#CCP4I VERSION CCP4Interface 1.3.13
#CCP4I SCRIPT LOG refmac5
#CCP4I DATE 19 Sep 2003  10:53:56
#CCP4I USER mgwt
#CCP4I PROJECT 2003test
#CCP4I JOB_ID 174
#CCP4I SCRATCH /tmp/mgwt
#CCP4I HOSTNAME bunyip
#CCP4I PID 23418

 
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 ### CCP4 5.0: Refmac_5.1.9999    5.1.9999            ##########
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 User: mgwt  Run date: 19/ 9/2003 Run time: 10:53:57 


 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.

 $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 ALL     hout NO     peptide YES     cispeptide YES     ssbridge YES     chain YES     symmetry YES     sugar YES     connectivity YES     link YES     format f exit Y
 Comment line--- # External script file:
 Data line--- END
 
    ****           Input and Default parameters#            ****
 
 
Input coordinate file.  Logical name - XYZIN actual file name  - /y/people/mgwt/CCP4/examples/tut2003/data/rnase_bad.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /y/people/mgwt/TEST/rnase_bad_refmac3.pdb
==> WARNING: No HKLIN has been defined
Output reflection file. Logical name - HKLOUT actual file name - HKLOUT
 
Cell from mtz :     0.000     0.000     0.000     0.000     0.000     0.000
Space group from mtz: number -    1; name - P1
 
  Refinement type                        : Restrained
 
 
    ****                 Makecif parameters                 ****
 
Dictionary files for restraints : /y/programs/xtal/ccp4-5.0.d/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /y/programs/xtal/ccp4-5.0.d/lib/data/monomers/ener_lib.cif
    Program will check all entries against dictionary
    Hydrogens will be restored in their riding positions
    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
 
 
  Residual                               : Rice Maximum Likelihood for Fs
 
    ****          Least-square scaling parameters           ****
 
Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
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      -1.0000
  Refinement of individual isotropic Bfactors
  Refinement resln        :   ********  0.0500
  Estimated number of reflections :          2
  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:    12.5000  0.5000
 
  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
 
 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                   0.00A
     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
B value  outliers      10.000
---------------------------------------------------------------
 
 Input file :/y/people/mgwt/CCP4/examples/tut2003/data/rnase_bad.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      4.3
 _lib_update       11/06/03
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          :  2432
                with complete description    :   449
  NUMBER OF MODIFICATIONS                    :    43
  NUMBER OF LINKS                            :    64
  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: /y/programs/xtal/ccp4-5.0.d/lib/data/atomsf.lib

  WARNING: "SCALE" card is absent in input PDB file
  Number of atoms    :    1724
  Number of residues :     417
  Number of chains   :       5
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : residue: ASP         1  chain:AA
            atom: "N   " is absent in coord_file
  WARNING : residue: CYS        96  chain:AA
            atom: "OXT " is absent in coord_file
  WARNING : residue: CYS        96  chain:BB
            atom: "OXT " is absent in coord_file
  WARNING : CIS peptide bond is found, angle =     16.01
            ch:AA res:  26  GLY      -->  27  PRO
  WARNING : CIS peptide bond is found, angle =      9.69
            ch:BB res:  26  GLY      -->  27  PRO
  WARNING : big distance for conn:TRANS    dist =     1.747
            ch:BB   res:  73  GLY     -->  74  GLU      ideal_dist=     1.329
  WARNING : big distance for conn:TRANS    dist =     1.863
            ch:BB   res:  75  ALA     -->  76  THR      ideal_dist=     1.329
  WARNING : link:SS       is found dist =     2.017 ideal_dist=     2.031
            ch:AA res:   7  CYS      at:SG  .->AA res:  96  CYS      at:SG  .
  WARNING : description of link:ARG-ARG  not found in the dictionary.
            link will be created with bond_lenth =   1.410
  WARNING : link:ARG-ARG  is found dist =     1.320 ideal_dist=     1.410
            ch:AA res:  40  ARG      at:NH1 .->BB res:  63  ARG      at:NE  .
  WARNING : description of link:ARG-ARG1 not found in the dictionary.
            link will be created with bond_lenth =   1.260
  WARNING : link:ARG-ARG1 is found dist =     1.411 ideal_dist=     1.260
            ch:AA res:  40  ARG      at:NH1 .->BB res:  63  ARG      at:CZ  .
  WARNING : description of link:ARG-ARG2 not found in the dictionary.
            link will be created with bond_lenth =   1.410
  WARNING : link:ARG-ARG2 is found dist =     1.489 ideal_dist=     1.410
            ch:AA res:  40  ARG      at:NH1 .->BB res:  63  ARG      at:NH2 .
  WARNING : link:SS       is found dist =     2.211 ideal_dist=     2.031
            ch:BB res:   7  CYS      at:SG  .->BB res:  96  CYS      at:SG  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  WARNING : atom :N    ASP      AA   1  is missing in the structure
  WARNING : atom :HA   ASP      AA   1  is missing in the structure
  WARNING : atom :HB1  ASP      AA   1  is missing in the structure
  WARNING : atom :HB2  ASP      AA   1  is missing in the structure
  WARNING : atom :H1   ASP      AA   1  is missing in the structure
  WARNING : atom :H2   ASP      AA   1  is missing in the structure
  WARNING : atom :H3   ASP      AA   1  is missing in the structure
  WARNING : atom :HA   VAL      AA   2  is missing in the structure
  WARNING : atom :HB   VAL      AA   2  is missing in the structure
  WARNING : atom :HG11 VAL      AA   2  is missing in the structure
  WARNING : atom :HG12 VAL      AA   2  is missing in the structure
  WARNING : atom :HG13 VAL      AA   2  is missing in the structure
  WARNING : atom :HG21 VAL      AA   2  is missing in the structure
  WARNING : atom :HG22 VAL      AA   2  is missing in the structure
  WARNING : atom :HG23 VAL      AA   2  is missing in the structure
  WARNING : atom :H    VAL      AA   2  is missing in the structure
  WARNING : atom :HA   SER      AA   3  is missing in the structure
  WARNING : atom :HB1  SER      AA   3  is missing in the structure
  WARNING : atom :HB2  SER      AA   3  is missing in the structure
  WARNING : atom :HG   SER      AA   3  is missing in the structure
   ... and more ...
  Number of chains                  :       5
  Total number of monomers          :     417
  Number of atoms                   :    3567
  Number of missing atoms           :    1838
  Number of rebuilt atoms           :    1839
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0
  I am writing new library:
  /y/people/mgwt/TEST/rnase_bad.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/mgwt/TEST/rnase_bad.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
 Refmac_5.1.9999:  New ligand has been encountered. Stopping now
Times: User:       5.4s System:    0.1s Elapsed:     0:09  
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: refmac5 XYZIN /y/people/mgwt/CCP4/examples/tut2003/data/rnase_bad.pdb XYZOUT /y/people/mgwt/TEST/rnase_bad_refmac3.pdb LIBOUT /y/people/mgwt/TEST/rnase_bad.cif 
has failed with error message
 Refmac_5.1.9999:  New ligand has been encountered. Stopping now
***************************************************************************


#CCP4I TERMINATION STATUS 0  Refmac_5.1.9999:  New ligand has been encountered. Stopping now
#CCP4I TERMINATION TIME 19 Sep 2003  10:54:06
#CCP4I TERMINATION OUTPUT_FILES  /y/people/mgwt/TEST/rnase_bad.cif 2003test
#CCP4I MESSAGE Task failed