#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 ############################################################### ############################################################### ############################################################### ### CCP4 5.0: Refmac_5.1.9999 5.1.9999 ########## ############################################################### 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