############################################################### ############################################################### ############################################################### ### CCP4 6.0: cbuccaneer version 1.0.0 : 04/10/07## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:08:08 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.Copyright 2002-2007 Kevin Cowtan and University of York. $TEXT:Reference: $$ Please reference $$ 'The Buccaneer software for automated model building' Cowtan K. (2006) Acta Cryst. D62, 1002-1011. $$ title [No title given] pdbin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.mtz colin-ref-fo /*/*/[FP.F_sigF.F,FP.F_sigF.sigF] colin-ref-hl /*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D] seqin-wrk /home/cowtan/test/1vjf.seq mtzin-wrk /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz colin-wrk-fo /*/*/[FP,SIGFP] colin-wrk-free /*/*/[FreeR_flag] colin-wrk-hl /*/*/[pirate.ABCD.A,pirate.ABCD.B,pirate.ABCD.C,pirate.ABCD.D] pdbout-wrk /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb find grow join link sequence correct filter ncsbuild prune rebuild cycles 3 sequence-reliability 0.95 new-residue-name UNK resolution 2.0 Cycle: 1 C-alphas after finding: 24 C-alphas after growing: 337 C-alphas after joining: 211 C-alphas linked: 0 C-alphas sequenced: 115 C-alphas corrected: 0 C-alphas after filtering: 211 C-alphas after NCS build: 211 C-alphas after pruning: 146 C-alphas after rebuilding: 146 Internal cycle 1 146 residues were built in 6 chains, the longest having 33 residues. 108 residues were sequenced, after pruning. Cycle: 2 C-alphas after finding: 170 C-alphas after growing: 421 C-alphas after joining: 218 C-alphas linked: 0 C-alphas sequenced: 146 C-alphas corrected: 0 C-alphas after filtering: 196 C-alphas after NCS build: 196 C-alphas after pruning: 170 C-alphas after rebuilding: 170 Internal cycle 2 170 residues were built in 5 chains, the longest having 73 residues. 128 residues were sequenced, after pruning. Cycle: 3 C-alphas after finding: 194 C-alphas after growing: 311 C-alphas after joining: 211 C-alphas linked: 1 C-alphas sequenced: 133 C-alphas corrected: 0 C-alphas after filtering: 199 C-alphas after NCS build: 199 C-alphas after pruning: 165 C-alphas after rebuilding: 165 Internal cycle 3 165 residues were built in 3 chains, the longest having 73 residues. 125 residues were sequenced, after pruning. $TEXT:Result: $$ $$ 165 residues were built in 3 chains, the longest having 73 residues. 125 residues were sequenced, after pruning. $$ cbuccaneer: Normal termination Times: User: 197.1s System: 0.4s Elapsed: 3:19 # /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/bin/refmac5 HKLIN /home/cowtan/test/1vjf-3.2A.mtz XYZIN /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb HKLOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz XYZOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
############################################################### ############################################################### ############################################################### ### CCP4 6.0: Refmac_5.3.0037 version 5.3.0037 : 03/29/06## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:11:28 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--- title [No title given] TITL Data line--- weight MATRIX 0.1 WEIG Data line--- labin HLA=pirate.ABCD.A HLB=pirate.ABCD.B HLC=pirate.ABCD.C HLD=pirate.ABCD.D FREE=FreeR_flag FP=FP SIGFP=SIGFP LABI Data line--- make check NONE MAKE Data line--- make hydrogen YES hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO MAKE Data line--- refi type REST PHASE SCBL 1.0 BBLU 0.0 resi MLKF meth CGMAT bref ISOT REFI Data line--- ncyc 10 NCYC Data line--- scal type SIMP LSSC ANISO EXPE SCAL Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8 SOLV 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 MONI Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB LABO Data line--- PNAME buccaneer PNAM Data line--- DNAME buccaneer DNAM Data line--- RSIZE 80 RSIZ Data line--- END END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /home/cowtan/test/1vjf-3.2A.mtz 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 **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb Output coordinate file. Logical name - XYZOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb Input reflection file. Logical name - HKLIN actual file name - /home/cowtan/test/1vjf-3.2A.mtz Output reflection file. Logical name - HKLOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz Cell from mtz : 50.903 50.903 121.411 90.000 90.000 90.000 Space group from mtz: number - 96; name - P43212 Refinement type : Restrained **** 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 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 : Phase modified Maximum Likelihood for Fs Phase Blurred by Scale*Exp(-B s**2) : 1.00 0.00 **** 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 1.400 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 0.0049 Refinement of individual isotropic Bfactors Refinement resln : 46.9323 3.2002 Estimated number of reflections : 3404 Free R exclusion - flag equals: 0 Weighting by comparison of trace of matrix Weighting parameters : 0.1000 Refinement cycles : 10 Scaling type : Wilson using 1 Gaussian using working set of reflns and experimental sigmas Estimation of SigmaA Using 2 Gaussians: using free set of reflns with experimental sigmas Input phases not used in SigmaA estimation Scaling and SigmaA resln: 46.9323 3.2002 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 :/home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 4.12 _lib_update 20/09/07 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 2436 with complete description : 454 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 Number of atoms : 1138 Number of residues : 165 Number of chains : 3 I am reading library. Please wait. mon_lib.cif INFO: link is found (not be used) dist= 1.389 ideal_dist= 1.500 ch:AA res: 137 ASP at:CG .->ch:BB res: 98 UNK at:CB . INFO: link is found (not be used) dist= 1.386 ideal_dist= 1.337 ch:AA res: 137 ASP at:OD1 .->ch:BB res: 98 UNK at:CB . INFO: link is found (not be used) dist= 1.364 ideal_dist= 1.337 ch:AA res: 137 ASP at:OD2 .->ch:BB res: 98 UNK at:CB . INFO: link is found (not be used) dist= 1.510 ideal_dist= 1.410 ch:BB res: 65 LYS at:NZ .->ch:BB res: 92 ARG at:NH1 . INFO: link is found (not be used) dist= 1.444 ideal_dist= 1.530 ch:CC res: 13 UNK at:CB .->ch:CC res: 18 UNK at:CB . -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:XX-XXX-XX -------------------------------- ATTENTION: atom:CB UNK 116 AA is missing in the structure ATTENTION: atom:CB UNK 123 AA is missing in the structure ATTENTION: atom:O VAL 179 AA is missing in the structure ATTENTION: atom:CB UNK 63 BB is missing in the structure ATTENTION: atom:O UNK 100 BB is missing in the structure ATTENTION: atom:O UNK 26 CC is missing in the structure Number of chains : 3 Total number of monomers : 165 Number of atoms : 1144 Number of missing atoms : 6 Number of rebuilt atoms : 0 Number of unknown atoms : 0 Number of deleted atoms : 0 Number of bonds restraints : 1154 Number of angles restraints : 1568 Number of torsions restraints : 769 Number of chiralities : 191 Number of planar groups : 205 loop_ _atom_type_symbol _atom_type_scat_Cromer_Mann_a1 _atom_type_scat_Cromer_Mann_b1 _atom_type_scat_Cromer_Mann_a2 _atom_type_scat_Cromer_Mann_b2 _atom_type_scat_Cromer_Mann_a3 _atom_type_scat_Cromer_Mann_b3 _atom_type_scat_Cromer_Mann_a4 _atom_type_scat_Cromer_Mann_b4 _atom_type_scat_Cromer_Mann_c N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290 C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156 O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508 S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 0.8669 Number of reflections in file 2948 Number of reflection read 2948 CGMAT cycle number = 1 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 107 UNK CA . - A 107 UNK C . mod.= 1.273 id.= 1.525 dev= 0.252 sig.= 0.021 A 108 UNK C . - A 109 UNK N . mod.= 1.082 id.= 1.329 dev= 0.247 sig.= 0.014 A 119 ILE C . - A 120 ASN N . mod.= 1.098 id.= 1.329 dev= 0.231 sig.= 0.014 A 143 PRO CD . - A 143 PRO N . mod.= 2.054 id.= 1.473 dev= -0.581 sig.= 0.014 A 143 PRO C . - A 144 LEU N . mod.= 1.157 id.= 1.329 dev= 0.172 sig.= 0.014 A 164 LEU C . - A 165 GLY N . mod.= 1.065 id.= 1.329 dev= 0.264 sig.= 0.014 A 168 PRO CD . - A 168 PRO N . mod.= 2.067 id.= 1.473 dev= -0.594 sig.= 0.014 B 36 UNK C . - B 37 UNK N . mod.= 1.077 id.= 1.329 dev= 0.252 sig.= 0.014 B 38 UNK C . - B 39 VAL N . mod.= 1.063 id.= 1.329 dev= 0.266 sig.= 0.014 B 53 PRO CD . - B 53 PRO N . mod.= 2.070 id.= 1.473 dev= -0.597 sig.= 0.014 B 56 HIS C . - B 57 THR N . mod.= 1.135 id.= 1.329 dev= 0.194 sig.= 0.014 B 58 LYS C . - B 59 ASN N . mod.= 0.920 id.= 1.329 dev= 0.409 sig.= 0.014 B 65 LYS C . - B 66 GLY N . mod.= 1.115 id.= 1.329 dev= 0.214 sig.= 0.014 B 74 LEU C . - B 75 GLY N . mod.= 0.684 id.= 1.329 dev= 0.645 sig.= 0.014 B 75 GLY C . - B 76 GLU N . mod.= 1.066 id.= 1.329 dev= 0.263 sig.= 0.014 B 86 HIS C . - B 87 VAL N . mod.= 1.089 id.= 1.329 dev= 0.240 sig.= 0.014 B 89 GLY C . - B 90 SER N . mod.= 1.137 id.= 1.329 dev= 0.192 sig.= 0.014 B 91 GLY N . - B 91 GLY CA . mod.= 1.200 id.= 1.458 dev= 0.258 sig.= 0.021 C 18 UNK C . - C 19 UNK N . mod.= 1.187 id.= 1.329 dev= 0.142 sig.= 0.014 C 19 UNK N . - C 19 UNK CA . mod.= 1.144 id.= 1.458 dev= 0.314 sig.= 0.021 C 19 UNK C . - C 20 UNK N . mod.= 1.117 id.= 1.329 dev= 0.212 sig.= 0.014 C 23 UNK C . - C 24 UNK N . mod.= 0.967 id.= 1.329 dev= 0.362 sig.= 0.014 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 110 UNK O - A 111 PRO N mod.= 95.24 id.= 123.00 dev= 27.757 sig.= 1.600 A 110 UNK CA - A 111 PRO N mod.= 143.93 id.= 116.90 dev=-27.030 sig.= 1.500 A 110 UNK C - A 111 PRO CD mod.= 57.78 id.= 125.00 dev= 67.217 sig.= 4.100 A 137 ASP C - A 138 PRO CD mod.= 82.23 id.= 125.00 dev= 42.771 sig.= 4.100 A 143 PRO CA - A 143 PRO CD mod.= 87.18 id.= 112.00 dev= 24.816 sig.= 1.400 A 143 PRO N - A 143 PRO CG mod.= 80.17 id.= 103.20 dev= 23.033 sig.= 1.500 A 144 LEU C - A 145 LYS CA mod.= 140.79 id.= 121.70 dev=-19.093 sig.= 1.800 A 164 LEU O - A 165 GLY N mod.= 100.92 id.= 123.00 dev= 22.076 sig.= 1.600 A 164 LEU CA - A 165 GLY N mod.= 138.22 id.= 116.20 dev=-22.020 sig.= 2.000 A 164 LEU C - A 165 GLY CA mod.= 148.71 id.= 121.70 dev=-27.006 sig.= 1.800 A 168 PRO CA - A 168 PRO CD mod.= 85.51 id.= 112.00 dev= 26.489 sig.= 1.400 A 168 PRO N - A 168 PRO CG mod.= 80.58 id.= 103.20 dev= 22.618 sig.= 1.500 B 53 PRO CA - B 53 PRO CD mod.= 85.32 id.= 112.00 dev= 26.676 sig.= 1.400 B 53 PRO N - B 53 PRO CG mod.= 80.58 id.= 103.20 dev= 22.625 sig.= 1.500 B 58 LYS O - B 59 ASN N mod.= 93.56 id.= 123.00 dev= 29.442 sig.= 1.600 B 58 LYS CA - B 59 ASN N mod.= 145.52 id.= 116.20 dev=-29.320 sig.= 2.000 B 58 LYS C - B 59 ASN CA mod.= 148.69 id.= 121.70 dev=-26.988 sig.= 1.800 B 74 LEU O - B 75 GLY N mod.= 100.90 id.= 123.00 dev= 22.099 sig.= 1.600 B 74 LEU CA - B 75 GLY N mod.= 138.20 id.= 116.20 dev=-22.001 sig.= 2.000 B 74 LEU C - B 75 GLY CA mod.= 151.95 id.= 121.70 dev=-30.253 sig.= 1.800 B 90 SER C - B 91 GLY CA mod.= 154.09 id.= 121.70 dev=-32.390 sig.= 1.800 B 91 GLY N - B 91 GLY C mod.= 147.32 id.= 112.50 dev=-34.817 sig.= 2.900 C 19 UNK N - C 19 UNK C mod.= 141.21 id.= 111.20 dev=-30.009 sig.= 2.800 C 19 UNK O - C 20 UNK N mod.= 106.68 id.= 123.00 dev= 16.315 sig.= 1.600 **** Large deviation of atoms from planarity **** Deviations from the planarity >10.000Sigma will be monitored Atom: A 111 PRO N deviation= 0.25 sigma.= 0.02 Atom: A 138 PRO N deviation= -0.35 sigma.= 0.02 Atom: A 143 PRO N deviation= -0.29 sigma.= 0.02 Atom: A 168 PRO N deviation= 0.33 sigma.= 0.02 Atom: B 52 MET C deviation= 0.21 sigma.= 0.02 Atom: B 53 PRO N deviation= -0.42 sigma.= 0.02 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored A 122 THR CB . - B 65 LYS NZ . mod.= 1.140 id.= 3.550 dev= -2.41 sig.= 0.20 sym.= 4 0 -1 0 A 122 THR CB . - B 65 LYS CE . mod.= 1.632 id.= 3.870 dev= -2.24 sig.= 0.20 sym.= 4 0 -1 0 A 122 THR CG2 . - B 65 LYS NZ . mod.= 1.286 id.= 3.540 dev= -2.25 sig.= 0.20 sym.= 4 0 -1 0 A 137 ASP CG . - B 98 UNK CB . mod.= 1.389 id.= 3.690 dev= -2.30 sig.= 0.20 sym.= 1 0 0 0 A 137 ASP OD1 . - B 98 UNK CB . mod.= 1.386 id.= 3.460 dev= -2.07 sig.= 0.20 sym.= 1 0 0 0 A 137 ASP OD2 . - B 98 UNK CB . mod.= 1.364 id.= 3.460 dev= -2.10 sig.= 0.20 sym.= 1 0 0 0 C 13 UNK CB . - C 18 UNK CB . mod.= 1.444 id.= 3.880 dev= -2.44 sig.= 0.20 sym.= 1 0 0 0 weigth matrix 0.1000000 special position ----------- 3.338314 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1154 0.055 0.022 Bond angles : refined atoms 1568 4.884 1.952 Torsion angles, period 1. refined 162 4.652 5.000 Torsion angles, period 2. refined 37 40.119 23.514 Torsion angles, period 3. refined 163 6.804 15.000 Torsion angles, period 4. refined 6 8.389 15.000 Chiral centres: refined atoms 191 0.179 0.200 Planar groups: refined atoms 861 0.031 0.020 VDW repulsions: refined atoms 668 0.563 0.200 VDW; torsion: refined atoms 815 0.350 0.200 HBOND: refined atoms 48 0.248 0.200 VDW repulsions; symmetry: refined atoms 89 0.703 0.200 HBOND; symmetry: refined atoms 4 0.364 0.200 M. chain bond B values: refined atoms 810 0.000 1.500 M. chain angle B values: refined atoms 1256 0.000 2.000 S. chain bond B values: refined atoms 344 0.000 3.000 S. chain angle B values: refined atoms 312 0.000 4.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.518, B = -41.796 Partial structure 1: scale = 0.289, B = 1.832 Overall anisotropic scale factors B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 1. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 1.
############################################################### ############################################################### ############################################################### ### CCP4 6.0: cbuccaneer version 1.0.0 : 04/10/07## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:11:37 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.Copyright 2002-2007 Kevin Cowtan and University of York. $TEXT:Reference: $$ Please reference $$ 'The Buccaneer software for automated model building' Cowtan K. (2006) Acta Cryst. D62, 1002-1011. $$ title [No title given] pdbin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.mtz colin-ref-fo /*/*/[FP.F_sigF.F,FP.F_sigF.sigF] colin-ref-hl /*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D] seqin-wrk /home/cowtan/test/1vjf.seq mtzin-wrk /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz colin-wrk-fo /*/*/[FP,SIGFP] colin-wrk-free /*/*/[FreeR_flag] colin-wrk-phifom /*/*/[PHCOMB,FOM] pdbin-wrk /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb pdbout-wrk /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb find grow join link sequence correct filter ncsbuild prune rebuild cycles 1 correlation-mode sequence-reliability 0.95 new-residue-name UNK resolution 2.0 Cycle: 1 C-alphas after finding: 189 C-alphas after growing: 355 C-alphas after joining: 213 C-alphas linked: 0 C-alphas sequenced: 149 C-alphas corrected: 2 C-alphas after filtering: 210 C-alphas after NCS build: 210 C-alphas after pruning: 175 C-alphas after rebuilding: 175 Internal cycle 1 175 residues were built in 3 chains, the longest having 84 residues. 141 residues were sequenced, after pruning. $TEXT:Result: $$ $$ 175 residues were built in 3 chains, the longest having 84 residues. 141 residues were sequenced, after pruning. $$ cbuccaneer: Normal termination Times: User: 110.4s System: 0.3s Elapsed: 1:50 # /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/bin/refmac5 HKLIN /home/cowtan/test/1vjf-3.2A.mtz XYZIN /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb HKLOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz XYZOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
############################################################### ############################################################### ############################################################### ### CCP4 6.0: Refmac_5.3.0037 version 5.3.0037 : 03/29/06## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:13:27 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--- title [No title given] TITL Data line--- weight MATRIX 0.1 WEIG Data line--- labin HLA=pirate.ABCD.A HLB=pirate.ABCD.B HLC=pirate.ABCD.C HLD=pirate.ABCD.D FREE=FreeR_flag FP=FP SIGFP=SIGFP LABI Data line--- make check NONE MAKE Data line--- make hydrogen YES hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO MAKE Data line--- refi type REST PHASE SCBL 1.0 BBLU 0.0 resi MLKF meth CGMAT bref ISOT REFI Data line--- ncyc 10 NCYC Data line--- scal type SIMP LSSC ANISO EXPE SCAL Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8 SOLV 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 MONI Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB LABO Data line--- PNAME buccaneer PNAM Data line--- DNAME buccaneer DNAM Data line--- RSIZE 80 RSIZ Data line--- END END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /home/cowtan/test/1vjf-3.2A.mtz 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 **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb Output coordinate file. Logical name - XYZOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb Input reflection file. Logical name - HKLIN actual file name - /home/cowtan/test/1vjf-3.2A.mtz Output reflection file. Logical name - HKLOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz Cell from mtz : 50.903 50.903 121.411 90.000 90.000 90.000 Space group from mtz: number - 96; name - P43212 Refinement type : Restrained **** 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 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 : Phase modified Maximum Likelihood for Fs Phase Blurred by Scale*Exp(-B s**2) : 1.00 0.00 **** 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 1.400 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 0.0049 Refinement of individual isotropic Bfactors Refinement resln : 46.9323 3.2002 Estimated number of reflections : 3404 Free R exclusion - flag equals: 0 Weighting by comparison of trace of matrix Weighting parameters : 0.1000 Refinement cycles : 10 Scaling type : Wilson using 1 Gaussian using working set of reflns and experimental sigmas Estimation of SigmaA Using 2 Gaussians: using free set of reflns with experimental sigmas Input phases not used in SigmaA estimation Scaling and SigmaA resln: 46.9323 3.2002 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 :/home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 4.12 _lib_update 20/09/07 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 2436 with complete description : 454 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 Number of atoms : 1236 Number of residues : 175 Number of chains : 3 I am reading library. Please wait. mon_lib.cif INFO: link is found (not be used) dist= 1.447 ideal_dist= 1.450 ch:AA res: 97 UNK at:N .->ch:AA res: 124 ARG at:CG . INFO: link is found (not be used) dist= 0.948 ideal_dist= 1.450 ch:AA res: 97 UNK at:N .->ch:AA res: 124 ARG at:CD . INFO: link is found (not be used) dist= 1.290 ideal_dist= 1.524 ch:AA res: 97 UNK at:CA .->ch:AA res: 124 ARG at:CD . INFO: link is found (not be used) dist= 1.643 ideal_dist= 1.510 ch:AA res: 97 UNK at:C .->ch:AA res: 124 ARG at:CD . INFO: link is found (not be used) dist= 0.991 ideal_dist= 1.339 ch:AA res: 97 UNK at:C .->ch:AA res: 124 ARG at:NE . INFO: link is found (not be used) dist= 1.589 ideal_dist= 1.460 ch:AA res: 97 UNK at:C .->ch:AA res: 124 ARG at:CZ . INFO: link is found (not be used) dist= 1.146 ideal_dist= 1.240 ch:AA res: 97 UNK at:O .->ch:AA res: 124 ARG at:NE . INFO: link is found (not be used) dist= 0.881 ideal_dist= 1.330 ch:AA res: 97 UNK at:O .->ch:AA res: 124 ARG at:CZ . INFO: link is found (not be used) dist= 1.207 ideal_dist= 1.240 ch:AA res: 97 UNK at:O .->ch:AA res: 124 ARG at:NH1 . INFO: link is found (not be used) dist= 1.275 ideal_dist= 1.337 ch:AA res: 99 UNK at:CB .->ch:AA res: 103 GLU at:OE1 . INFO: link is found (not be used) dist= 1.666 ideal_dist= 1.420 ch:AA res: 111 SER at:CB .->ch:AA res: 146 ASN at:OD1 . INFO: link is found (not be used) dist= 1.365 ideal_dist= 1.462 ch:AA res: 124 ARG at:NH1 .->ch:BB res: 68 LEU at:CD1 . INFO: link is found (not be used) dist= 1.396 ideal_dist= 1.337 ch:BB res: 40 ARG at:CG .->ch:BB res: 42 GLU at:OE1 . INFO: link is found (not be used) dist= 1.515 ideal_dist= 1.337 ch:BB res: 40 ARG at:CD .->ch:BB res: 42 GLU at:OE1 . INFO: link is found (not be used) dist= 1.289 ideal_dist= 1.339 ch:BB res: 40 ARG at:NE .->ch:BB res: 42 GLU at:CD . INFO: link is found (not be used) dist= 1.479 ideal_dist= 1.275 ch:BB res: 40 ARG at:NE .->ch:BB res: 42 GLU at:OE1 . INFO: link is found (not be used) dist= 0.773 ideal_dist= 1.510 ch:BB res: 40 ARG at:CZ .->ch:BB res: 42 GLU at:CG . INFO: link is found (not be used) dist= 1.181 ideal_dist= 1.460 ch:BB res: 40 ARG at:CZ .->ch:BB res: 42 GLU at:CD . INFO: link is found (not be used) dist= 0.497 ideal_dist= 1.457 ch:BB res: 40 ARG at:NH1 .->ch:BB res: 42 GLU at:CB . INFO: link is found (not be used) dist= 1.076 ideal_dist= 1.457 ch:BB res: 40 ARG at:NH1 .->ch:BB res: 42 GLU at:CG . INFO: link is found (not be used) dist= 1.278 ideal_dist= 1.457 ch:BB res: 40 ARG at:NH2 .->ch:BB res: 42 GLU at:CG . INFO: link is found (not be used) dist= 1.416 ideal_dist= 1.275 ch:BB res: 63 ASP at:OD1 .->ch:BB res: 67 GLN at:N . INFO: link is found (not be used) dist= 1.628 ideal_dist= 1.413 ch:BB res: 35 UNK at:CB .->ch:CC res: 24 UNK at:O . -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:XX-XXX-XX -------------------------------- ATTENTION: atom:O UNK 180 AA is missing in the structure ATTENTION: atom:O GLN 98 BB is missing in the structure ATTENTION: atom:O UNK 26 CC is missing in the structure Number of chains : 3 Total number of monomers : 175 Number of atoms : 1239 Number of missing atoms : 3 Number of rebuilt atoms : 0 Number of unknown atoms : 0 Number of deleted atoms : 0 Number of bonds restraints : 1254 Number of angles restraints : 1703 Number of torsions restraints : 838 Number of chiralities : 208 Number of planar groups : 221 loop_ _atom_type_symbol _atom_type_scat_Cromer_Mann_a1 _atom_type_scat_Cromer_Mann_b1 _atom_type_scat_Cromer_Mann_a2 _atom_type_scat_Cromer_Mann_b2 _atom_type_scat_Cromer_Mann_a3 _atom_type_scat_Cromer_Mann_b3 _atom_type_scat_Cromer_Mann_a4 _atom_type_scat_Cromer_Mann_b4 _atom_type_scat_Cromer_Mann_c N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290 C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156 O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508 S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 0.8669 Number of reflections in file 2948 Number of reflection read 2948 CGMAT cycle number = 1 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 99 UNK C . - A 100 UNK N . mod.= 1.170 id.= 1.329 dev= 0.159 sig.= 0.014 A 107 VAL C . - A 108 THR N . mod.= 1.157 id.= 1.329 dev= 0.172 sig.= 0.014 A 108 THR C . - A 109 PRO N . mod.= 1.088 id.= 1.341 dev= 0.253 sig.= 0.016 A 109 PRO N . - A 109 PRO CA . mod.= 1.240 id.= 1.458 dev= 0.218 sig.= 0.021 A 109 PRO CD . - A 109 PRO N . mod.= 1.933 id.= 1.473 dev= -0.460 sig.= 0.014 A 120 ASP CA . - A 120 ASP C . mod.= 1.260 id.= 1.525 dev= 0.265 sig.= 0.021 A 120 ASP C . - A 121 THR N . mod.= 1.139 id.= 1.329 dev= 0.190 sig.= 0.014 B 34 UNK N . - B 34 UNK CA . mod.= 1.987 id.= 1.491 dev= -0.496 sig.= 0.021 B 34 UNK C . - B 35 UNK N . mod.= 1.095 id.= 1.329 dev= 0.234 sig.= 0.014 B 37 PRO CD . - B 37 PRO N . mod.= 2.196 id.= 1.473 dev= -0.723 sig.= 0.014 B 37 PRO CA . - B 37 PRO C . mod.= 1.805 id.= 1.525 dev= -0.280 sig.= 0.021 B 52 PRO CD . - B 52 PRO N . mod.= 1.953 id.= 1.473 dev= -0.480 sig.= 0.014 B 56 THR N . - B 56 THR CA . mod.= 1.245 id.= 1.458 dev= 0.213 sig.= 0.021 B 56 THR C . - B 57 LYS N . mod.= 1.186 id.= 1.329 dev= 0.143 sig.= 0.014 B 65 LYS C . - B 66 GLY N . mod.= 0.983 id.= 1.329 dev= 0.346 sig.= 0.014 B 75 GLY C . - B 76 GLU N . mod.= 1.181 id.= 1.329 dev= 0.148 sig.= 0.014 B 89 GLY N . - B 89 GLY CA . mod.= 1.684 id.= 1.458 dev= -0.226 sig.= 0.021 C 12 UNK C . - C 13 UNK N . mod.= 1.112 id.= 1.329 dev= 0.217 sig.= 0.014 C 20 UNK C . - C 21 UNK N . mod.= 1.006 id.= 1.329 dev= 0.323 sig.= 0.014 C 21 UNK C . - C 22 UNK N . mod.= 1.060 id.= 1.329 dev= 0.269 sig.= 0.014 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 106 GLY O - A 107 VAL N mod.= 94.73 id.= 123.00 dev= 28.266 sig.= 1.600 A 106 GLY CA - A 107 VAL N mod.= 144.33 id.= 116.20 dev=-28.132 sig.= 2.000 A 106 GLY C - A 107 VAL CA mod.= 145.83 id.= 121.70 dev=-24.129 sig.= 1.800 A 107 VAL O - A 108 THR N mod.= 99.42 id.= 123.00 dev= 23.579 sig.= 1.600 A 107 VAL CA - A 108 THR N mod.= 139.62 id.= 116.20 dev=-23.421 sig.= 2.000 A 108 THR C - A 109 PRO CD mod.= 68.32 id.= 125.00 dev= 56.682 sig.= 4.100 A 109 PRO N - A 109 PRO CG mod.= 78.82 id.= 103.20 dev= 24.380 sig.= 1.500 A 120 ASP O - A 121 THR N mod.= 100.87 id.= 123.00 dev= 22.132 sig.= 1.600 A 120 ASP CA - A 121 THR N mod.= 138.24 id.= 116.20 dev=-22.039 sig.= 2.000 B 37 PRO CA - B 37 PRO CD mod.= 81.71 id.= 112.00 dev= 30.292 sig.= 1.400 B 37 PRO N - B 37 PRO CG mod.= 79.63 id.= 103.20 dev= 23.565 sig.= 1.500 B 52 PRO CA - B 52 PRO CD mod.= 88.44 id.= 112.00 dev= 23.556 sig.= 1.400 B 52 PRO N - B 52 PRO CG mod.= 81.54 id.= 103.20 dev= 21.657 sig.= 1.500 B 67 GLN N - B 67 GLN C mod.= 150.46 id.= 111.20 dev=-39.264 sig.= 2.800 C 25 UNK N - C 25 UNK C mod.= 82.46 id.= 111.20 dev= 28.740 sig.= 2.800 **** Torsion angle outliers **** Torsion angle deviations from the ideal >10.000Sigma will be monitored A 136 SER CA - A 137 ASP CA mod.=-119.67 id.= 180.00 per.= 1 dev= -60.33 sig.= 5.00 B 34 UNK CA - B 35 UNK CA mod.= 117.72 id.= 180.00 per.= 1 dev= 62.28 sig.= 5.00 B 52 PRO CA - B 53 GLY CA mod.=-125.50 id.= 180.00 per.= 1 dev= -54.50 sig.= 5.00 B 53 GLY CA - B 54 GLY CA mod.=-119.90 id.= 180.00 per.= 1 dev= -60.10 sig.= 5.00 B 90 SER CA - B 91 GLY CA mod.= -99.30 id.= 180.00 per.= 1 dev= -80.70 sig.= 5.00 **** Large deviation of atoms from planarity **** Deviations from the planarity >10.000Sigma will be monitored Atom: A 108 THR C deviation= 0.21 sigma.= 0.02 Atom: A 109 PRO N deviation= -0.38 sigma.= 0.02 Atom: B 36 UNK C deviation= 0.20 sigma.= 0.02 Atom: B 37 PRO N deviation= -0.44 sigma.= 0.02 Atom: B 52 PRO N deviation= -0.26 sigma.= 0.02 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored A 97 UNK N . - A 124 ARG CG . mod.= 1.447 id.= 3.520 dev= -2.07 sig.= 0.20 sym.= 1 0 0 0 A 97 UNK N . - A 124 ARG CD . mod.= 0.948 id.= 3.520 dev= -2.57 sig.= 0.20 sym.= 1 0 0 0 A 97 UNK CA . - A 124 ARG CD . mod.= 1.290 id.= 3.870 dev= -2.58 sig.= 0.20 sym.= 1 0 0 0 A 97 UNK C . - A 124 ARG CD . mod.= 1.643 id.= 3.670 dev= -2.03 sig.= 0.20 sym.= 1 0 0 0 A 97 UNK C . - A 124 ARG NE . mod.= 0.991 id.= 3.350 dev= -2.36 sig.= 0.20 sym.= 1 0 0 0 A 97 UNK O . - A 124 ARG CZ . mod.= 0.881 id.= 3.270 dev= -2.39 sig.= 0.20 sym.= 1 0 0 0 A 99 UNK CB . - A 103 GLU OE1 . mod.= 1.275 id.= 3.460 dev= -2.19 sig.= 0.20 sym.= 1 0 0 0 A 105 LEU CD2 . - A 117 LEU CD2 . mod.= 1.792 id.= 3.880 dev= -2.09 sig.= 0.20 sym.= 1 0 0 0 A 124 ARG NH1 . - B 68 LEU CD1 . mod.= 1.365 id.= 3.540 dev= -2.18 sig.= 0.20 sym.= 1 0 0 0 A 137 ASP OD1 . - A 138 PRO CD . mod.= 0.788 id.= 3.440 dev= -2.65 sig.= 0.20 sym.= 1 0 0 0 B 40 ARG CG . - B 42 GLU OE1 . mod.= 1.396 id.= 3.440 dev= -2.04 sig.= 0.20 sym.= 1 0 0 0 B 40 ARG NE . - B 42 GLU CD . mod.= 1.289 id.= 3.350 dev= -2.06 sig.= 0.20 sym.= 1 0 0 0 B 40 ARG CZ . - B 42 GLU CG . mod.= 0.773 id.= 3.670 dev= -2.90 sig.= 0.20 sym.= 1 0 0 0 B 40 ARG CZ . - B 42 GLU CD . mod.= 1.181 id.= 3.500 dev= -2.32 sig.= 0.20 sym.= 1 0 0 0 B 40 ARG NH1 . - B 42 GLU CG . mod.= 1.076 id.= 3.520 dev= -2.44 sig.= 0.20 sym.= 1 0 0 0 B 40 ARG NH1 . - B 42 GLU CB . mod.= 0.497 id.= 3.520 dev= -3.02 sig.= 0.20 sym.= 1 0 0 0 B 40 ARG NH2 . - B 42 GLU CG . mod.= 1.278 id.= 3.520 dev= -2.24 sig.= 0.20 sym.= 1 0 0 0 weigth matrix 0.1000000 special position ----------- 3.193648 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1254 0.050 0.022 Bond angles : refined atoms 1703 4.403 1.960 Torsion angles, period 1. refined 172 15.113 5.000 Torsion angles, period 2. refined 42 37.997 24.048 Torsion angles, period 3. refined 189 6.834 15.000 Torsion angles, period 4. refined 6 5.919 15.000 Chiral centres: refined atoms 208 0.179 0.200 Planar groups: refined atoms 928 0.025 0.020 VDW repulsions: refined atoms 865 0.654 0.200 VDW; torsion: refined atoms 867 0.362 0.200 HBOND: refined atoms 53 0.563 0.200 VDW repulsions; symmetry: refined atoms 42 0.457 0.200 M. chain bond B values: refined atoms 863 0.000 1.500 M. chain angle B values: refined atoms 1350 0.000 2.000 S. chain bond B values: refined atoms 391 0.000 3.000 S. chain angle B values: refined atoms 353 0.000 4.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.480, B = -47.873 Partial structure 1: scale = 0.311, B = 21.740 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 1. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 1.
############################################################### ############################################################### ############################################################### ### CCP4 6.0: cbuccaneer version 1.0.0 : 04/10/07## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:13:36 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.Copyright 2002-2007 Kevin Cowtan and University of York. $TEXT:Reference: $$ Please reference $$ 'The Buccaneer software for automated model building' Cowtan K. (2006) Acta Cryst. D62, 1002-1011. $$ title [No title given] pdbin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.mtz colin-ref-fo /*/*/[FP.F_sigF.F,FP.F_sigF.sigF] colin-ref-hl /*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D] seqin-wrk /home/cowtan/test/1vjf.seq mtzin-wrk /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz colin-wrk-fo /*/*/[FP,SIGFP] colin-wrk-free /*/*/[FreeR_flag] colin-wrk-phifom /*/*/[PHCOMB,FOM] pdbin-wrk /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb pdbout-wrk /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb find grow join link sequence correct filter ncsbuild prune rebuild cycles 1 correlation-mode sequence-reliability 0.95 new-residue-name UNK resolution 2.0 Cycle: 1 C-alphas after finding: 199 C-alphas after growing: 273 C-alphas after joining: 193 C-alphas linked: 0 C-alphas sequenced: 169 C-alphas corrected: 0 C-alphas after filtering: 179 C-alphas after NCS build: 179 C-alphas after pruning: 170 C-alphas after rebuilding: 170 Internal cycle 1 170 residues were built in 2 chains, the longest having 127 residues. 165 residues were sequenced, after pruning. $TEXT:Result: $$ $$ 170 residues were built in 2 chains, the longest having 127 residues. 165 residues were sequenced, after pruning. $$ cbuccaneer: Normal termination Times: User: 90.1s System: 0.3s Elapsed: 1:31 # /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/bin/refmac5 HKLIN /home/cowtan/test/1vjf-3.2A.mtz XYZIN /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb HKLOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz XYZOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
############################################################### ############################################################### ############################################################### ### CCP4 6.0: Refmac_5.3.0037 version 5.3.0037 : 03/29/06## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:15:07 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--- title [No title given] TITL Data line--- weight MATRIX 0.1 WEIG Data line--- labin HLA=pirate.ABCD.A HLB=pirate.ABCD.B HLC=pirate.ABCD.C HLD=pirate.ABCD.D FREE=FreeR_flag FP=FP SIGFP=SIGFP LABI Data line--- make check NONE MAKE Data line--- make hydrogen YES hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO MAKE Data line--- refi type REST PHASE SCBL 1.0 BBLU 0.0 resi MLKF meth CGMAT bref ISOT REFI Data line--- ncyc 10 NCYC Data line--- scal type SIMP LSSC ANISO EXPE SCAL Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8 SOLV 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 MONI Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB LABO Data line--- PNAME buccaneer PNAM Data line--- DNAME buccaneer DNAM Data line--- RSIZE 80 RSIZ Data line--- END END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /home/cowtan/test/1vjf-3.2A.mtz 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 **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb Output coordinate file. Logical name - XYZOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb Input reflection file. Logical name - HKLIN actual file name - /home/cowtan/test/1vjf-3.2A.mtz Output reflection file. Logical name - HKLOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz Cell from mtz : 50.903 50.903 121.411 90.000 90.000 90.000 Space group from mtz: number - 96; name - P43212 Refinement type : Restrained **** 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 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 : Phase modified Maximum Likelihood for Fs Phase Blurred by Scale*Exp(-B s**2) : 1.00 0.00 **** 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 1.400 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 0.0049 Refinement of individual isotropic Bfactors Refinement resln : 46.9323 3.2002 Estimated number of reflections : 3404 Free R exclusion - flag equals: 0 Weighting by comparison of trace of matrix Weighting parameters : 0.1000 Refinement cycles : 10 Scaling type : Wilson using 1 Gaussian using working set of reflns and experimental sigmas Estimation of SigmaA Using 2 Gaussians: using free set of reflns with experimental sigmas Input phases not used in SigmaA estimation Scaling and SigmaA resln: 46.9323 3.2002 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 :/home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 4.12 _lib_update 20/09/07 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 2436 with complete description : 454 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 Number of atoms : 1287 Number of residues : 170 Number of chains : 2 I am reading library. Please wait. mon_lib.cif WARNING : CIS peptide bond is found, angle = 88.83 ch:BB res: 138 PRO --> 139 VAL INFO: link is found (not be used) dist= 1.616 ideal_dist= 1.457 ch:AA res: 117 LEU at:CD1 .->ch:AA res: 127 PHE at:CZ . INFO: link is found (not be used) dist= 1.526 ideal_dist= 1.195 ch:AA res: 137 ASP at:OD1 .->ch:BB res: 138 PRO at:N . INFO: link is found (not be used) dist= 1.473 ideal_dist= 1.337 ch:AA res: 137 ASP at:OD1 .->ch:BB res: 138 PRO at:CG . INFO: link is found (not be used) dist= 1.426 ideal_dist= 1.337 ch:AA res: 137 ASP at:OD1 .->ch:BB res: 138 PRO at:CD . -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:XX-XXX-XX -------------------------------- ATTENTION: atom:O ASP 137 AA is missing in the structure ATTENTION: atom:O UNK 180 BB is missing in the structure Number of chains : 2 Total number of monomers : 170 Number of atoms : 1289 Number of missing atoms : 2 Number of rebuilt atoms : 0 Number of unknown atoms : 0 Number of deleted atoms : 0 Number of bonds restraints : 1313 Number of angles restraints : 1777 Number of torsions restraints : 898 Number of chiralities : 207 Number of planar groups : 229 loop_ _atom_type_symbol _atom_type_scat_Cromer_Mann_a1 _atom_type_scat_Cromer_Mann_b1 _atom_type_scat_Cromer_Mann_a2 _atom_type_scat_Cromer_Mann_b2 _atom_type_scat_Cromer_Mann_a3 _atom_type_scat_Cromer_Mann_b3 _atom_type_scat_Cromer_Mann_a4 _atom_type_scat_Cromer_Mann_b4 _atom_type_scat_Cromer_Mann_c N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290 C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156 O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508 S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 0.8669 Number of reflections in file 2948 Number of reflection read 2948 CGMAT cycle number = 1 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 27 GLY C . - A 28 VAL N . mod.= 0.972 id.= 1.329 dev= 0.357 sig.= 0.014 A 28 VAL C . - A 29 ASP N . mod.= 1.067 id.= 1.329 dev= 0.262 sig.= 0.014 A 29 ASP N . - A 29 ASP CA . mod.= 1.152 id.= 1.458 dev= 0.306 sig.= 0.021 A 30 HIS C . - A 31 LYS N . mod.= 1.043 id.= 1.329 dev= 0.286 sig.= 0.014 A 32 THR CA . - A 32 THR C . mod.= 1.295 id.= 1.525 dev= 0.230 sig.= 0.021 A 36 PRO CD . - A 36 PRO N . mod.= 2.226 id.= 1.473 dev= -0.753 sig.= 0.014 A 37 PRO CD . - A 37 PRO N . mod.= 2.082 id.= 1.473 dev= -0.609 sig.= 0.014 A 52 PRO CD . - A 52 PRO N . mod.= 1.990 id.= 1.473 dev= -0.517 sig.= 0.014 A 105 LEU C . - A 106 GLY N . mod.= 1.176 id.= 1.329 dev= 0.153 sig.= 0.014 A 109 PRO CD . - A 109 PRO N . mod.= 1.790 id.= 1.473 dev= -0.317 sig.= 0.014 B 138 PRO CD . - B 138 PRO N . mod.= 2.059 id.= 1.473 dev= -0.586 sig.= 0.014 B 138 PRO C . - B 139 VAL N . mod.= 1.103 id.= 1.329 dev= 0.226 sig.= 0.014 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 30 HIS O - A 31 LYS N mod.= 91.04 id.= 123.00 dev= 31.965 sig.= 1.600 A 30 HIS CA - A 31 LYS N mod.= 148.06 id.= 116.20 dev=-31.864 sig.= 2.000 A 30 HIS C - A 31 LYS CA mod.= 151.13 id.= 121.70 dev=-29.426 sig.= 1.800 A 32 THR O - A 33 LEU N mod.= 105.57 id.= 123.00 dev= 17.428 sig.= 1.600 A 35 HIS O - A 36 PRO N mod.= 85.16 id.= 123.00 dev= 37.840 sig.= 1.600 A 35 HIS CA - A 36 PRO N mod.= 154.01 id.= 116.90 dev=-37.106 sig.= 1.500 A 36 PRO CA - A 36 PRO CD mod.= 80.63 id.= 112.00 dev= 31.373 sig.= 1.400 A 36 PRO N - A 36 PRO CG mod.= 79.49 id.= 103.20 dev= 23.713 sig.= 1.500 A 37 PRO CA - A 37 PRO CD mod.= 82.94 id.= 112.00 dev= 29.060 sig.= 1.400 A 37 PRO N - A 37 PRO CG mod.= 81.37 id.= 103.20 dev= 21.826 sig.= 1.500 A 52 PRO CA - A 52 PRO CD mod.= 88.49 id.= 112.00 dev= 23.509 sig.= 1.400 A 52 PRO N - A 52 PRO CG mod.= 80.85 id.= 103.20 dev= 22.348 sig.= 1.500 A 105 LEU O - A 106 GLY N mod.= 91.18 id.= 123.00 dev= 31.821 sig.= 1.600 A 105 LEU CA - A 106 GLY N mod.= 147.90 id.= 116.20 dev=-31.705 sig.= 2.000 A 106 GLY C - A 107 VAL CA mod.= 103.57 id.= 121.70 dev= 18.126 sig.= 1.800 A 107 VAL N - A 107 VAL C mod.= 142.13 id.= 111.20 dev=-30.925 sig.= 2.800 A 109 PRO N - A 109 PRO CG mod.= 80.41 id.= 103.20 dev= 22.793 sig.= 1.500 B 138 PRO CA - B 138 PRO CD mod.= 88.71 id.= 112.00 dev= 23.294 sig.= 1.400 B 138 PRO N - B 138 PRO CG mod.= 79.50 id.= 103.20 dev= 23.695 sig.= 1.500 B 138 PRO O - B 139 VAL N mod.= 64.86 id.= 123.00 dev= 58.135 sig.= 1.600 B 138 PRO CA - B 139 VAL N mod.= 174.26 id.= 116.20 dev=-58.064 sig.= 2.000 B 138 PRO C - B 139 VAL CA mod.= 168.43 id.= 121.70 dev=-46.729 sig.= 1.800 **** Torsion angle outliers **** Torsion angle deviations from the ideal >10.000Sigma will be monitored A 52 PRO CA - A 53 GLY CA mod.=-123.55 id.= 180.00 per.= 1 dev= -56.45 sig.= 5.00 A 90 SER CA - A 91 GLY CA mod.= -93.24 id.= 180.00 per.= 1 dev= -86.76 sig.= 5.00 B 138 PRO CA - B 139 VAL CA mod.= -88.83 id.= 0.00 per.= 1 dev= 88.83 sig.= 5.00 **** Large deviation of atoms from planarity **** Deviations from the planarity >10.000Sigma will be monitored Atom: A 37 PRO N deviation= -0.32 sigma.= 0.02 Atom: A 52 PRO N deviation= -0.33 sigma.= 0.02 Atom: A 109 PRO N deviation= -0.22 sigma.= 0.02 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored A 32 THR CG2 . - B 150 THR CG2 . mod.= 1.776 id.= 3.880 dev= -2.10 sig.= 0.20 sym.= 1 0 0 0 A 117 LEU CD1 . - A 127 PHE CZ . mod.= 1.616 id.= 3.760 dev= -2.14 sig.= 0.20 sym.= 1 0 0 0 A 137 ASP OD1 . - B 138 PRO CD . mod.= 1.426 id.= 3.440 dev= -2.01 sig.= 0.20 sym.= 1 0 0 0 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1313 0.047 0.022 Bond angles : refined atoms 1777 5.127 1.960 Torsion angles, period 1. refined 168 16.126 5.000 Torsion angles, period 2. refined 54 37.237 23.889 Torsion angles, period 3. refined 218 7.072 15.000 Torsion angles, period 4. refined 7 8.813 15.000 Chiral centres: refined atoms 207 0.180 0.200 Planar groups: refined atoms 976 0.020 0.020 VDW repulsions: refined atoms 815 0.502 0.200 VDW; torsion: refined atoms 903 0.363 0.200 HBOND: refined atoms 52 0.359 0.200 VDW repulsions; symmetry: refined atoms 59 0.604 0.200 HBOND; symmetry: refined atoms 4 0.441 0.200 M. chain bond B values: refined atoms 840 0.000 1.500 M. chain angle B values: refined atoms 1342 0.000 2.000 S. chain bond B values: refined atoms 473 0.000 3.000 S. chain angle B values: refined atoms 435 0.000 4.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.513, B = -44.340 Partial structure 1: scale = 0.331, B = 19.044 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 1. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 1.