############################################################### ############################################################### ############################################################### ### CCP4 6.0: Refmac_5.2.0019 version 5.2.0019 : 06/09/05## ############################################################### User: chris Run date: 1/10/2008 Run time: 11:43:59 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 NONE Data line--- make hydrogen YES hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO Data line--- refi type REST resi MLKF meth CGMAT bref ISOT Data line--- ncyc 20 Data line--- scal type BULK reso 2.300 166.667 LSSC ANISO EXPE Data line--- solvent YES VDWProb 1.2 IONProb 0.8 RSHRink 0.8 Data line--- weight MATRIX 0.08 Data line--- monitor MEDIUM torsion 10.0 distance 10.0 angle 10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere 10.0 rbond 10.0 ncsr 10.0 Data line--- labin FP=F_combined_Hr_Lr SIGFP=SIGF_combined_Hr_Lr FREE=FreeR_flag Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM Data line--- PNAME SSADH Data line--- DNAME combined_Hr_Lr Data line--- RSIZE 80 Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /Users/chris/SSADH/AS_march08/Comb_ccp4/SSADH_comb_P4_scala2.mtz Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /usr/local/lib/solve//syminfo.lib **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - /Users/chris/SSADH/AS_march08/Comb_ccp4/Refmac92_molprobity_flip-coot-1.pdb Output coordinate file. Logical name - XYZOUT actual file name - /tmp/chris/SSADH_comb_94_2_pdb_1.tmp Input reflection file. Logical name - HKLIN actual file name - /Users/chris/SSADH/AS_march08/Comb_ccp4/SSADH_comb_P4_scala2.mtz Output reflection file. Logical name - HKLOUT actual file name - /tmp/chris/SSADH_comb_94_4_mtz_1.tmp Cell from mtz : 151.885 151.885 165.772 90.000 90.000 90.000 Space group from mtz: number - 90; name - P 4 21 2 Refinement type : Restrained **** Makecif parameters **** Dictionary files for restraints : /usr/local/ccp4-6.0.2/lib/data/monomers/mon*cif Parameters for new entry and VDW: /usr/local/ccp4-6.0.2/lib/data/monomers/ener_lib.cif Program will rely on residue and atom names. No checking If this option is used then monomers should be checked carefully before using Hydrogens in input coordinate file will be kept Links between monomers will be checked. Only those links present in the coordinate file will be used 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 Bulk solvent based on Babinet"s principle 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 0.0095 Refinement of individual isotropic Bfactors Refinement resln : 166.6667 2.3000 Estimated number of reflections : 104863 Free R exclusion - flag equals: 0 Weighting by comparison of trace of matrix Weighting parameters : 0.0800 Refinement cycles : 20 Scaling type : Bulk solvent using using Babinet principle using working set of reflns and 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: 166.6670 2.3000 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 :/Users/chris/SSADH/AS_march08/Comb_ccp4/Refmac92_molprobity_flip-c ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 4.11 _lib_update 15/04/05 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 2432 with complete description : 449 NUMBER OF MODIFICATIONS : 46 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: /usr/local/ccp4-6.0.2/lib/data/atomsf.lib Number of atoms : 15192 Number of residues : 2457 Number of chains : 9 I am reading library. Please wait. mon_lib.cif WARNING : TRANS peptide bond (not be changed CIS) angle = 163.08 ch:DD res: 2 LEU --> 3 ASN WARNING : TRANS peptide bond (not be changed CIS) angle = 172.56 ch:DD res: 4 ASP --> 5 SER WARNING : CIS peptide bond is found, angle = 65.32 ch:DD res: 5 SER --> 6 ASN WARNING : TRANS peptide bond (not be changed CIS) angle = 165.53 ch:DD res: 134 GLN --> 135 ALA WARNING : CIS peptide bond is found, angle = 15.29 ch:DD res: 135 ALA --> 136 ASP WARNING : TRANS peptide bond (not be changed CIS) angle = 160.03 ch:DD res: 355 CYS --> 356 GLY WARNING : CIS peptide bond is found, angle = 7.56 ch:DD res: 356 GLY --> 357 GLY WARNING : TRANS peptide bond (not be changed CIS) angle = 173.75 ch:DD res: 362 ARG --> 363 GLY WARNING : CIS peptide bond is found, angle = 8.72 ch:DD res: 363 GLY --> 364 GLY INFO: link is found (not be used) dist= 1.694 ideal_dist= 1.400 ch:BB res: 279 LYS at:NZ .->ch:BB res: 389 LEU at:O . -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:XX-XXX-9- -------------------------------- ATTENTION: atom:CG LYS AA 357 is missing in the structure ATTENTION: atom:CD LYS AA 357 is missing in the structure ATTENTION: atom:CE LYS AA 357 is missing in the structure ATTENTION: atom:NZ LYS AA 357 is missing in the structure ATTENTION: atom:CG GLU BB 332 is missing in the structure ATTENTION: atom:CD GLU BB 332 is missing in the structure ATTENTION: atom:OE1 GLU BB 332 is missing in the structure ATTENTION: atom:OE2 GLU BB 332 is missing in the structure ATTENTION: atom:CG GLU CC 332 is missing in the structure ATTENTION: atom:CD GLU CC 332 is missing in the structure ATTENTION: atom:OE1 GLU CC 332 is missing in the structure ATTENTION: atom:OE2 GLU CC 332 is missing in the structure ATTENTION: atom:CE LYS CC 333 is missing in the structure ATTENTION: atom:NZ LYS CC 333 is missing in the structure ATTENTION: atom:CG GLU CC 409 is missing in the structure ATTENTION: atom:CD GLU CC 409 is missing in the structure ATTENTION: atom:OE1 GLU CC 409 is missing in the structure ATTENTION: atom:OE2 GLU CC 409 is missing in the structure ATTENTION: atom:CG GLU DD 333 is missing in the structure ATTENTION: atom:CD GLU DD 333 is missing in the structure ... and more ... WARNING : atom :P2B NAP EE 1 is absent in the library WARNING : atom :O2B NAP EE 1 is absent in the library WARNING : atom :C2B NAP EE 1 is absent in the library WARNING : atom :C3B NAP EE 1 is absent in the library WARNING : atom :O3B NAP EE 1 is absent in the library WARNING : atom :C1B NAP EE 1 is absent in the library WARNING : atom :N9A NAP EE 1 is absent in the library WARNING : atom :C8A NAP EE 1 is absent in the library WARNING : atom :N7A NAP EE 1 is absent in the library WARNING : atom :C5A NAP EE 1 is absent in the library WARNING : atom :C4A NAP EE 1 is absent in the library WARNING : atom :N3A NAP EE 1 is absent in the library WARNING : atom :C2A NAP EE 1 is absent in the library WARNING : atom :N1A NAP EE 1 is absent in the library WARNING : atom :C6A NAP EE 1 is absent in the library WARNING : atom :N6A NAP EE 1 is absent in the library WARNING : atom :O4B NAP EE 1 is absent in the library WARNING : atom :C4B NAP EE 1 is absent in the library WARNING : atom :C5B NAP EE 1 is absent in the library WARNING : atom :O5B NAP EE 1 is absent in the library ... and more ... Number of chains : 9 Total number of monomers : 2457 Number of atoms : 15407 Number of missing atoms : 215 Number of rebuilt atoms : 0 Number of unknown atoms : 176 Number of deleted atoms : 0 Number of bonds restraints : 14731 Number of angles restraints : 19940 Number of torsions restraints : 10034 Number of chiralities : 2231 Number of planar groups : 2638 IERR = 1 There is error. See above ===> Error: Fatal error. Cannot continue Refmac_5.2.0019: Fatal error. Cannot continue Times: User: 57.1s System: 0.8s Elapsed: 0:59 *************************************************************************** * Information from CCP4Interface script *************************************************************************** The program run with command: refmac5 XYZIN "/Users/chris/SSADH/AS_march08/Comb_ccp4/Refmac92_molprobity_flip-coot-1.pdb" XYZOUT "/tmp/chris/SSADH_comb_94_2_pdb_1.tmp" HKLIN "/Users/chris/SSADH/AS_march08/Comb_ccp4/SSADH_comb_P4_scala2.mtz" HKLOUT "/tmp/chris/SSADH_comb_94_4_mtz_1.tmp" LIBOUT "/Users/chris/SSADH/AS_march08/Comb_ccp4/SSADH_comb_94_lib.cif" has failed with error message Refmac_5.2.0019: Fatal error. Cannot continue *************************************************************************** #CCP4I TERMINATION STATUS 0 Refmac_5.2.0019: Fatal error. Cannot continue #CCP4I TERMINATION TIME 01 Oct 2008 11:44:58 #CCP4I MESSAGE Task failed