (C4D -N_D -C1D )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -NR5 -FE    108.000 (C4D -N_D -FE  )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -NR5 -FE    108.000 (C1D -N_D -FE  )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -H     120.000 (C1D -CHD -HHD )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -CR5   120.000 (C1D -CHD -C4C )
  WARNING : MHM      : default angle value will used
                  chem_type : H   -C   -CR5   120.000 (HHD -CHD -C4C )
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -C       1.015 (HHD -CHD )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -H     120.000 (C3C -CAC -HAC )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -C     120.000 (C3C -CAC -CBC )
  WARNING : MHM      : default angle value will used
                  chem_type : H   -C   -C     120.000 (HAC -CAC -CBC )
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -C       1.015 (HAC -CAC )
  WARNING : MHM      : default angle value will used
                  chem_type : C   -C   -H     120.000 (CAC -CBC -HBC2)
  WARNING : MHM      : default angle value will used
                  chem_type : C   -C   -H     120.000 (CAC -CBC -HBC )
  WARNING : MHM      : default angle value will used
                  chem_type : H   -C   -H     120.000 (HBC2-CBC -HBC )
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -C       1.015 (HBC2-CBC )
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -C       1.015 (HBC -CBC )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -NR5 -FE    108.000 (C1C -N_C -FE  )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -NR5 -CR5   108.000 (C1C -N_C -C4C )
  WARNING : MHM      : default angle value will used
                  chem_type : FE  -NR5 -CR5   108.000 (FE  -N_C -C4C )
  WARNING : MHM      : default angle value will used
                  chem_type : NR5 -FE  -NR5   180.000 (N_C -FE  -N_A )
  WARNING : MHM      : default angle value will used
                  chem_type : NR5 -FE  -NR5    90.000 (N_C -FE  -N_B )
  WARNING : MHM      : default angle value will used
                  chem_type : NR5 -FE  -NR5    90.000 (N_C -FE  -N_D )
  WARNING : MHM      : default angle value will used
                  chem_type : NR5 -FE  -NR5    90.000 (N_A -FE  -N_B )
  WARNING : MHM      : default angle value will used
                  chem_type : NR5 -FE  -NR5    90.000 (N_A -FE  -N_D )
  WARNING : MHM      : default angle value will used
                  chem_type : NR5 -FE  -NR5   180.000 (N_B -FE  -N_D )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -H     120.000 (C1C -CHC -HHC )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -CR5   120.000 (C1C -CHC -C4B )
  WARNING : MHM      : default angle value will used
                  chem_type : H   -C   -CR5   120.000 (HHC -CHC -C4B )
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -C       1.015 (HHC -CHC )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -NR5 -CR5   108.000 (C4B -N_B -C1B )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -NR5 -FE    108.000 (C4B -N_B -FE  )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -NR5 -FE    108.000 (C1B -N_B -FE  )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -H     120.000 (C3B -CAB -HAB )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -C     120.000 (C3B -CAB -CBB )
  WARNING : MHM      : default angle value will used
                  chem_type : H   -C   -C     120.000 (HAB -CAB -CBB )
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -C       1.015 (HAB -CAB )
  WARNING : MHM      : default angle value will used
                  chem_type : C   -C   -H     120.000 (CAB -CBB -HBB2)
  WARNING : MHM      : default angle value will used
                  chem_type : C   -C   -H     120.000 (CAB -CBB -HBB )
  WARNING : MHM      : default angle value will used
                  chem_type : H   -C   -H     120.000 (HBB2-CBB -HBB )
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -C       1.015 (HBB2-CBB )
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -C       1.015 (HBB -CBB )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -H     120.000 (C1B -CHB -HHB )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -C   -CR5   120.000 (C1B -CHB -C4A )
  WARNING : MHM      : default angle value will used
                  chem_type : H   -C   -CR5   120.000 (HHB -CHB -C4A )
  WARNING : MHM      : default bond legnth will used
                  chem_type: H   -C       1.015 (HHB -CHB )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -NR5 -FE    108.000 (C4A -N_A -FE  )
  WARNING : MHM      : default angle value will used
                  chem_type : CR5 -NR5 -CR5   108.000 (C4A -N_A -C1A )
  WARNING : MHM      : default angle value will used
                  chem_type : FE  -NR5 -CR5   108.000 (FE  -N_A -C1A )
 * Plotfile: /var/tmp/refmac5_temp.04504_new_MHM.ps
  INFO:     connection is found (not be used) dist=   2.054 ideal_dist=   1.935
            ch:XX res:  23  HIS      at:NE2  --> ch:Xa res: 300  HEM      at:FE
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------

 FORMATTED      OLD     file opened on unit   8
 Logical name: SYMOP, Full name: /usr/share/local/ccp4_master/ccp4/lib/data/symop.lib

  Number of chains                  :       3
  Total number of monomers          :     391
  Number of atoms                   :    1812
  Number of missing atoms           :       0
  Number of rebuilding atoms        :       0
  Number of unknoun atoms           :       0
  Number of deleted atoms           :       0

  Number of bonds restraints    :    1669
  Number of angles restraints   :    2272
  Number of torsions restraints :    1174
  Number of chiralities         :     230
  Number of planar groups       :     294
  I am writing new library:
  new.lib
 
Important, important important!!!!!
 
Your coordinate file has ligand which either have minimum or no description
New ligand description has been added to new.lib
Picture of new ligand can be viewd using postscript file. See above
Check description in that file and if satisfied use it as input library
If not satisfied either change atom types accordingly and rerun refmac or use libcheck
See documentation "how to make new ligand" section for a help
It is strongly recommended that dictionary  entry should be checked carfully before using it
Best way of creating dictionary entry is  using sketcher whcih is part of ccp4i
If you are sure in the library description then use keyword (MAKE CHECK 0)
I.e. do not check correctness of the coordinates
===> Error: New ligand has been encountered. Stopping now
<!--SUMMARY_BEGIN-->
 Refmac_5.0.27:  New ligand has been encountered. Stopping now
 Times: User:      15.6s System:    0.5s Elapsed:    0:16
<!--SUMMARY_END-->
ATOM   1580 FE   HEM   300      14.255   7.860  19.858 1.000 20.79
ATOM   1581  N_A HEM   300      13.553   8.414  18.096 1.000 22.98
ATOM   1582  N_B HEM   300      12.525   7.036  20.336 1.000 20.26
ATOM   1583  N_C HEM   300      14.879   7.624  21.736 1.000 16.67
ATOM   1584  N_D HEM   300      15.939   8.811  19.434 1.000 20.59
ATOM   1585  C1A HEM   300      14.119   9.241  17.133 1.000 23.72
ATOM   1586  CHA HEM   300      15.481   9.537  17.115 1.000 24.14
ATOM   1587  C4D HEM   300      16.334   9.303  18.203 1.000 21.66
ATOM   1588  C1B HEM   300      11.372   7.006  19.567 1.000 23.83
ATOM   1589  CHB HEM   300      11.253   7.601  18.309 1.000 20.76
ATOM   1590  C4A HEM   300      12.343   8.016  17.553 1.000 22.91
ATOM   1591  C1C HEM   300      14.125   7.192  22.808 1.000 20.77
ATOM   1592  CHC HEM   300      12.901   6.535  22.709 1.000 24.48
ATOM   1593  C4B HEM   300      12.135   6.457  21.532 1.000 21.54
ATOM   1594  C1D HEM   300      17.090   8.878  20.205 1.000 19.95
ATOM   1595  CHD HEM   300      17.175   8.462  21.527 1.000 16.27
ATOM   1596  C4C HEM   300      16.084   8.013  22.292 1.000 18.51
ATOM   1597  C2A HEM   300      13.252   9.350  15.980 1.000 24.63
ATOM   1598  CAA HEM   300      13.390  10.278  14.780 1.000 22.74
ATOM   1599  C3A HEM   300      12.166   8.579  16.230 1.000 25.64
ATOM   1600  CMA HEM   300      10.820   8.572  15.514 1.000 28.80
ATOM   1601  CBA HEM   300      12.899  11.701  14.981 1.000 28.80
ATOM   1602  CGA HEM   300      13.158  12.564  13.754 1.000 32.61
ATOM   1603  O1A HEM   300      14.094  12.218  12.999 1.000 36.32
ATOM   1604  O2A HEM   300      12.429  13.563  13.558 1.000 33.95
ATOM   1605  C2B HEM   300      10.295   6.331  20.244 1.000 20.68
ATOM   1606  CMB HEM   300       8.980   5.934  19.567 1.000 27.93
ATOM   1607  C3B HEM   300      10.755   6.018  21.473 1.000 23.64
ATOM   1608  CAB HEM   300      10.042   5.446  22.519 1.000 23.62
ATOM   1609  CBB HEM   300       9.058   4.479  22.524 1.000 21.46
ATOM   1610  C2C HEM   300      14.926   7.105  24.009 1.000 19.04
ATOM   1611  CMC HEM   300      14.331   6.775  25.382 1.000 20.22
ATOM   1612  C3C HEM   300      16.134   7.612  23.681 1.000 19.84
ATOM   1613  CAC HEM   300      17.310   7.684  24.424 1.000 21.83
ATOM   1614  CBC HEM   300      17.528   7.477  25.761 1.000 26.87
ATOM   1615  C2D HEM   300      18.180   9.487  19.483 1.000 25.25
ATOM   1616  CMD HEM   300      19.574   9.790  20.027 1.000 21.36
ATOM   1617  C3D HEM   300      17.699   9.745  18.246 1.000 23.92
ATOM   1618  CAD HEM   300      18.373  10.537  17.144 1.000 27.29
ATOM   1619  CBD HEM   300      18.770   9.706  15.922 1.000 23.29
ATOM   1620  CGD HEM   300      19.599  10.563  14.975 1.000 30.36
ATOM   1621  O1D HEM   300      20.826  10.645  15.168 1.000 23.65
ATOM   1622  O2D HEM   300      18.994  11.155  14.063 1.000 29.19
#!/bin/csh -f
#
refmac5 \
HKLIN   ../../mtz/data_free.mtz \
HKLOUT   refm01.mtz \
XYZIN   start.pdb \
XYZOUT   refm01.pdb \
>refmac.out \
<<EOF
#
LABIN FP=FP11 SIGFP=SIGFP11  FREE=FreeR_flag
LABO FC=FC PHIC=PHIC    FWT=2FOFCWT PHWT=PH2FOFCWT -
                     DELFWT=FOFCWT  PHDELWT=PHFOFCWT
MAKE HYDR Y
REFI TYPE REST
REFI RESI MLKF
REFI BREF MIXED
#
#
SCAL TYPE BULK
NCYC 5
MONI FEW
end
EOF
#
exit