############################################################### ############################################################### ############################################################### ### CCP4 6.0: Refmac_5.4.0065 version 5.4.0065 : 12/02/07## ############################################################### User: ccp4 Run date: 6/ 2/2008 Run time: 15:18:12 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 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 Logical name: ATOMSF, Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/atomsf.lib 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 Refmac_5.4.0065: New ligand has been encountered. Stopping now Times: User: 3.8s System: 0.1s Elapsed: 0:04 *************************************************************************** * Information from CCP4Interface script *************************************************************************** The program run with command: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/bin/refmac_linintel XYZIN "/y/people/ccp4/projects/buccaneer/oleg/final_pdbset1_refmac1-coot-0.pdb" XYZOUT "/y/people/ccp4/projects/testing/final_pdbset1_refmac1.pdb" LIBOUT "/y/people/ccp4/projects/testing/final_pdbset1_refmac1-coot-0.cif" has failed with error message Refmac_5.4.0065: New ligand has been encountered. Stopping now *************************************************************************** #CCP4I TERMINATION STATUS 0 Refmac_5.4.0065: New ligand has been encountered. Stopping now #CCP4I TERMINATION TIME 06 Feb 2008 15:18:16 #CCP4I TERMINATION OUTPUT_FILES /y/people/ccp4/projects/testing/final_pdbset1_refmac1-coot-0.cif testing #CCP4I MESSAGE Task failed