############################################################### ############################################################### ############################################################### ### CCP4 6.4: cbuccaneer version 1.5.2 : 06/10/11## ############################################################### User: unknown Run date: 17/ 7/2014 Run time: 18:53:36 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 2002-2010 Kevin Cowtan and University of York. $TEXT:Reference: $$ Please reference $$ 'Fitting molecular fragments into electron density' Cowtan K. (2008) Acta Cryst. D64, 83-89. $$ $TEXT:Reference: $$ Please reference $$ 'The Buccaneer software for automated model building' Cowtan K. (2006) Acta Cryst. D62, 1002-1011. $$ title buccaneer auto-build pdbin-ref /home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /home/jmht/ccp4-6.4.0/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 /data1/jmht/polya_helices/3PP5/search_polya_15/input/3PP5_1.fasta mtzin /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz colin-fo FP, SIGFP colin-phifom PHIC, FOM colin-fc FWT, PHWT colin-free FREE pdbin /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.pdb pdbout buccaneer_pipeline/build.pdb anisotropy-correction fast cycles 3 sequence-reliability 0.95 new-residue-name UNK resolution 2.0 MTZ file: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz Number of reflections: 16180 Number of columns: 17 Applying anisotropy correction: | -1.01e-14, 5.538e-17, 6.293e-18| | 5.538e-17, 0,-1.187e-17| | 6.293e-18,-1.187e-17, -0.1121| PDB file: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.pdb Number of atoms read: 315 Cycle: 1 C-alphas after finding: 81 C-alphas after growing: 101 C-alphas after joining: 69 C-alphas linked: 0 C-alphas sequenced: 57 C-alphas corrected: 0 C-alphas after filtering: 60 C-alphas after NCS build: 60 C-alphas after pruning: 60 C-alphas after rebuilding: 60 Internal cycle 1 60 residues were built in 1 fragments, the longest having 60 residues. 56 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) Cycle: 2 C-alphas after finding: 76 C-alphas after growing: 116 C-alphas after joining: 76 C-alphas linked: 0 C-alphas sequenced: 57 C-alphas corrected: 0 C-alphas after filtering: 60 C-alphas after NCS build: 60 C-alphas after pruning: 60 C-alphas after rebuilding: 60 Internal cycle 2 60 residues were built in 1 fragments, the longest having 60 residues. 56 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) Cycle: 3 C-alphas after finding: 76 C-alphas after growing: 116 C-alphas after joining: 76 C-alphas linked: 0 C-alphas sequenced: 57 C-alphas corrected: 0 C-alphas after filtering: 60 C-alphas after NCS build: 60 C-alphas after pruning: 60 C-alphas after rebuilding: 60 Internal cycle 3 60 residues were built in 1 fragments, the longest having 60 residues. 56 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) $TEXT:Result: $$ $$ 60 residues were built in 1 fragments, the longest having 60 residues. 56 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) $$ cbuccaneer: Normal termination Times: User: 17.9s System: 0.0s Elapsed: 0:17
############################################################### ############################################################### ############################################################### ### CCP4 6.4: Refmac_5.8.0049 version 5.8.0049 : 30/06/13## ############################################################### User: unknown Run date: 17/ 7/2014 Run time: 18:53:53 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up.$TEXT:Reference1: $$ Main reference $$ "REFMAC5 for the refinement of macromolecular crystal structures:" G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) Acta Crystallogr. D67, 355-367 $$ $SUMMARY :Reference1: $$ Refmac: $$ :TEXT:Reference1: $$ $TEXT:Reference2: $$ Secondary reference $$ "Refinement of Macromolecular Structures by the Maximum-Likelihood Method:" G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997) Acta Crystallogr. D53, 240-255 EU Validation contract: BIO2CT-92-0524 $$ $SUMMARY :Reference2: $$ Refmac: $$ :TEXT:Reference2: $$ Data line--- title buccaneer auto-build Data line--- ncyc 10 Data line--- labin PHIB=PHIC FOM= FOM FREE=FREE FP=FP SIGFP= SIGFP Data line--- weight AUTO Data line--- make check NONE Data line--- make hydrogen NO hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO Data line--- refi type REST PHASE resi MLKF meth CGMAT bref ISOT Data line--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8 Data line--- PHOUT Data line--- PNAME buccaneer Data line--- DNAME buccaneer Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /home/jmht/ccp4-6.4.0/lib/data/syminfo.lib **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - buccaneer_pipeline/build.pdb Output coordinate file. Logical name - XYZOUT actual file name - buccaneer_pipeline/refine.pdb Input reflection file. Logical name - HKLIN actual file name - /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_outpu Output reflection file. Logical name - HKLOUT actual file name - buccaneer_pipeline/refine.mtz Cell from mtz : 39.140 39.140 118.190 90.000 90.000 120.000 Space group from mtz: number - 173; name - P 63 Refinement type : Restrained **** Makecif parameters **** Dictionary files for restraints : /home/jmht/ccp4-6.4.0/lib/data/monomers/mon*cif Parameters for new entry and VDW: /home/jmht/ccp4-6.4.0/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 will not be written to the output file 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 **** Map sharpening parameters and methods **** No map sharpening will be performed Method of minimisation : Sparse Matrix Experimental sigmas used for weighting Number of Bins and width: 20 0.0223 Refinement of individual isotropic Bfactors Refinement resln : 18.5778 1.4990 Estimated number of reflections : 26875 Free R exclusion - flag equals: 0 Auto weighting. An attempt Refinement cycles : 10 Scaling type : Wilson using 1 Gaussian Estimation of D/Sigma in resolution bins using free set of reflns with experimental sigmas Input phases not used in SigmaA estimation Scaling and SigmaA resln: 18.5778 1.4990 Damping factors: 1.0000 1.0000 **** Geometry restraints and weights **** Sigma: Bonding distances Weight = 1.00 Bond angles Weight = 1.00 Planar groups (all and main chain) WEIGHT= 1.00 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) 1.5A**2 Main chain angle (1-3 neighbour) 2.0A**2 Side chain bond 3.0A**2 Side chain angle 4.5A**2 RESTRAINTS AGAINST EXCESSIVE SHIFTS Positional parameters 0.00A Thermal parameters 0.00A Occupancy parameters 0.00 RADIUS OF CONFIDENCE Positional parameters 0.00A Thermal parameters 0.00A**2 Occupancy parameters 0.00 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 :buccaneer_pipeline/build.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 5.41 _lib_update 11/02/13 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 11464 with complete description : 11464 NUMBER OF MODIFICATIONS : 56 NUMBER OF LINKS : 68 I am reading libraries. Please wait. - energy parameters - monomer"s description (links & mod ) FORMATTED OLD file opened on unit 45 Logical name: ATOMSF, Filename: /home/jmht/ccp4-6.4.0/lib/data/atomsf.lib Number of atoms : 483 Number of residues : 60 Number of chains : 1 I am reading library. Please wait. mon_lib.cif -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:XX-XXX-XX -------------------------------- ATTENTION: atom:CG UNK 9 AA is missing in the structure ATTENTION: atom:CG UNK 10 AA is missing in the structure ATTENTION: atom:CG PHE 36 AA is missing in the structure ATTENTION: atom:CD1 PHE 36 AA is missing in the structure ATTENTION: atom:CE1 PHE 36 AA is missing in the structure ATTENTION: atom:CZ PHE 36 AA is missing in the structure ATTENTION: atom:CE2 PHE 36 AA is missing in the structure ATTENTION: atom:CD2 PHE 36 AA is missing in the structure ATTENTION: atom:CG GLU 41 AA is missing in the structure ATTENTION: atom:CD GLU 41 AA is missing in the structure ATTENTION: atom:OE1 GLU 41 AA is missing in the structure ATTENTION: atom:OE2 GLU 41 AA is missing in the structure ATTENTION: atom:CG UNK 63 AA is missing in the structure ATTENTION: atom:CG UNK 68 AA is missing in the structure Number of chains : 1 Total number of monomers : 60 Number of atoms : 497 Number of missing atoms : 14 Number of rebuilt atoms : 0 Number of unknown atoms : 0 Number of deleted atoms : 0 Number of bonds restraints : 486 Number of angles restraints : 654 Number of torsions restraints : 322 Number of chiralities : 79 Number of planar groups : 84 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 distances : 0 Number of angles : 0 Number of torsions : 0 Number of planes : 0 Number of chirals : 0 Number of intervals : 0 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Standard External All Bonds: 486 0 486 Angles: 654 0 654 Chirals: 79 0 79 Planes: 84 0 84 Torsions: 322 0 322 Intervals: 0 0 0 -------------------------------------------------------------------------------- Number of harmonic restraints = 0 Number of atoms in special position = 0 ----------------------------------------------------- **** Info from mtz file **** FreeR flag 0 Number of "free" reflections 809 Number of all reflections 16180 -------------------------------------------------------------------------------- Number of reflections in file 16180 Number of reflections read 16180 CGMAT cycle number = 1 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 96 96 288 Maximuum H,K,L : 27 27 78 Minimum acceptable grid spacing: 59 59 178 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 96 96 288 Maximuum H,K,L : 27 27 78 Minimum acceptable grid spacing: 59 59 178 Weight matrix 0.54462564 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 141. Norm of Geom. positional gradient 30.9 Norm of X_ray B-factor gradient 0.194E+04 Norm of Geom. B-factor gradient 0.00 Product of X_ray and Geom posit. gradients 0.130E+06 Cosine of angle between them 0.021 Product of X_ray and Geom B-fact gradients 0.00 Cosine of angle between them 0.000 Residuals: XRAY= 0.2781E+06 GEOM= 978.0 TOTAL= 0.2791E+06 function value 279114.66 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 486 0.011 0.020 Bond angles : refined atoms 654 1.169 1.978 Torsion angles, period 1. refined 59 2.730 5.000 Torsion angles, period 2. refined 25 29.835 26.400 Torsion angles, period 3. refined 99 10.676 15.000 Torsion angles, period 4. refined 3 5.427 15.000 Chiral centres: refined atoms 79 0.074 0.200 Planar groups: refined atoms 351 0.000 0.020 VDW repulsions: refined_atoms 208 0.301 0.200 VDW; torsion: refined_atoms 360 0.302 0.200 HBOND: refined_atoms 8 0.333 0.200 VDW repulsions: symmetry: refined_atoms 35 0.367 0.200 HBOND: symmetry: refined_atoms 2 0.098 0.200 M. chain bond B values: refined atoms 239 0.000 3.948 M. chain angle B values: refined atoms 297 0.000 5.922 S. chain bond B values: refined atoms 242 0.000 3.948 S. chain angle B values: refined atoms 356 0.000 5.922 Long range B values: refined atoms 739 0.000 32.630 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.776, B = -22.530 Partial structure 1: scale = 0.443, B = 53.346 Overall anisotropic scale factors B11 = -0.11 B22 = -0.11 B33 = 0.37 B12 = -0.06 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 6.4: cbuccaneer version 1.5.2 : 06/10/11## ############################################################### User: unknown Run date: 17/ 7/2014 Run time: 18:54:36 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 2002-2010 Kevin Cowtan and University of York. $TEXT:Reference: $$ Please reference $$ 'Fitting molecular fragments into electron density' Cowtan K. (2008) Acta Cryst. D64, 83-89. $$ $TEXT:Reference: $$ Please reference $$ 'The Buccaneer software for automated model building' Cowtan K. (2006) Acta Cryst. D62, 1002-1011. $$ title buccaneer auto-build pdbin-ref /home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /home/jmht/ccp4-6.4.0/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 /data1/jmht/polya_helices/3PP5/search_polya_15/input/3PP5_1.fasta mtzin buccaneer_pipeline/refine.mtz colin-fo FP, SIGFP colin-hl HLACOMB,HLBCOMB,HLCCOMB,HLDCOMB colin-fc FWT,PHWT colin-free FREE pdbin buccaneer_pipeline/refine.pdb pdbout buccaneer_pipeline/build.pdb anisotropy-correction fast cycles 2 sequence-reliability 0.95 correlation-mode new-residue-name UNK resolution 2.0 MTZ file: buccaneer_pipeline/refine.mtz Number of reflections: 16180 Number of columns: 22 Applying anisotropy correction: |-9.483e-15, 4.866e-17, 5.728e-17| | 4.866e-17, 0,-1.927e-17| | 5.728e-17,-1.927e-17, -0.1077| PDB file: buccaneer_pipeline/refine.pdb Number of atoms read: 483 Cycle: 1 C-alphas after finding: 76 C-alphas after growing: 110 C-alphas after joining: 76 C-alphas linked: 0 C-alphas sequenced: 73 C-alphas corrected: 0 C-alphas after filtering: 76 C-alphas after NCS build: 120 C-alphas after pruning: 60 C-alphas after rebuilding: 60 Internal cycle 1 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) Cycle: 2 C-alphas after finding: 76 C-alphas after growing: 135 C-alphas after joining: 76 C-alphas linked: 0 C-alphas sequenced: 73 C-alphas corrected: 0 C-alphas after filtering: 76 C-alphas after NCS build: 120 C-alphas after pruning: 60 C-alphas after rebuilding: 60 Internal cycle 2 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) $TEXT:Result: $$ $$ 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) $$ cbuccaneer: Normal termination Times: User: 19.8s System: 0.0s Elapsed: 0:20
############################################################### ############################################################### ############################################################### ### CCP4 6.4: Refmac_5.8.0049 version 5.8.0049 : 30/06/13## ############################################################### User: unknown Run date: 17/ 7/2014 Run time: 18:54:56 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: $$ Main reference $$ "REFMAC5 for the refinement of macromolecular crystal structures:" G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) Acta Crystallogr. D67, 355-367 $$ $SUMMARY :Reference1: $$ Refmac: $$ :TEXT:Reference1: $$ $TEXT:Reference2: $$ Secondary reference $$ "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 $$ $SUMMARY :Reference2: $$ Refmac: $$ :TEXT:Reference2: $$ Data line--- title buccaneer auto-build Data line--- ncyc 10 Data line--- labin PHIB=PHIC FOM= FOM FREE=FREE FP=FP SIGFP= SIGFP Data line--- weight AUTO Data line--- make check NONE Data line--- make hydrogen NO hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO Data line--- refi type REST PHASE resi MLKF meth CGMAT bref ISOT Data line--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8 Data line--- PHOUT Data line--- PNAME buccaneer Data line--- DNAME buccaneer Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /home/jmht/ccp4-6.4.0/lib/data/syminfo.lib **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - buccaneer_pipeline/build.pdb Output coordinate file. Logical name - XYZOUT actual file name - buccaneer_pipeline/refine.pdb Input reflection file. Logical name - HKLIN actual file name - /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_outpu Output reflection file. Logical name - HKLOUT actual file name - buccaneer_pipeline/refine.mtz Cell from mtz : 39.140 39.140 118.190 90.000 90.000 120.000 Space group from mtz: number - 173; name - P 63 Refinement type : Restrained **** Makecif parameters **** Dictionary files for restraints : /home/jmht/ccp4-6.4.0/lib/data/monomers/mon*cif Parameters for new entry and VDW: /home/jmht/ccp4-6.4.0/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 will not be written to the output file 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 **** Map sharpening parameters and methods **** No map sharpening will be performed Method of minimisation : Sparse Matrix Experimental sigmas used for weighting Number of Bins and width: 20 0.0223 Refinement of individual isotropic Bfactors Refinement resln : 18.5778 1.4990 Estimated number of reflections : 26875 Free R exclusion - flag equals: 0 Auto weighting. An attempt Refinement cycles : 10 Scaling type : Wilson using 1 Gaussian Estimation of D/Sigma in resolution bins using free set of reflns with experimental sigmas Input phases not used in SigmaA estimation Scaling and SigmaA resln: 18.5778 1.4990 Damping factors: 1.0000 1.0000 **** Geometry restraints and weights **** Sigma: Bonding distances Weight = 1.00 Bond angles Weight = 1.00 Planar groups (all and main chain) WEIGHT= 1.00 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) 1.5A**2 Main chain angle (1-3 neighbour) 2.0A**2 Side chain bond 3.0A**2 Side chain angle 4.5A**2 RESTRAINTS AGAINST EXCESSIVE SHIFTS Positional parameters 0.00A Thermal parameters 0.00A Occupancy parameters 0.00 RADIUS OF CONFIDENCE Positional parameters 0.00A Thermal parameters 0.00A**2 Occupancy parameters 0.00 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 :buccaneer_pipeline/build.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 5.41 _lib_update 11/02/13 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 11464 with complete description : 11464 NUMBER OF MODIFICATIONS : 56 NUMBER OF LINKS : 68 I am reading libraries. Please wait. - energy parameters - monomer"s description (links & mod ) FORMATTED OLD file opened on unit 45 Logical name: ATOMSF, Filename: /home/jmht/ccp4-6.4.0/lib/data/atomsf.lib Number of atoms : 501 Number of residues : 60 Number of chains : 1 I am reading library. Please wait. mon_lib.cif -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:XX-XXX-XX -------------------------------- ATTENTION: atom:CG UNK 9 AA is missing in the structure ATTENTION: atom:CG UNK 10 AA is missing in the structure ATTENTION: atom:CG UNK 68 AA is missing in the structure Number of chains : 1 Total number of monomers : 60 Number of atoms : 504 Number of missing atoms : 3 Number of rebuilt atoms : 0 Number of unknown atoms : 0 Number of deleted atoms : 0 Number of bonds restraints : 506 Number of angles restraints : 680 Number of torsions restraints : 340 Number of chiralities : 78 Number of planar groups : 88 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 distances : 0 Number of angles : 0 Number of torsions : 0 Number of planes : 0 Number of chirals : 0 Number of intervals : 0 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Standard External All Bonds: 506 0 506 Angles: 680 0 680 Chirals: 78 0 78 Planes: 88 0 88 Torsions: 340 0 340 Intervals: 0 0 0 -------------------------------------------------------------------------------- Number of harmonic restraints = 0 Number of atoms in special position = 0 ----------------------------------------------------- **** Info from mtz file **** FreeR flag 0 Number of "free" reflections 809 Number of all reflections 16180 -------------------------------------------------------------------------------- Number of reflections in file 16180 Number of reflections read 16180 CGMAT cycle number = 1 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 96 96 288 Maximuum H,K,L : 27 27 78 Minimum acceptable grid spacing: 59 59 178 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 96 96 288 Maximuum H,K,L : 27 27 78 Minimum acceptable grid spacing: 59 59 178 Weight matrix 0.51820004 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 189. Norm of Geom. positional gradient 39.7 Norm of X_ray B-factor gradient 0.186E+04 Norm of Geom. B-factor gradient 0.00 Product of X_ray and Geom posit. gradients 0.462E+06 Cosine of angle between them 0.041 Product of X_ray and Geom B-fact gradients 0.00 Cosine of angle between them 0.000 Residuals: XRAY= 0.2811E+06 GEOM= 1062. TOTAL= 0.2822E+06 function value 282174.66 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 506 0.011 0.020 Bond angles : refined atoms 680 1.303 1.970 Torsion angles, period 1. refined 59 2.214 5.000 Torsion angles, period 2. refined 29 30.763 26.207 Torsion angles, period 3. refined 103 10.504 15.000 Torsion angles, period 4. refined 3 11.394 15.000 Chiral centres: refined atoms 78 0.070 0.200 Planar groups: refined atoms 374 0.000 0.020 VDW repulsions: refined_atoms 224 0.259 0.200 VDW; torsion: refined_atoms 370 0.310 0.200 HBOND: refined_atoms 5 0.361 0.200 VDW repulsions: symmetry: refined_atoms 40 0.430 0.200 HBOND: symmetry: refined_atoms 3 0.489 0.200 M. chain bond B values: refined atoms 239 0.000 3.948 M. chain angle B values: refined atoms 297 0.000 5.922 S. chain bond B values: refined atoms 263 0.000 3.948 S. chain angle B values: refined atoms 382 0.000 5.922 Long range B values: refined atoms 781 0.000 32.710 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.774, B = -22.286 Partial structure 1: scale = 0.464, B = 45.334 Overall anisotropic scale factors B11 = -0.12 B22 = -0.12 B33 = 0.37 B12 = -0.06 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 6.4: cbuccaneer version 1.5.2 : 06/10/11## ############################################################### User: unknown Run date: 17/ 7/2014 Run time: 18:55:39 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 2002-2010 Kevin Cowtan and University of York. $TEXT:Reference: $$ Please reference $$ 'Fitting molecular fragments into electron density' Cowtan K. (2008) Acta Cryst. D64, 83-89. $$ $TEXT:Reference: $$ Please reference $$ 'The Buccaneer software for automated model building' Cowtan K. (2006) Acta Cryst. D62, 1002-1011. $$ title buccaneer auto-build pdbin-ref /home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /home/jmht/ccp4-6.4.0/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 /data1/jmht/polya_helices/3PP5/search_polya_15/input/3PP5_1.fasta mtzin buccaneer_pipeline/refine.mtz colin-fo FP, SIGFP colin-hl HLACOMB,HLBCOMB,HLCCOMB,HLDCOMB colin-fc FWT,PHWT colin-free FREE pdbin buccaneer_pipeline/refine.pdb pdbout buccaneer_pipeline/build.pdb anisotropy-correction fast cycles 2 sequence-reliability 0.95 correlation-mode new-residue-name UNK resolution 2.0 MTZ file: buccaneer_pipeline/refine.mtz Number of reflections: 16180 Number of columns: 22 Applying anisotropy correction: |-9.168e-15, 1.095e-16,-8.236e-17| | 1.095e-16, 0,-2.269e-17| |-8.236e-17,-2.269e-17, -0.1084| PDB file: buccaneer_pipeline/refine.pdb Number of atoms read: 501 Cycle: 1 C-alphas after finding: 76 C-alphas after growing: 118 C-alphas after joining: 60 C-alphas linked: 0 C-alphas sequenced: 57 C-alphas corrected: 0 C-alphas after filtering: 60 C-alphas after NCS build: 60 C-alphas after pruning: 60 C-alphas after rebuilding: 60 Internal cycle 1 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) Cycle: 2 C-alphas after finding: 76 C-alphas after growing: 141 C-alphas after joining: 70 C-alphas linked: 0 C-alphas sequenced: 67 C-alphas corrected: 0 C-alphas after filtering: 70 C-alphas after NCS build: 70 C-alphas after pruning: 60 C-alphas after rebuilding: 60 Internal cycle 2 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) $TEXT:Result: $$ $$ 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) $$ cbuccaneer: Normal termination Times: User: 19.4s System: 0.0s Elapsed: 0:20
############################################################### ############################################################### ############################################################### ### CCP4 6.4: Refmac_5.8.0049 version 5.8.0049 : 30/06/13## ############################################################### User: unknown Run date: 17/ 7/2014 Run time: 18:55:59 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up.$TEXT:Reference1: $$ Main reference $$ "REFMAC5 for the refinement of macromolecular crystal structures:" G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) Acta Crystallogr. D67, 355-367 $$ $SUMMARY :Reference1: $$ Refmac: $$ :TEXT:Reference1: $$ $TEXT:Reference2: $$ Secondary reference $$ "Refinement of Macromolecular Structures by the Maximum-Likelihood Method:" G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997) Acta Crystallogr. D53, 240-255 EU Validation contract: BIO2CT-92-0524 $$ $SUMMARY :Reference2: $$ Refmac: $$ :TEXT:Reference2: $$ Data line--- title buccaneer auto-build Data line--- ncyc 10 Data line--- labin PHIB=PHIC FOM= FOM FREE=FREE FP=FP SIGFP= SIGFP Data line--- weight AUTO Data line--- make check NONE Data line--- make hydrogen NO hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO Data line--- refi type REST PHASE resi MLKF meth CGMAT bref ISOT Data line--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8 Data line--- PHOUT Data line--- PNAME buccaneer Data line--- DNAME buccaneer Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /home/jmht/ccp4-6.4.0/lib/data/syminfo.lib **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - buccaneer_pipeline/build.pdb Output coordinate file. Logical name - XYZOUT actual file name - buccaneer_pipeline/refine.pdb Input reflection file. Logical name - HKLIN actual file name - /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_outpu Output reflection file. Logical name - HKLOUT actual file name - buccaneer_pipeline/refine.mtz Cell from mtz : 39.140 39.140 118.190 90.000 90.000 120.000 Space group from mtz: number - 173; name - P 63 Refinement type : Restrained **** Makecif parameters **** Dictionary files for restraints : /home/jmht/ccp4-6.4.0/lib/data/monomers/mon*cif Parameters for new entry and VDW: /home/jmht/ccp4-6.4.0/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 will not be written to the output file 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 **** Map sharpening parameters and methods **** No map sharpening will be performed Method of minimisation : Sparse Matrix Experimental sigmas used for weighting Number of Bins and width: 20 0.0223 Refinement of individual isotropic Bfactors Refinement resln : 18.5778 1.4990 Estimated number of reflections : 26875 Free R exclusion - flag equals: 0 Auto weighting. An attempt Refinement cycles : 10 Scaling type : Wilson using 1 Gaussian Estimation of D/Sigma in resolution bins using free set of reflns with experimental sigmas Input phases not used in SigmaA estimation Scaling and SigmaA resln: 18.5778 1.4990 Damping factors: 1.0000 1.0000 **** Geometry restraints and weights **** Sigma: Bonding distances Weight = 1.00 Bond angles Weight = 1.00 Planar groups (all and main chain) WEIGHT= 1.00 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) 1.5A**2 Main chain angle (1-3 neighbour) 2.0A**2 Side chain bond 3.0A**2 Side chain angle 4.5A**2 RESTRAINTS AGAINST EXCESSIVE SHIFTS Positional parameters 0.00A Thermal parameters 0.00A Occupancy parameters 0.00 RADIUS OF CONFIDENCE Positional parameters 0.00A Thermal parameters 0.00A**2 Occupancy parameters 0.00 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 :buccaneer_pipeline/build.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 5.41 _lib_update 11/02/13 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 11464 with complete description : 11464 NUMBER OF MODIFICATIONS : 56 NUMBER OF LINKS : 68 I am reading libraries. Please wait. - energy parameters - monomer"s description (links & mod ) FORMATTED OLD file opened on unit 45 Logical name: ATOMSF, Filename: /home/jmht/ccp4-6.4.0/lib/data/atomsf.lib Number of atoms : 501 Number of residues : 60 Number of chains : 1 I am reading library. Please wait. mon_lib.cif -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:XX-XXX-XX -------------------------------- ATTENTION: atom:CG UNK 9 AA is missing in the structure ATTENTION: atom:CG UNK 10 AA is missing in the structure ATTENTION: atom:CG UNK 68 AA is missing in the structure Number of chains : 1 Total number of monomers : 60 Number of atoms : 504 Number of missing atoms : 3 Number of rebuilt atoms : 0 Number of unknown atoms : 0 Number of deleted atoms : 0 Number of bonds restraints : 506 Number of angles restraints : 680 Number of torsions restraints : 340 Number of chiralities : 78 Number of planar groups : 88 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 distances : 0 Number of angles : 0 Number of torsions : 0 Number of planes : 0 Number of chirals : 0 Number of intervals : 0 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Standard External All Bonds: 506 0 506 Angles: 680 0 680 Chirals: 78 0 78 Planes: 88 0 88 Torsions: 340 0 340 Intervals: 0 0 0 -------------------------------------------------------------------------------- Number of harmonic restraints = 0 Number of atoms in special position = 0 ----------------------------------------------------- **** Info from mtz file **** FreeR flag 0 Number of "free" reflections 809 Number of all reflections 16180 -------------------------------------------------------------------------------- Number of reflections in file 16180 Number of reflections read 16180 CGMAT cycle number = 1 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 12 ASN C . - A 13 ILE N . mod.= 0.844 id.= 1.329 dev= 0.485 sig.= 0.014 A 68 UNK CA . - A 68 UNK C . mod.= 1.042 id.= 1.500 dev= 0.458 sig.= 0.020 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 12 ASN CA - A 13 ILE N mod.= 170.77 id.= 116.20 dev=-54.566 sig.= 2.000 A 12 ASN C - A 13 ILE CA mod.= 169.61 id.= 121.70 dev=-47.914 sig.= 1.800 A 12 ASN O - A 13 ILE N mod.= 68.28 id.= 123.00 dev= 54.717 sig.= 1.600 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 96 96 288 Maximuum H,K,L : 27 27 78 Minimum acceptable grid spacing: 59 59 178 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 96 96 288 Maximuum H,K,L : 27 27 78 Minimum acceptable grid spacing: 59 59 178 Weight matrix 0.50224590 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 199. Norm of Geom. positional gradient 176. Norm of X_ray B-factor gradient 0.178E+04 Norm of Geom. B-factor gradient 0.00 Product of X_ray and Geom posit. gradients 0.410E+07 Cosine of angle between them 0.078 Product of X_ray and Geom B-fact gradients 0.00 Cosine of angle between them 0.000 Residuals: XRAY= 0.2882E+06 GEOM= 4247. TOTAL= 0.2924E+06 function value 292449.03 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 506 0.033 0.020 Bond angles : refined atoms 680 3.937 1.970 Torsion angles, period 1. refined 59 2.791 5.000 Torsion angles, period 2. refined 29 30.728 26.207 Torsion angles, period 3. refined 103 11.000 15.000 Torsion angles, period 4. refined 3 11.391 15.000 Chiral centres: refined atoms 78 0.152 0.200 Planar groups: refined atoms 374 0.000 0.020 VDW repulsions: refined_atoms 212 0.265 0.200 VDW; torsion: refined_atoms 373 0.319 0.200 HBOND: refined_atoms 7 0.321 0.200 VDW repulsions: symmetry: refined_atoms 28 0.407 0.200 M. chain bond B values: refined atoms 239 0.000 3.948 M. chain angle B values: refined atoms 297 0.000 5.922 S. chain bond B values: refined atoms 263 0.000 3.948 S. chain angle B values: refined atoms 383 0.000 5.922 Long range B values: refined atoms 773 0.000 32.640 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.763, B = -22.434 Partial structure 1: scale = 0.484, B = 47.099 Overall anisotropic scale factors B11 = -0.12 B22 = -0.12 B33 = 0.40 B12 = -0.06 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 6.4: cbuccaneer version 1.5.2 : 06/10/11## ############################################################### User: unknown Run date: 17/ 7/2014 Run time: 18:56:42 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 2002-2010 Kevin Cowtan and University of York. $TEXT:Reference: $$ Please reference $$ 'Fitting molecular fragments into electron density' Cowtan K. (2008) Acta Cryst. D64, 83-89. $$ $TEXT:Reference: $$ Please reference $$ 'The Buccaneer software for automated model building' Cowtan K. (2006) Acta Cryst. D62, 1002-1011. $$ title buccaneer auto-build pdbin-ref /home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /home/jmht/ccp4-6.4.0/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 /data1/jmht/polya_helices/3PP5/search_polya_15/input/3PP5_1.fasta mtzin buccaneer_pipeline/refine.mtz colin-fo FP, SIGFP colin-hl HLACOMB,HLBCOMB,HLCCOMB,HLDCOMB colin-fc FWT,PHWT colin-free FREE pdbin buccaneer_pipeline/refine.pdb pdbout buccaneer_pipeline/build.pdb anisotropy-correction fast cycles 2 sequence-reliability 0.95 correlation-mode new-residue-name UNK resolution 2.0 MTZ file: buccaneer_pipeline/refine.mtz Number of reflections: 16180 Number of columns: 22 Applying anisotropy correction: |-9.083e-15, 5.552e-17, 1.547e-17| | 5.552e-17, 0,-1.145e-17| | 1.547e-17,-1.145e-17, -0.1098| PDB file: buccaneer_pipeline/refine.pdb Number of atoms read: 501 Cycle: 1 C-alphas after finding: 76 C-alphas after growing: 101 C-alphas after joining: 60 C-alphas linked: 0 C-alphas sequenced: 57 C-alphas corrected: 0 C-alphas after filtering: 60 C-alphas after NCS build: 60 C-alphas after pruning: 60 C-alphas after rebuilding: 60 Internal cycle 1 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) Cycle: 2 C-alphas after finding: 76 C-alphas after growing: 93 C-alphas after joining: 60 C-alphas linked: 0 C-alphas sequenced: 57 C-alphas corrected: 0 C-alphas after filtering: 60 C-alphas after NCS build: 60 C-alphas after pruning: 60 C-alphas after rebuilding: 60 Internal cycle 2 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) $TEXT:Result: $$ $$ 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) $$ cbuccaneer: Normal termination Times: User: 16.9s System: 0.0s Elapsed: 0:17
############################################################### ############################################################### ############################################################### ### CCP4 6.4: Refmac_5.8.0049 version 5.8.0049 : 30/06/13## ############################################################### User: unknown Run date: 17/ 7/2014 Run time: 18:56:59 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: $$ Main reference $$ "REFMAC5 for the refinement of macromolecular crystal structures:" G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) Acta Crystallogr. D67, 355-367 $$ $SUMMARY :Reference1: $$ Refmac: $$ :TEXT:Reference1: $$ $TEXT:Reference2: $$ Secondary reference $$ "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 $$ $SUMMARY :Reference2: $$ Refmac: $$ :TEXT:Reference2: $$ Data line--- title buccaneer auto-build Data line--- ncyc 10 Data line--- labin PHIB=PHIC FOM= FOM FREE=FREE FP=FP SIGFP= SIGFP Data line--- weight AUTO Data line--- make check NONE Data line--- make hydrogen NO hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO Data line--- refi type REST PHASE resi MLKF meth CGMAT bref ISOT Data line--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8 Data line--- PHOUT Data line--- PNAME buccaneer Data line--- DNAME buccaneer Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /home/jmht/ccp4-6.4.0/lib/data/syminfo.lib **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - buccaneer_pipeline/build.pdb Output coordinate file. Logical name - XYZOUT actual file name - buccaneer_pipeline/refine.pdb Input reflection file. Logical name - HKLIN actual file name - /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_outpu Output reflection file. Logical name - HKLOUT actual file name - buccaneer_pipeline/refine.mtz Cell from mtz : 39.140 39.140 118.190 90.000 90.000 120.000 Space group from mtz: number - 173; name - P 63 Refinement type : Restrained **** Makecif parameters **** Dictionary files for restraints : /home/jmht/ccp4-6.4.0/lib/data/monomers/mon*cif Parameters for new entry and VDW: /home/jmht/ccp4-6.4.0/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 will not be written to the output file 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 **** Map sharpening parameters and methods **** No map sharpening will be performed Method of minimisation : Sparse Matrix Experimental sigmas used for weighting Number of Bins and width: 20 0.0223 Refinement of individual isotropic Bfactors Refinement resln : 18.5778 1.4990 Estimated number of reflections : 26875 Free R exclusion - flag equals: 0 Auto weighting. An attempt Refinement cycles : 10 Scaling type : Wilson using 1 Gaussian Estimation of D/Sigma in resolution bins using free set of reflns with experimental sigmas Input phases not used in SigmaA estimation Scaling and SigmaA resln: 18.5778 1.4990 Damping factors: 1.0000 1.0000 **** Geometry restraints and weights **** Sigma: Bonding distances Weight = 1.00 Bond angles Weight = 1.00 Planar groups (all and main chain) WEIGHT= 1.00 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) 1.5A**2 Main chain angle (1-3 neighbour) 2.0A**2 Side chain bond 3.0A**2 Side chain angle 4.5A**2 RESTRAINTS AGAINST EXCESSIVE SHIFTS Positional parameters 0.00A Thermal parameters 0.00A Occupancy parameters 0.00 RADIUS OF CONFIDENCE Positional parameters 0.00A Thermal parameters 0.00A**2 Occupancy parameters 0.00 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 :buccaneer_pipeline/build.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 5.41 _lib_update 11/02/13 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 11464 with complete description : 11464 NUMBER OF MODIFICATIONS : 56 NUMBER OF LINKS : 68 I am reading libraries. Please wait. - energy parameters - monomer"s description (links & mod ) FORMATTED OLD file opened on unit 45 Logical name: ATOMSF, Filename: /home/jmht/ccp4-6.4.0/lib/data/atomsf.lib Number of atoms : 501 Number of residues : 60 Number of chains : 1 I am reading library. Please wait. mon_lib.cif -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:XX-XXX-XX -------------------------------- ATTENTION: atom:CG UNK 9 AA is missing in the structure ATTENTION: atom:CG UNK 10 AA is missing in the structure ATTENTION: atom:CG UNK 68 AA is missing in the structure Number of chains : 1 Total number of monomers : 60 Number of atoms : 504 Number of missing atoms : 3 Number of rebuilt atoms : 0 Number of unknown atoms : 0 Number of deleted atoms : 0 Number of bonds restraints : 506 Number of angles restraints : 680 Number of torsions restraints : 340 Number of chiralities : 78 Number of planar groups : 88 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 distances : 0 Number of angles : 0 Number of torsions : 0 Number of planes : 0 Number of chirals : 0 Number of intervals : 0 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Standard External All Bonds: 506 0 506 Angles: 680 0 680 Chirals: 78 0 78 Planes: 88 0 88 Torsions: 340 0 340 Intervals: 0 0 0 -------------------------------------------------------------------------------- Number of harmonic restraints = 0 Number of atoms in special position = 0 ----------------------------------------------------- **** Info from mtz file **** FreeR flag 0 Number of "free" reflections 809 Number of all reflections 16180 -------------------------------------------------------------------------------- Number of reflections in file 16180 Number of reflections read 16180 CGMAT cycle number = 1 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 96 96 288 Maximuum H,K,L : 27 27 78 Minimum acceptable grid spacing: 59 59 178 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 96 96 288 Maximuum H,K,L : 27 27 78 Minimum acceptable grid spacing: 59 59 178 Weight matrix 0.52774316 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 152. Norm of Geom. positional gradient 40.8 Norm of X_ray B-factor gradient 0.188E+04 Norm of Geom. B-factor gradient 0.00 Product of X_ray and Geom posit. gradients -0.336E+06 Cosine of angle between them -0.036 Product of X_ray and Geom B-fact gradients 0.00 Cosine of angle between them 0.000 Residuals: XRAY= 0.2776E+06 GEOM= 1085. TOTAL= 0.2786E+06 function value 278641.31 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 506 0.013 0.020 Bond angles : refined atoms 680 1.410 1.970 Torsion angles, period 1. refined 59 3.224 5.000 Torsion angles, period 2. refined 29 26.058 26.207 Torsion angles, period 3. refined 103 10.626 15.000 Torsion angles, period 4. refined 3 11.132 15.000 Chiral centres: refined atoms 78 0.077 0.200 Planar groups: refined atoms 374 0.000 0.020 VDW repulsions: refined_atoms 209 0.247 0.200 VDW; torsion: refined_atoms 368 0.312 0.200 HBOND: refined_atoms 5 0.383 0.200 VDW repulsions: symmetry: refined_atoms 37 0.454 0.200 HBOND: symmetry: refined_atoms 2 0.073 0.200 M. chain bond B values: refined atoms 239 0.000 3.948 M. chain angle B values: refined atoms 297 0.000 5.922 S. chain bond B values: refined atoms 264 0.000 3.948 S. chain angle B values: refined atoms 383 0.000 5.922 Long range B values: refined atoms 762 0.000 32.541 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.783, B = -22.082 Partial structure 1: scale = 0.468, B = 43.156 Overall anisotropic scale factors B11 = -0.12 B22 = -0.12 B33 = 0.38 B12 = -0.06 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 6.4: cbuccaneer version 1.5.2 : 06/10/11## ############################################################### User: unknown Run date: 17/ 7/2014 Run time: 18:57:42 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 2002-2010 Kevin Cowtan and University of York. $TEXT:Reference: $$ Please reference $$ 'Fitting molecular fragments into electron density' Cowtan K. (2008) Acta Cryst. D64, 83-89. $$ $TEXT:Reference: $$ Please reference $$ 'The Buccaneer software for automated model building' Cowtan K. (2006) Acta Cryst. D62, 1002-1011. $$ title buccaneer auto-build pdbin-ref /home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /home/jmht/ccp4-6.4.0/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 /data1/jmht/polya_helices/3PP5/search_polya_15/input/3PP5_1.fasta mtzin buccaneer_pipeline/refine.mtz colin-fo FP, SIGFP colin-hl HLACOMB,HLBCOMB,HLCCOMB,HLDCOMB colin-fc FWT,PHWT colin-free FREE pdbin buccaneer_pipeline/refine.pdb pdbout buccaneer_pipeline/build.pdb anisotropy-correction fast cycles 2 sequence-reliability 0.95 correlation-mode new-residue-name UNK resolution 2.0 MTZ file: buccaneer_pipeline/refine.mtz Number of reflections: 16180 Number of columns: 22 Applying anisotropy correction: |-9.393e-15, 5.745e-17, 4.529e-18| | 5.745e-17, 0,-1.019e-17| | 4.529e-18,-1.019e-17, -0.1105| PDB file: buccaneer_pipeline/refine.pdb Number of atoms read: 501 Cycle: 1 C-alphas after finding: 76 C-alphas after growing: 109 C-alphas after joining: 60 C-alphas linked: 0 C-alphas sequenced: 57 C-alphas corrected: 0 C-alphas after filtering: 60 C-alphas after NCS build: 60 C-alphas after pruning: 60 C-alphas after rebuilding: 60 Internal cycle 1 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) Cycle: 2 C-alphas after finding: 76 C-alphas after growing: 100 C-alphas after joining: 60 C-alphas linked: 0 C-alphas sequenced: 57 C-alphas corrected: 0 C-alphas after filtering: 60 C-alphas after NCS build: 60 C-alphas after pruning: 60 C-alphas after rebuilding: 60 Internal cycle 2 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) $TEXT:Result: $$ $$ 60 residues were built in 1 fragments, the longest having 60 residues. 57 residues were sequenced, after pruning. 60 residues were uniquely allocated to 1 chains. Completeness by residues built: 100.0% Completeness of chains (number): 82.2% (1) $$ cbuccaneer: Normal termination Times: User: 17.5s System: 0.0s Elapsed: 0:18
############################################################### ############################################################### ############################################################### ### CCP4 6.4: Refmac_5.8.0049 version 5.8.0049 : 30/06/13## ############################################################### User: unknown Run date: 17/ 7/2014 Run time: 18:58:00 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up.$TEXT:Reference1: $$ Main reference $$ "REFMAC5 for the refinement of macromolecular crystal structures:" G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) Acta Crystallogr. D67, 355-367 $$ $SUMMARY :Reference1: $$ Refmac: $$ :TEXT:Reference1: $$ $TEXT:Reference2: $$ Secondary reference $$ "Refinement of Macromolecular Structures by the Maximum-Likelihood Method:" G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997) Acta Crystallogr. D53, 240-255 EU Validation contract: BIO2CT-92-0524 $$ $SUMMARY :Reference2: $$ Refmac: $$ :TEXT:Reference2: $$ Data line--- title buccaneer auto-build Data line--- ncyc 10 Data line--- labin PHIB=PHIC FOM= FOM FREE=FREE FP=FP SIGFP= SIGFP Data line--- weight AUTO Data line--- make check NONE Data line--- make hydrogen NO hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO Data line--- refi type REST PHASE resi MLKF meth CGMAT bref ISOT Data line--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8 Data line--- PHOUT Data line--- PNAME buccaneer Data line--- DNAME buccaneer Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /home/jmht/ccp4-6.4.0/lib/data/syminfo.lib **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - buccaneer_pipeline/build.pdb Output coordinate file. Logical name - XYZOUT actual file name - buccaneer_pipeline/refine.pdb Input reflection file. Logical name - HKLIN actual file name - /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_outpu Output reflection file. Logical name - HKLOUT actual file name - buccaneer_pipeline/refine.mtz Cell from mtz : 39.140 39.140 118.190 90.000 90.000 120.000 Space group from mtz: number - 173; name - P 63 Refinement type : Restrained **** Makecif parameters **** Dictionary files for restraints : /home/jmht/ccp4-6.4.0/lib/data/monomers/mon*cif Parameters for new entry and VDW: /home/jmht/ccp4-6.4.0/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 will not be written to the output file 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 **** Map sharpening parameters and methods **** No map sharpening will be performed Method of minimisation : Sparse Matrix Experimental sigmas used for weighting Number of Bins and width: 20 0.0223 Refinement of individual isotropic Bfactors Refinement resln : 18.5778 1.4990 Estimated number of reflections : 26875 Free R exclusion - flag equals: 0 Auto weighting. An attempt Refinement cycles : 10 Scaling type : Wilson using 1 Gaussian Estimation of D/Sigma in resolution bins using free set of reflns with experimental sigmas Input phases not used in SigmaA estimation Scaling and SigmaA resln: 18.5778 1.4990 Damping factors: 1.0000 1.0000 **** Geometry restraints and weights **** Sigma: Bonding distances Weight = 1.00 Bond angles Weight = 1.00 Planar groups (all and main chain) WEIGHT= 1.00 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) 1.5A**2 Main chain angle (1-3 neighbour) 2.0A**2 Side chain bond 3.0A**2 Side chain angle 4.5A**2 RESTRAINTS AGAINST EXCESSIVE SHIFTS Positional parameters 0.00A Thermal parameters 0.00A Occupancy parameters 0.00 RADIUS OF CONFIDENCE Positional parameters 0.00A Thermal parameters 0.00A**2 Occupancy parameters 0.00 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 :buccaneer_pipeline/build.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 5.41 _lib_update 11/02/13 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 11464 with complete description : 11464 NUMBER OF MODIFICATIONS : 56 NUMBER OF LINKS : 68 I am reading libraries. Please wait. - energy parameters - monomer"s description (links & mod ) FORMATTED OLD file opened on unit 45 Logical name: ATOMSF, Filename: /home/jmht/ccp4-6.4.0/lib/data/atomsf.lib Number of atoms : 501 Number of residues : 60 Number of chains : 1 I am reading library. Please wait. mon_lib.cif -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:XX-XXX-XX -------------------------------- ATTENTION: atom:CG UNK 9 AA is missing in the structure ATTENTION: atom:CG UNK 10 AA is missing in the structure ATTENTION: atom:CG UNK 68 AA is missing in the structure Number of chains : 1 Total number of monomers : 60 Number of atoms : 504 Number of missing atoms : 3 Number of rebuilt atoms : 0 Number of unknown atoms : 0 Number of deleted atoms : 0 Number of bonds restraints : 506 Number of angles restraints : 680 Number of torsions restraints : 340 Number of chiralities : 78 Number of planar groups : 88 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 distances : 0 Number of angles : 0 Number of torsions : 0 Number of planes : 0 Number of chirals : 0 Number of intervals : 0 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Standard External All Bonds: 506 0 506 Angles: 680 0 680 Chirals: 78 0 78 Planes: 88 0 88 Torsions: 340 0 340 Intervals: 0 0 0 -------------------------------------------------------------------------------- Number of harmonic restraints = 0 Number of atoms in special position = 0 ----------------------------------------------------- **** Info from mtz file **** FreeR flag 0 Number of "free" reflections 809 Number of all reflections 16180 -------------------------------------------------------------------------------- Number of reflections in file 16180 Number of reflections read 16180 CGMAT cycle number = 1 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 96 96 288 Maximuum H,K,L : 27 27 78 Minimum acceptable grid spacing: 59 59 178 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 96 96 288 Maximuum H,K,L : 27 27 78 Minimum acceptable grid spacing: 59 59 178 Weight matrix 0.58211029 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 182. Norm of Geom. positional gradient 43.6 Norm of X_ray B-factor gradient 0.200E+04 Norm of Geom. B-factor gradient 0.00 Product of X_ray and Geom posit. gradients -0.637E+04 Cosine of angle between them -0.001 Product of X_ray and Geom B-fact gradients 0.00 Cosine of angle between them 0.000 Residuals: XRAY= 0.2787E+06 GEOM= 1076. TOTAL= 0.2798E+06 function value 279757.09 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 506 0.013 0.020 Bond angles : refined atoms 680 1.334 1.970 Torsion angles, period 1. refined 59 2.845 5.000 Torsion angles, period 2. refined 29 30.720 26.207 Torsion angles, period 3. refined 103 12.251 15.000 Torsion angles, period 4. refined 3 11.127 15.000 Chiral centres: refined atoms 78 0.073 0.200 Planar groups: refined atoms 374 0.000 0.020 VDW repulsions: refined_atoms 201 0.254 0.200 VDW; torsion: refined_atoms 368 0.311 0.200 HBOND: refined_atoms 6 0.327 0.200 VDW repulsions: symmetry: refined_atoms 36 0.442 0.200 HBOND: symmetry: refined_atoms 1 0.105 0.200 M. chain bond B values: refined atoms 239 0.000 3.948 M. chain angle B values: refined atoms 297 0.000 5.922 S. chain bond B values: refined atoms 264 0.000 3.948 S. chain angle B values: refined atoms 382 0.000 5.922 Long range B values: refined atoms 758 0.000 32.504 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.777, B = -22.205 Partial structure 1: scale = 0.458, B = 44.326 Overall anisotropic scale factors B11 = -0.12 B22 = -0.12 B33 = 0.37 B12 = -0.06 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.