1201_refmac5_review-orig.log

 $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: $$
 :TEXT:Reference1: $$

 Data line ---> make check ALL
 Data line ---> 
 make     hydrogen YES     hout NO     peptide YES     cispeptide YES     ssbrid
 ge YES     symmetry YES     sugar YES     connectivity YES     link YES     for
 mat f exit Y
 Data line ---> END
===> Warning: Reflections file has not been defined
===> Warning: Switching to the idealisation mode
 
    ****           Input and Default parameters#            ****
 
Input coordinate file.  Logical name - XYZIN actual file name  - /y/people/ccp4/projects/buccaneer/oleg/final_pdbset1_refmac1-coot-0.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /y/people/ccp4/projects/testing/final_pdbset1_refmac1.pdb
 
  Refinement type                        : Idealisation
 
    ****                 Makecif parameters                 ****
 
Dictionary files for restraints : /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/ener_lib.cif
    Program will check all entries against dictionary
    Hydrogens in input coordinate file will be kept
    L-D peptides will be checked and corrected
    Links between monomers will be checked and corrected
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically
 
  Method of minimisation                 : Sparse Matrix
 
  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                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)
 
 TORSION ANGLES
          Weight= 1.00
 
 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00
 
 RADIUS OF CONFIDENCE
     Positional parameters 0.30A
     Thermal parameters    0.03A**2
     Occupancy parameters  0.50
 
Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
---------------------------------------------------------------
 
 Input file :/y/people/ccp4/projects/buccaneer/oleg/final_pdbset1_refmac1-coot-
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      4.13
 _lib_update       18/01/08
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          :  2436
                with complete description    :   455
  NUMBER OF MODIFICATIONS                    :    47
  NUMBER OF LINKS                            :    64
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/syminfo.lib

  WARNING : D-peptide : LYS  203  chain:A1
  WARNING : D-peptide : LYS  204  chain:A1
  Number of atoms    :    1599
  Number of residues :     304
  Number of chains   :       2
  I am reading library. Please wait.
                mon_lib.cif

  WARNING : CIS peptide bond is found, angle =      6.48
            ch:AA   res: 204  LYS-D    --> 205  GLY
  WARNING : description of link:LYS-D-GL is not in the dictionary.
            link will be created with bond_lenth =   1.510
  WARNING : link:LYS-D-GL is found dist =     1.699 ideal_dist=     1.510
            ch:AA   res: 203  LYS-D    at:C   .->AA   res: 205  GLY      at:CA  .
  WARNING : description of link:LYS-D-GL is not in the dictionary.
            link will be created with bond_lenth =   1.240
  WARNING : link:LYS-D-GL is found dist =     1.201 ideal_dist=     1.240
            ch:AA   res: 203  LYS-D    at:O   .->AA   res: 205  GLY      at:N   .
  WARNING : description of link:LYS-D-GL is not in the dictionary.
            link will be created with bond_lenth =   1.420
  WARNING : link:LYS-D-GL is found dist =     1.183 ideal_dist=     1.420
            ch:AA   res: 203  LYS-D    at:O   .->AA   res: 205  GLY      at:CA  .

  --------------------------------
  --- title of input coord file ---
 
  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-9-
  --------------------------------
  Number of chains                  :       2
  Total number of monomers          :     304
  Number of atoms                   :    1599
  Number of missing atoms           :       0
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0
 
  Number of bonds restraints    :    1509
  Number of angles restraints   :    2033
  Number of torsions restraints :    1037
  Number of chiralities         :     213
  Number of planar groups       :     274
  I am writing new library:
  /y/people/ccp4/projects/testing/final_pdbset1_refmac1-coot-0.cif

Important, Important, Important!!!!!
 
Your coordinate file has a ligand which has either minimum or no description in the library
$$
A new ligand description has been added to /y/people/ccp4/projects/testing/final_pdbset1_refmac1-coot-0.cif
Picture of the new ligand can be viewed using postscript file. See above
Check description in this file and, if satisfied, use it as the input library
Otherwise either edit bond orders manually or use CCP4i Sketcher to view and edit the ligand
and create a library entry by running libcheck
It is strongly recommended that dictionary  entry should be checked carefully before using it
If you are happy with the library description then use the keyword (MAKE CHECK NONE)
I.e. do not check correctness of the coordinates
===> Error: New ligand has been encountered. Stopping now