The logfile is composed of output from the following programs:
Result:
165 residues were built in 3 chains, the longest having 73 residues. 125 residues were sequenced, after pruning.
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############################################################### ############################################################### ############################################################### ### 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
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Initial | After 10 cycles | |
---|---|---|
R factor | 0.443 | 0.326 |
Rfree | 0.500 | 0.458 |
The following tables were found in the logfile: Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. Fom(<cos(DelPhi)>-acentric, centric, overall v resln |
Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Rfactor analysis, stats vs cycle |
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############################################################### ############################################################### ############################################################### ### 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. v. resln :N:1,6,7,11,12: :Cycle 1. and v. resln :N:1,4,5,9,10: :Cycle 1. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.003 46 96.23 516.0 431.4 0.43 0.49 5 601.5 556.7 0.62 0.71 0.008 70 98.63 768.0 621.3 0.38 0.44 2 450.6 291.3 0.35 0.38 0.013 80 100.00 698.3 604.0 0.39 0.39 9 593.0 462.6 0.35 0.37 0.017 93 100.00 497.0 525.5 0.44 0.42 6 534.3 360.5 0.61 0.64 0.022 102 100.00 479.9 535.6 0.44 0.45 4 658.6 580.2 0.44 0.39 0.027 129 100.00 499.1 499.1 0.43 0.43 2 771.5 358.8 0.60 0.58 0.032 112 98.41 494.6 472.2 0.46 0.45 12 559.9 415.0 0.48 0.43 0.037 125 100.00 633.2 565.5 0.43 0.43 9 674.1 479.8 0.47 0.39 0.042 141 100.00 699.4 613.7 0.44 0.44 5 803.5 334.9 0.58 0.57 0.047 148 100.00 678.1 600.1 0.41 0.42 3 618.1 489.3 0.77 0.74 0.051 159 100.00 680.3 598.2 0.40 0.41 6 823.6 566.0 0.51 0.49 0.056 159 100.00 768.1 591.9 0.40 0.39 4 602.3 555.9 0.48 0.47 0.061 158 100.00 686.6 551.0 0.44 0.43 9 679.9 289.6 0.66 0.58 0.066 167 100.00 608.9 518.6 0.47 0.46 6 664.6 554.7 0.43 0.49 0.071 181 100.00 628.0 522.2 0.46 0.44 5 820.1 702.5 0.30 0.33 0.076 180 100.00 636.7 570.9 0.48 0.45 11 650.4 455.0 0.37 0.35 0.081 178 100.00 611.6 508.9 0.42 0.43 14 487.6 457.2 0.64 0.53 0.085 185 100.00 549.9 498.8 0.54 0.50 8 439.0 457.9 0.64 0.46 0.090 194 100.00 516.8 465.5 0.48 0.47 11 688.3 512.9 0.39 0.38 0.095 192 100.00 542.7 456.1 0.47 0.46 12 393.7 432.5 0.53 0.48 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 1. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 1. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0029 13 0.980 33 0.901 46 0.923 0.821 0.0077 30 0.944 40 0.956 70 0.951 0.824 0.0126 41 0.917 39 0.875 80 0.897 0.827 0.0175 56 0.936 37 0.819 93 0.889 0.829 0.0223 64 0.919 38 0.852 102 0.894 0.831 0.0272 81 0.922 48 0.816 129 0.882 0.833 0.0320 73 0.919 39 0.845 112 0.893 0.834 0.0369 86 0.915 39 0.814 125 0.883 0.836 0.0418 100 0.945 41 0.842 141 0.915 0.837 0.0466 109 0.920 39 0.840 148 0.899 0.839 0.0515 113 0.917 46 0.825 159 0.891 0.840 0.0563 114 0.932 45 0.874 159 0.916 0.841 0.0612 122 0.928 36 0.811 158 0.902 0.842 0.0661 124 0.886 43 0.796 167 0.863 0.843 0.0709 141 0.891 40 0.699 181 0.848 0.844 0.0758 133 0.902 47 0.658 180 0.838 0.845 0.0806 140 0.884 38 0.816 178 0.870 0.846 0.0855 145 0.875 40 0.762 185 0.851 0.847 0.0904 152 0.856 42 0.741 194 0.831 0.848 0.0952 151 0.876 41 0.735 192 0.846 0.849 $$ Resolution limits = 46.932 3.200 Number of used reflections = 2799 Percentage observed = 99.8303 Percentage of free reflections = 4.8606 Overall R factor = 0.4435 Free R factor = 0.5000 Overall weighted R factor = 0.4392 Free weighted R factor = 0.4651 Overall correlation coefficient = 0.5028 Free correlation coefficient = 0.3590 DPI based on free R factor = 1.0380 Overall figure of merit = 0.8772 ML based su of positional parameters = 0.9914 ML based su of thermal parameters = 54.7370 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Not converging with gamma equal 0.0000000E+00 Trying gamma equal 5.5000003E-02 Gamma decreased to 4.4000003E-02 CGMAT cycle number = 2 weigth matrix 0.1000000 special position ----------- 3.612395 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1154 0.063 0.022 Bond angles : refined atoms 1568 4.546 1.952 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.504, B = -11.506 Partial structure 1: scale = 0.294, B = -10.000 Overall anisotropic scale factors B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3782 Free R factor = 0.4797 Overall figure of merit = 0.8844 ----------------------------------------------------------------------------- Trying gamma equal 4.4000003E-02 Gamma decreased to 3.4000002E-02 CGMAT cycle number = 3 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1154 0.069 0.022 Bond angles : refined atoms 1568 4.618 1.952 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.503, B = -11.736 Partial structure 1: scale = 0.298, B = -9.111 Overall anisotropic scale factors B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3564 Free R factor = 0.4762 Overall figure of merit = 0.8857 ----------------------------------------------------------------------------- Trying gamma equal 3.4000002E-02 Gamma decreased to 2.4909092E-02 CGMAT cycle number = 4 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1154 0.072 0.022 Bond angles : refined atoms 1568 4.715 1.952 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.503, B = -11.962 Partial structure 1: scale = 0.297, B = -9.771 Overall anisotropic scale factors B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3437 Free R factor = 0.4699 Overall figure of merit = 0.8860 ----------------------------------------------------------------------------- Trying gamma equal 2.4909092E-02 Gamma decreased to 1.6644629E-02 CGMAT cycle number = 5 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1154 0.073 0.022 Bond angles : refined atoms 1568 4.787 1.952 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.503, B = -12.135 Partial structure 1: scale = 0.298, B = -8.520 Overall anisotropic scale factors B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3362 Free R factor = 0.4677 Overall figure of merit = 0.8860 ----------------------------------------------------------------------------- Trying gamma equal 1.6644629E-02 Gamma decreased to 9.1314809E-03 CGMAT cycle number = 6 weigth matrix 9.9999994E-02 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1154 0.074 0.022 Bond angles : refined atoms 1568 4.826 1.952 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.502, B = -12.606 Partial structure 1: scale = 0.298, B = -6.905 Overall anisotropic scale factors B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3302 Free R factor = 0.4636 Overall figure of merit = 0.8861 ----------------------------------------------------------------------------- Trying gamma equal 9.1314809E-03 Gamma decreased to 2.3013467E-03 CGMAT cycle number = 7 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1154 0.074 0.022 Bond angles : refined atoms 1568 4.851 1.952 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.505, B = -12.493 Partial structure 1: scale = 0.311, B = -2.434 Overall anisotropic scale factors B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3259 Free R factor = 0.4576 Overall figure of merit = 0.8864 ----------------------------------------------------------------------------- Trying gamma equal 2.3013467E-03 Gamma decreased to 0.0000000E+00 CGMAT cycle number = 8 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1154 0.074 0.022 Bond angles : refined atoms 1568 4.872 1.952 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.505, B = -12.666 Partial structure 1: scale = 0.312, B = -0.640 Overall anisotropic scale factors B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3222 Free R factor = 0.4524 Overall figure of merit = 0.8868 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Gamma decreased to 0.0000000E+00 CGMAT cycle number = 9 weigth matrix 9.9999994E-02 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1154 0.073 0.022 Bond angles : refined atoms 1568 4.890 1.952 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.508, B = -12.231 Partial structure 1: scale = 0.312, B = -4.475 Overall anisotropic scale factors B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3205 Free R factor = 0.4512 Overall figure of merit = 0.8876 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Gamma decreased to 0.0000000E+00 CGMAT cycle number = 10 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 127 PHE CE1 . - A 127 PHE CZ . mod.= 1.788 id.= 1.382 dev= -0.406 sig.= 0.030 A 137 ASP CB . - A 137 ASP CG . mod.= 1.916 id.= 1.516 dev= -0.400 sig.= 0.025 A 137 ASP C . - A 137 ASP O . mod.= 1.521 id.= 1.231 dev= -0.290 sig.= 0.020 A 145 LYS CB . - A 145 LYS CG . mod.= 1.896 id.= 1.520 dev= -0.376 sig.= 0.030 B 35 UNK C . - B 35 UNK O . mod.= 1.540 id.= 1.231 dev= -0.309 sig.= 0.020 B 35 UNK C . - B 36 UNK N . mod.= 0.765 id.= 1.329 dev= 0.564 sig.= 0.014 B 36 UNK N . - B 36 UNK CA . mod.= 1.769 id.= 1.458 dev= -0.311 sig.= 0.021 B 36 UNK C . - B 36 UNK O . mod.= 1.478 id.= 1.231 dev= -0.247 sig.= 0.020 B 36 UNK C . - B 37 UNK N . mod.= 1.186 id.= 1.329 dev= 0.143 sig.= 0.014 B 37 UNK C . - B 37 UNK O . mod.= 1.660 id.= 1.231 dev= -0.429 sig.= 0.020 B 38 UNK CA . - B 38 UNK C . mod.= 2.086 id.= 1.525 dev= -0.561 sig.= 0.021 B 38 UNK C . - B 39 VAL N . mod.= 1.120 id.= 1.329 dev= 0.209 sig.= 0.014 B 39 VAL N . - B 39 VAL CA . mod.= 1.719 id.= 1.458 dev= -0.261 sig.= 0.021 B 60 LEU CG . - B 60 LEU CD2 . mod.= 2.005 id.= 1.521 dev= -0.484 sig.= 0.033 B 63 UNK N . - B 63 UNK CA . mod.= 1.678 id.= 1.458 dev= -0.220 sig.= 0.021 B 63 UNK C . - B 64 ALA N . mod.= 1.548 id.= 1.329 dev= -0.219 sig.= 0.014 B 92 ARG CG . - B 92 ARG CD . mod.= 1.841 id.= 1.520 dev= -0.321 sig.= 0.030 C 16 UNK CA . - C 16 UNK CB . mod.= 1.865 id.= 1.521 dev= -0.344 sig.= 0.033 C 24 UNK C . - C 24 UNK O . mod.= 0.986 id.= 1.231 dev= 0.245 sig.= 0.020 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 111 PRO CA - A 111 PRO CD mod.= 97.38 id.= 112.00 dev= 14.622 sig.= 1.400 B 36 UNK N - B 36 UNK C mod.= 69.35 id.= 111.20 dev= 41.847 sig.= 2.800 B 37 UNK N - B 37 UNK C mod.= 81.76 id.= 111.20 dev= 29.442 sig.= 2.800 B 65 LYS O - B 66 GLY N mod.= 105.51 id.= 123.00 dev= 17.492 sig.= 1.600 C 25 UNK N - C 25 UNK C mod.= 80.83 id.= 111.20 dev= 30.367 sig.= 2.800 **** Torsion angle outliers **** Torsion angle deviations from the ideal >10.000Sigma will be monitored A 118 LEU CA - A 119 ILE CA mod.= 111.01 id.= 180.00 per.= 1 dev= 68.99 sig.= 5.00 A 136 SER CA - A 137 ASP CA mod.=-119.95 id.= 180.00 per.= 1 dev= -60.05 sig.= 5.00 B 35 UNK CA - B 36 UNK CA mod.= 116.07 id.= 180.00 per.= 1 dev= 63.93 sig.= 5.00 B 53 PRO CA - B 54 GLY CA mod.=-124.71 id.= 180.00 per.= 1 dev= -55.29 sig.= 5.00 B 54 GLY CA - B 55 GLY CA mod.=-118.21 id.= 180.00 per.= 1 dev= -61.79 sig.= 5.00 B 90 SER CA - B 91 GLY CA mod.= -99.86 id.= 180.00 per.= 1 dev= -80.14 sig.= 5.00 B 98 UNK CA - B 99 UNK CA mod.=-129.80 id.= 180.00 per.= 1 dev= -50.20 sig.= 5.00 **** Large deviation of atoms from planarity **** Deviations from the planarity >10.000Sigma will be monitored Atom: A 111 PRO N deviation= 0.23 sigma.= 0.02 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1154 0.082 0.022 Bond angles : refined atoms 1568 5.176 1.952 Torsion angles, period 1. refined 162 18.727 5.000 Torsion angles, period 2. refined 37 39.096 23.514 Torsion angles, period 3. refined 163 24.335 15.000 Torsion angles, period 4. refined 6 22.756 15.000 Chiral centres: refined atoms 191 0.300 0.200 Planar groups: refined atoms 861 0.020 0.020 VDW repulsions: refined atoms 552 0.406 0.200 VDW; torsion: refined atoms 793 0.393 0.200 HBOND: refined atoms 39 0.259 0.200 VDW repulsions; symmetry: refined atoms 82 0.576 0.200 HBOND; symmetry: refined atoms 1 0.134 0.200 M. chain bond B values: refined atoms 855 0.117 1.500 M. chain angle B values: refined atoms 1256 0.155 2.000 S. chain bond B values: refined atoms 367 1.545 3.000 S. chain angle B values: refined atoms 312 1.954 4.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.505, B = -12.824 Partial structure 1: scale = 0.313, B = -1.678 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 10. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 10. v. resln :N:1,6,7,11,12: :Cycle 10. and v. resln :N:1,4,5,9,10: :Cycle 10. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.003 46 96.23 528.6 428.2 0.48 0.54 5 616.2 516.3 0.54 0.59 0.008 70 98.63 786.7 678.0 0.36 0.41 2 461.7 48.4 0.90 0.86 0.013 80 100.00 715.4 602.5 0.34 0.35 9 607.5 468.2 0.34 0.34 0.017 93 100.00 509.2 535.0 0.35 0.35 6 547.4 392.2 0.57 0.58 0.022 102 100.00 491.7 491.6 0.38 0.39 4 674.7 551.2 0.37 0.41 0.027 129 100.00 511.3 495.4 0.40 0.40 2 790.4 532.1 0.39 0.39 0.032 112 98.41 506.7 474.1 0.45 0.44 12 573.6 447.2 0.52 0.50 0.037 125 100.00 648.7 621.1 0.35 0.36 9 690.5 567.1 0.51 0.49 0.042 141 100.00 716.5 672.5 0.31 0.31 5 823.1 472.9 0.43 0.43 0.047 148 100.00 694.7 637.7 0.31 0.33 3 633.2 385.3 0.46 0.37 0.051 159 100.00 696.9 652.3 0.28 0.28 6 843.7 689.4 0.30 0.29 0.056 159 100.00 786.8 703.6 0.27 0.27 4 617.0 595.7 0.58 0.56 0.061 158 100.00 703.4 611.1 0.29 0.29 9 696.5 519.0 0.45 0.40 0.066 167 100.00 623.7 591.6 0.31 0.30 6 680.8 540.4 0.66 0.68 0.071 181 100.00 643.3 583.0 0.31 0.30 5 840.1 767.6 0.33 0.38 0.076 180 100.00 652.2 611.4 0.30 0.29 11 666.3 568.3 0.33 0.37 0.081 178 100.00 626.6 580.5 0.28 0.28 14 499.6 521.2 0.46 0.41 0.085 185 100.00 563.3 555.9 0.30 0.29 8 449.8 401.2 0.61 0.49 0.090 194 100.00 529.4 493.7 0.32 0.29 11 705.1 534.0 0.43 0.40 0.095 192 100.00 556.0 537.9 0.31 0.29 12 403.4 442.3 0.46 0.39 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 10. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 10. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0029 13 0.980 33 0.880 46 0.908 0.885 0.0077 30 0.950 40 0.945 70 0.947 0.885 0.0126 41 0.925 39 0.893 80 0.909 0.884 0.0175 56 0.938 37 0.823 93 0.892 0.884 0.0223 64 0.921 38 0.845 102 0.893 0.884 0.0272 81 0.928 48 0.825 129 0.890 0.884 0.0320 73 0.926 39 0.860 112 0.903 0.883 0.0369 86 0.921 39 0.828 125 0.892 0.883 0.0418 100 0.947 41 0.830 141 0.913 0.883 0.0466 109 0.929 39 0.858 148 0.910 0.883 0.0515 113 0.925 46 0.841 159 0.901 0.883 0.0563 114 0.943 45 0.865 159 0.921 0.882 0.0612 122 0.937 36 0.786 158 0.903 0.882 0.0661 124 0.904 43 0.826 167 0.884 0.882 0.0709 141 0.899 40 0.702 181 0.856 0.882 0.0758 133 0.914 47 0.657 180 0.847 0.882 0.0806 140 0.897 38 0.824 178 0.881 0.882 0.0855 145 0.894 40 0.801 185 0.874 0.882 0.0904 152 0.877 42 0.753 194 0.850 0.881 0.0952 151 0.885 41 0.790 192 0.864 0.881 $$ Resolution limits = 46.932 3.200 Number of used reflections = 2799 Percentage observed = 99.8303 Percentage of free reflections = 4.8606 Overall R factor = 0.3194 Free R factor = 0.4564 Overall weighted R factor = 0.3215 Free weighted R factor = 0.4437 Overall correlation coefficient = 0.7458 Free correlation coefficient = 0.5074 DPI based on free R factor = 0.9476 Overall figure of merit = 0.8869 ML based su of positional parameters = 0.7466 ML based su of thermal parameters = 40.9093 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Gamma decreased to 0.0000000E+00 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 118 LEU C . - A 119 ILE N . mod.= 1.058 id.= 1.329 dev= 0.271 sig.= 0.014 A 119 ILE N . - A 119 ILE CA . mod.= 1.820 id.= 1.458 dev= -0.362 sig.= 0.021 A 119 ILE CA . - A 119 ILE C . mod.= 1.837 id.= 1.525 dev= -0.312 sig.= 0.021 A 119 ILE C . - A 120 ASN N . mod.= 1.530 id.= 1.329 dev= -0.201 sig.= 0.014 A 120 ASN CA . - A 120 ASN C . mod.= 1.242 id.= 1.525 dev= 0.283 sig.= 0.021 A 120 ASN C . - A 120 ASN O . mod.= 0.973 id.= 1.231 dev= 0.258 sig.= 0.020 A 121 ASP CG . - A 121 ASP OD2 . mod.= 1.598 id.= 1.249 dev= -0.349 sig.= 0.019 A 127 PHE CE1 . - A 127 PHE CZ . mod.= 1.795 id.= 1.382 dev= -0.413 sig.= 0.030 A 137 ASP CB . - A 137 ASP CG . mod.= 1.924 id.= 1.516 dev= -0.408 sig.= 0.025 A 137 ASP C . - A 137 ASP O . mod.= 1.517 id.= 1.231 dev= -0.286 sig.= 0.020 A 145 LYS CB . - A 145 LYS CG . mod.= 1.879 id.= 1.520 dev= -0.359 sig.= 0.030 B 35 UNK N . - B 35 UNK CA . mod.= 1.988 id.= 1.491 dev= -0.497 sig.= 0.021 B 35 UNK C . - B 35 UNK O . mod.= 1.540 id.= 1.231 dev= -0.309 sig.= 0.020 B 35 UNK C . - B 36 UNK N . mod.= 1.096 id.= 1.329 dev= 0.233 sig.= 0.014 B 38 UNK CA . - B 38 UNK C . mod.= 1.805 id.= 1.525 dev= -0.280 sig.= 0.021 B 60 LEU CG . - B 60 LEU CD2 . mod.= 1.929 id.= 1.521 dev= -0.408 sig.= 0.033 B 63 UNK C . - B 64 ALA N . mod.= 1.534 id.= 1.329 dev= -0.205 sig.= 0.014 B 65 LYS CD . - B 65 LYS CE . mod.= 2.084 id.= 1.520 dev= -0.564 sig.= 0.030 B 65 LYS CE . - B 65 LYS NZ . mod.= 1.930 id.= 1.489 dev= -0.441 sig.= 0.030 B 65 LYS C . - B 66 GLY N . mod.= 1.826 id.= 1.329 dev= -0.497 sig.= 0.014 B 66 GLY CA . - B 66 GLY C . mod.= 1.754 id.= 1.516 dev= -0.238 sig.= 0.018 B 69 TRP NE1 . - B 69 TRP CE2 . mod.= 1.535 id.= 1.370 dev= -0.165 sig.= 0.011 B 89 GLY N . - B 89 GLY CA . mod.= 1.685 id.= 1.458 dev= -0.227 sig.= 0.021 B 92 ARG CG . - B 92 ARG CD . mod.= 1.876 id.= 1.520 dev= -0.356 sig.= 0.030 C 16 UNK CA . - C 16 UNK CB . mod.= 1.868 id.= 1.521 dev= -0.347 sig.= 0.033 C 23 UNK C . - C 23 UNK O . mod.= 1.444 id.= 1.231 dev= -0.213 sig.= 0.020 C 23 UNK C . - C 24 UNK N . mod.= 1.495 id.= 1.329 dev= -0.166 sig.= 0.014 C 24 UNK C . - C 25 UNK N . mod.= 1.562 id.= 1.329 dev= -0.233 sig.= 0.014 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 107 UNK N - A 107 UNK C mod.= 78.94 id.= 111.20 dev= 32.261 sig.= 2.800 A 118 LEU N - A 118 LEU CB mod.= 91.27 id.= 110.50 dev= 19.226 sig.= 1.700 A 118 LEU CA - A 118 LEU O mod.= 103.70 id.= 120.80 dev= 17.102 sig.= 1.700 A 119 ILE CA - A 120 ASN N mod.= 92.64 id.= 116.20 dev= 23.559 sig.= 2.000 A 119 ILE C - A 120 ASN CA mod.= 100.90 id.= 121.70 dev= 20.805 sig.= 1.800 A 120 ASN CA - A 120 ASN O mod.= 99.49 id.= 120.80 dev= 21.307 sig.= 1.700 B 35 UNK N - B 35 UNK CB mod.= 133.52 id.= 110.40 dev=-23.116 sig.= 1.500 B 65 LYS CG - B 65 LYS CE mod.= 87.48 id.= 111.30 dev= 23.816 sig.= 2.300 B 65 LYS O - B 66 GLY N mod.= 106.62 id.= 123.00 dev= 16.382 sig.= 1.600 B 65 LYS CA - B 66 GLY N mod.= 136.28 id.= 116.20 dev=-20.084 sig.= 2.000 B 66 GLY CA - B 66 GLY O mod.= 149.47 id.= 120.80 dev=-28.674 sig.= 1.700 C 25 UNK N - C 25 UNK C mod.= 82.47 id.= 111.20 dev= 28.734 sig.= 2.800 **** Torsion angle outliers **** Torsion angle deviations from the ideal >10.000Sigma will be monitored A 118 LEU CA - A 119 ILE CA mod.= 118.93 id.= 180.00 per.= 1 dev= 61.07 sig.= 5.00 A 136 SER CA - A 137 ASP CA mod.=-119.72 id.= 180.00 per.= 1 dev= -60.28 sig.= 5.00 B 35 UNK CA - B 36 UNK CA mod.= 117.71 id.= 180.00 per.= 1 dev= 62.29 sig.= 5.00 B 53 PRO CA - B 54 GLY CA mod.=-125.50 id.= 180.00 per.= 1 dev= -54.50 sig.= 5.00 B 54 GLY CA - B 55 GLY CA mod.=-119.84 id.= 180.00 per.= 1 dev= -60.16 sig.= 5.00 B 90 SER CA - B 91 GLY CA mod.= -99.24 id.= 180.00 per.= 1 dev= -80.76 sig.= 5.00 **** Large deviation of atoms from planarity **** Deviations from the planarity >10.000Sigma will be monitored Atom: A 111 PRO N deviation= 0.23 sigma.= 0.02 WRITTEN OUTPUT MTZ FILE Logical Name: HKLOUT Filename: /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1154 0.087 0.022 Bond angles : refined atoms 1568 5.566 1.952 Torsion angles, period 1. refined 162 19.402 5.000 Torsion angles, period 2. refined 37 39.300 23.514 Torsion angles, period 3. refined 163 24.091 15.000 Torsion angles, period 4. refined 6 25.144 15.000 Chiral centres: refined atoms 191 0.283 0.200 Planar groups: refined atoms 861 0.024 0.020 VDW repulsions: refined atoms 562 0.418 0.200 VDW; torsion: refined atoms 779 0.393 0.200 HBOND: refined atoms 39 0.293 0.200 VDW repulsions; symmetry: refined atoms 75 0.565 0.200 HBOND; symmetry: refined atoms 1 0.085 0.200 M. chain bond B values: refined atoms 857 0.090 1.500 M. chain angle B values: refined atoms 1256 0.124 2.000 S. chain bond B values: refined atoms 365 1.340 3.000 S. chain angle B values: refined atoms 312 1.822 4.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.510, B = -12.100 Partial structure 1: scale = 0.312, B = -8.977 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 11. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 11. v. resln :N:1,6,7,11,12: :Cycle 11. and v. resln :N:1,4,5,9,10: :Cycle 11. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.003 46 96.23 524.1 428.4 0.47 0.53 5 610.8 527.1 0.54 0.60 0.008 70 98.63 779.9 674.7 0.36 0.41 2 457.7 30.3 0.93 0.91 0.013 80 100.00 709.2 601.4 0.34 0.35 9 602.3 453.5 0.35 0.36 0.017 93 100.00 504.8 533.4 0.37 0.36 6 542.7 387.9 0.47 0.49 0.022 102 100.00 487.4 497.5 0.41 0.42 4 668.8 531.0 0.38 0.43 0.027 129 100.00 506.9 495.4 0.42 0.42 2 783.6 531.5 0.43 0.46 0.032 112 98.41 502.3 470.2 0.43 0.42 12 568.6 445.0 0.53 0.51 0.037 125 100.00 643.1 619.8 0.33 0.34 9 684.6 562.0 0.55 0.53 0.042 141 100.00 710.3 649.7 0.32 0.33 5 816.0 431.9 0.47 0.48 0.047 148 100.00 688.7 627.0 0.31 0.33 3 627.8 361.4 0.47 0.29 0.051 159 100.00 690.9 634.4 0.29 0.30 6 836.4 689.2 0.27 0.26 0.056 159 100.00 780.0 702.2 0.27 0.27 4 611.7 568.3 0.48 0.47 0.061 158 100.00 697.3 601.3 0.31 0.30 9 690.5 535.0 0.50 0.42 0.066 167 100.00 618.4 581.3 0.31 0.31 6 675.0 573.9 0.59 0.61 0.071 181 100.00 637.7 583.7 0.33 0.32 5 832.9 784.3 0.34 0.39 0.076 180 100.00 646.6 615.1 0.31 0.30 11 660.6 620.4 0.34 0.37 0.081 178 100.00 621.2 577.1 0.28 0.28 14 495.2 509.8 0.44 0.38 0.085 185 100.00 558.5 550.7 0.32 0.31 8 445.9 372.1 0.67 0.55 0.090 194 100.00 524.8 488.3 0.33 0.31 11 699.0 522.9 0.47 0.46 0.095 192 100.00 551.2 527.3 0.31 0.31 12 399.9 416.5 0.41 0.34 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 11. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 11. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0029 13 0.980 33 0.880 46 0.908 0.883 0.0077 30 0.947 40 0.944 70 0.945 0.883 0.0126 41 0.927 39 0.893 80 0.911 0.883 0.0175 56 0.938 37 0.829 93 0.895 0.884 0.0223 64 0.922 38 0.850 102 0.895 0.884 0.0272 81 0.929 48 0.830 129 0.892 0.884 0.0320 73 0.926 39 0.858 112 0.903 0.884 0.0369 86 0.920 39 0.825 125 0.890 0.884 0.0418 100 0.947 41 0.831 141 0.913 0.884 0.0466 109 0.929 39 0.864 148 0.912 0.884 0.0515 113 0.924 46 0.840 159 0.900 0.884 0.0563 114 0.944 45 0.867 159 0.922 0.885 0.0612 122 0.937 36 0.789 158 0.904 0.885 0.0661 124 0.903 43 0.818 167 0.881 0.885 0.0709 141 0.900 40 0.697 181 0.855 0.885 0.0758 133 0.914 47 0.656 180 0.847 0.885 0.0806 140 0.901 38 0.826 178 0.885 0.885 0.0855 145 0.897 40 0.797 185 0.876 0.885 0.0904 152 0.879 42 0.760 194 0.853 0.885 0.0952 151 0.883 41 0.807 192 0.866 0.885 $$ Resolution limits = 46.932 3.200 Number of used reflections = 2799 Percentage observed = 99.8303 Percentage of free reflections = 4.8606 Overall R factor = 0.3264 Free R factor = 0.4581 Overall weighted R factor = 0.3301 Free weighted R factor = 0.4436 Overall correlation coefficient = 0.7417 Free correlation coefficient = 0.5118 DPI based on free R factor = 0.9509 Overall figure of merit = 0.8877 ML based su of positional parameters = 0.7466 ML based su of thermal parameters = 40.9093 ----------------------------------------------------------------------------- Time in seconds: CPU = 5.34 Elapsed = 6.00 **** Things for loggraph, R factor and others vs cycle **** $TABLE: Rfactor analysis, stats vs cycle : $GRAPHS: vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LLG vs cycle :N:1,5: :Geometry vs cycle:N:1,6,7,8: $$ Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$ $$ 0 0.443 0.500 0.877 1296.8 0.055 4.884 0.179 1 0.378 0.480 0.884 642.8 0.063 4.546 0.209 2 0.356 0.476 0.886 439.1 0.069 4.618 0.258 3 0.344 0.470 0.886 323.4 0.072 4.715 0.267 4 0.336 0.468 0.886 257.8 0.073 4.787 0.259 5 0.330 0.464 0.886 223.0 0.074 4.826 0.259 6 0.326 0.458 0.886 165.7 0.074 4.851 0.260 7 0.322 0.452 0.887 129.1 0.074 4.872 0.260 8 0.321 0.451 0.888 86.6 0.073 4.890 0.259 9 0.319 0.456 0.887 121.7 0.082 5.176 0.300 10 0.326 0.458 0.888 111.4 0.087 5.566 0.283 $$
Refmac_5.3.0037: End of Refmac_5.3.0037 Times: User: 7.5s System: 0.3s Elapsed: 0:09
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Result:
175 residues were built in 3 chains, the longest having 84 residues. 141 residues were sequenced, after pruning.
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############################################################### ############################################################### ############################################################### ### 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
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Initial | After 10 cycles | |
---|---|---|
R factor | 0.390 | 0.274 |
Rfree | 0.441 | 0.386 |
The following tables were found in the logfile: Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. Fom(<cos(DelPhi)>-acentric, centric, overall v resln |
Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Rfactor analysis, stats vs cycle |
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############################################################### ############################################################### ############################################################### ### 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. v. resln :N:1,6,7,11,12: :Cycle 1. and v. resln :N:1,4,5,9,10: :Cycle 1. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.003 46 96.23 556.8 466.7 0.44 0.52 5 649.0 553.1 0.28 0.32 0.008 70 98.63 828.7 640.4 0.34 0.36 2 486.3 163.4 0.66 0.53 0.013 80 100.00 753.5 689.7 0.33 0.34 9 639.9 540.4 0.46 0.54 0.017 93 100.00 536.3 505.4 0.34 0.34 6 576.6 442.6 0.38 0.37 0.022 102 100.00 517.9 499.2 0.45 0.46 4 710.6 514.3 0.62 0.50 0.027 129 100.00 538.6 550.6 0.38 0.37 2 832.5 502.4 0.40 0.41 0.032 112 98.41 533.7 556.9 0.49 0.47 12 604.1 504.3 0.40 0.34 0.037 125 100.00 683.3 641.1 0.38 0.38 9 727.4 636.5 0.44 0.37 0.042 141 100.00 754.7 735.3 0.35 0.36 5 867.0 668.5 0.23 0.27 0.047 148 100.00 731.8 663.1 0.37 0.38 3 667.0 590.6 0.43 0.44 0.051 159 100.00 734.1 667.4 0.35 0.35 6 888.7 650.7 0.27 0.23 0.056 159 100.00 828.8 708.4 0.33 0.34 4 649.9 603.1 0.56 0.55 0.061 158 100.00 740.9 607.3 0.37 0.36 9 733.7 360.5 0.58 0.57 0.066 167 100.00 657.0 556.8 0.41 0.40 6 717.1 525.8 0.44 0.44 0.071 181 100.00 677.6 578.2 0.42 0.40 5 884.9 582.9 0.40 0.41 0.076 180 100.00 687.0 591.7 0.41 0.40 11 701.9 538.2 0.42 0.47 0.081 178 100.00 660.0 598.2 0.38 0.37 14 526.2 535.4 0.49 0.47 0.085 185 100.00 593.4 546.2 0.44 0.42 8 473.7 431.4 0.74 0.61 0.090 194 100.00 557.6 503.9 0.44 0.43 11 742.7 517.0 0.39 0.40 0.095 192 100.00 585.6 569.2 0.41 0.40 12 424.9 357.5 0.46 0.43 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 1. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 1. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0029 13 0.980 33 0.925 46 0.941 0.895 0.0077 30 0.948 40 0.941 70 0.944 0.892 0.0126 41 0.922 39 0.879 80 0.901 0.890 0.0175 56 0.934 37 0.797 93 0.880 0.889 0.0223 64 0.919 38 0.839 102 0.889 0.888 0.0272 81 0.932 48 0.837 129 0.897 0.887 0.0320 73 0.926 39 0.870 112 0.906 0.885 0.0369 86 0.916 39 0.864 125 0.900 0.884 0.0418 100 0.945 41 0.843 141 0.915 0.884 0.0466 109 0.929 39 0.833 148 0.904 0.883 0.0515 113 0.920 46 0.824 159 0.892 0.882 0.0563 114 0.934 45 0.902 159 0.925 0.881 0.0612 122 0.928 36 0.798 158 0.899 0.880 0.0661 124 0.895 43 0.825 167 0.877 0.880 0.0709 141 0.898 40 0.720 181 0.859 0.879 0.0758 133 0.906 47 0.655 180 0.841 0.878 0.0806 140 0.892 38 0.806 178 0.874 0.878 0.0855 145 0.886 40 0.754 185 0.857 0.877 0.0904 152 0.869 42 0.747 194 0.843 0.876 0.0952 151 0.878 41 0.798 192 0.861 0.876 $$ Resolution limits = 46.932 3.200 Number of used reflections = 2799 Percentage observed = 99.8303 Percentage of free reflections = 4.8606 Overall R factor = 0.3896 Free R factor = 0.4406 Overall weighted R factor = 0.3885 Free weighted R factor = 0.4340 Overall correlation coefficient = 0.6297 Free correlation coefficient = 0.5329 DPI based on free R factor = 0.9531 Overall figure of merit = 0.8837 ML based su of positional parameters = 0.8548 ML based su of thermal parameters = 47.1747 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Convergence reached with no gamma cycles CGMAT cycle number = 2 weigth matrix 0.1000000 special position ----------- 3.340322 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1254 0.065 0.022 Bond angles : refined atoms 1703 5.299 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.483, B = -13.479 Partial structure 1: scale = 0.311, B = -6.884 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3314 Free R factor = 0.4055 Overall figure of merit = 0.8893 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Not converging with gamma equal 0.0000000E+00 Trying gamma equal 5.5000003E-02 Gamma decreased to 4.4000003E-02 CGMAT cycle number = 3 weigth matrix 0.1000000 special position ----------- 3.866606 special position ----------- 3.413604 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1254 0.061 0.022 Bond angles : refined atoms 1703 4.758 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.483, B = -13.581 Partial structure 1: scale = 0.312, B = -1.015 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3105 Free R factor = 0.3929 Overall figure of merit = 0.8917 ----------------------------------------------------------------------------- Trying gamma equal 4.4000003E-02 Gamma decreased to 3.4000002E-02 CGMAT cycle number = 4 weigth matrix 9.9999994E-02 special position ----------- 3.785506 special position ----------- 3.482043 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1254 0.062 0.022 Bond angles : refined atoms 1703 4.654 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.484, B = -13.679 Partial structure 1: scale = 0.312, B = -0.111 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2993 Free R factor = 0.3864 Overall figure of merit = 0.8933 ----------------------------------------------------------------------------- Trying gamma equal 3.4000002E-02 Gamma decreased to 2.4909092E-02 CGMAT cycle number = 5 weigth matrix 0.1000000 special position ----------- 3.820793 special position ----------- 3.556735 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1254 0.063 0.022 Bond angles : refined atoms 1703 4.614 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.484, B = -13.938 Partial structure 1: scale = 0.310, B = 1.072 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2925 Free R factor = 0.3862 Overall figure of merit = 0.8941 ----------------------------------------------------------------------------- Trying gamma equal 2.4909092E-02 Gamma decreased to 1.6644629E-02 CGMAT cycle number = 6 weigth matrix 0.1000000 special position ----------- 3.717989 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1254 0.063 0.022 Bond angles : refined atoms 1703 4.574 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.484, B = -14.011 Partial structure 1: scale = 0.310, B = 0.654 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2874 Free R factor = 0.3847 Overall figure of merit = 0.8947 ----------------------------------------------------------------------------- Trying gamma equal 1.6644629E-02 Gamma decreased to 9.1314809E-03 CGMAT cycle number = 7 weigth matrix 0.1000000 special position ----------- 3.892307 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1254 0.062 0.022 Bond angles : refined atoms 1703 4.537 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.484, B = -14.207 Partial structure 1: scale = 0.310, B = 1.120 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2835 Free R factor = 0.3827 Overall figure of merit = 0.8949 ----------------------------------------------------------------------------- Trying gamma equal 9.1314809E-03 Gamma decreased to 2.3013467E-03 CGMAT cycle number = 8 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1254 0.062 0.022 Bond angles : refined atoms 1703 4.500 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.485, B = -14.339 Partial structure 1: scale = 0.310, B = 2.082 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2801 Free R factor = 0.3849 Overall figure of merit = 0.8950 ----------------------------------------------------------------------------- Trying gamma equal 2.3013467E-03 Not converging with gamma equal 2.3013467E-03 Trying gamma equal 3.6452018E-02 Gamma decreased to 2.9621884E-02 CGMAT cycle number = 9 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1254 0.062 0.022 Bond angles : refined atoms 1703 4.462 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.485, B = -14.313 Partial structure 1: scale = 0.308, B = 0.494 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2781 Free R factor = 0.3841 Overall figure of merit = 0.8953 ----------------------------------------------------------------------------- Trying gamma equal 2.9621884E-02 Gamma decreased to 2.3412671E-02 CGMAT cycle number = 10 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 137 ASP C . - A 138 PRO N . mod.= 1.517 id.= 1.341 dev= -0.176 sig.= 0.016 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 106 GLY C - A 107 VAL CA mod.= 101.87 id.= 121.70 dev= 19.833 sig.= 1.800 A 107 VAL N - A 107 VAL C mod.= 141.06 id.= 111.20 dev=-29.859 sig.= 2.800 **** Torsion angle outliers **** Torsion angle deviations from the ideal >10.000Sigma will be monitored A 137 ASP CA - A 138 PRO CA mod.= 114.58 id.= 180.00 per.= 1 dev= 65.42 sig.= 5.00 B 34 UNK CA - B 35 UNK CA mod.= 120.39 id.= 180.00 per.= 1 dev= 59.61 sig.= 5.00 B 52 PRO CA - B 53 GLY CA mod.=-123.26 id.= 180.00 per.= 1 dev= -56.74 sig.= 5.00 B 90 SER CA - B 91 GLY CA mod.= -93.50 id.= 180.00 per.= 1 dev= -86.50 sig.= 5.00 **** Large deviation of atoms from planarity **** Deviations from the planarity >10.000Sigma will be monitored Atom: A 109 PRO N deviation= -0.20 sigma.= 0.02 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored A 137 ASP OD1 . - A 138 PRO CD . mod.= 1.371 id.= 3.440 dev= -2.07 sig.= 0.20 sym.= 1 0 0 0 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1254 0.061 0.022 Bond angles : refined atoms 1703 4.427 1.960 Torsion angles, period 1. refined 172 16.779 5.000 Torsion angles, period 2. refined 42 41.314 24.048 Torsion angles, period 3. refined 189 22.708 15.000 Torsion angles, period 4. refined 6 18.244 15.000 Chiral centres: refined atoms 208 0.267 0.200 Planar groups: refined atoms 928 0.016 0.020 VDW repulsions: refined atoms 710 0.462 0.200 VDW; torsion: refined atoms 863 0.388 0.200 HBOND: refined atoms 54 0.340 0.200 VDW repulsions; symmetry: refined atoms 35 0.305 0.200 HBOND; symmetry: refined atoms 1 0.110 0.200 M. chain bond B values: refined atoms 894 0.000 1.500 M. chain angle B values: refined atoms 1350 0.000 2.000 S. chain bond B values: refined atoms 413 0.799 3.000 S. chain angle B values: refined atoms 353 1.473 4.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.487, B = -13.964 Partial structure 1: scale = 0.308, B = -2.091 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 10. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 10. v. resln :N:1,6,7,11,12: :Cycle 10. and v. resln :N:1,4,5,9,10: :Cycle 10. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.003 46 96.23 547.9 470.8 0.39 0.47 5 638.6 521.6 0.38 0.46 0.008 70 98.63 815.4 651.2 0.32 0.35 2 478.5 204.5 0.76 0.64 0.013 80 100.00 741.4 686.9 0.27 0.29 9 629.6 514.2 0.30 0.33 0.017 93 100.00 527.7 517.6 0.32 0.32 6 567.3 397.9 0.45 0.45 0.022 102 100.00 509.5 496.7 0.39 0.40 4 699.2 413.4 0.44 0.36 0.027 129 100.00 530.0 523.8 0.36 0.37 2 819.2 530.4 0.35 0.39 0.032 112 98.41 525.1 536.5 0.38 0.38 12 594.4 490.1 0.41 0.38 0.037 125 100.00 672.3 649.2 0.32 0.33 9 715.7 791.8 0.32 0.31 0.042 141 100.00 742.6 732.5 0.26 0.26 5 853.1 632.6 0.26 0.27 0.047 148 100.00 720.0 677.5 0.24 0.24 3 656.3 451.2 0.69 0.64 0.051 159 100.00 722.3 698.7 0.25 0.25 6 874.4 736.8 0.18 0.17 0.056 159 100.00 815.5 738.6 0.25 0.25 4 639.4 640.4 0.36 0.36 0.061 158 100.00 729.0 664.2 0.25 0.26 9 721.9 390.2 0.51 0.53 0.066 167 100.00 646.4 608.5 0.26 0.27 6 705.6 618.7 0.40 0.37 0.071 181 100.00 666.7 612.3 0.26 0.27 5 870.7 792.7 0.16 0.18 0.076 180 100.00 676.0 625.1 0.26 0.26 11 690.6 569.8 0.39 0.39 0.081 178 100.00 649.4 607.2 0.25 0.25 14 517.7 559.2 0.41 0.39 0.085 185 100.00 583.8 586.7 0.26 0.25 8 466.1 375.7 0.58 0.49 0.090 194 100.00 548.7 527.7 0.27 0.26 11 730.8 582.7 0.35 0.32 0.095 192 100.00 576.2 564.4 0.26 0.25 12 418.0 399.7 0.50 0.47 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 10. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 10. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0029 13 0.981 33 0.905 46 0.926 0.915 0.0077 30 0.954 40 0.950 70 0.952 0.915 0.0126 41 0.927 39 0.888 80 0.908 0.916 0.0175 56 0.937 37 0.825 93 0.892 0.916 0.0223 64 0.928 38 0.855 102 0.901 0.916 0.0272 81 0.934 48 0.843 129 0.900 0.917 0.0320 73 0.934 39 0.869 112 0.911 0.917 0.0369 86 0.927 39 0.860 125 0.906 0.917 0.0418 100 0.953 41 0.843 141 0.921 0.917 0.0466 109 0.938 39 0.865 148 0.918 0.917 0.0515 113 0.928 46 0.838 159 0.902 0.918 0.0563 114 0.947 45 0.904 159 0.935 0.918 0.0612 122 0.941 36 0.837 158 0.917 0.918 0.0661 124 0.910 43 0.824 167 0.888 0.918 0.0709 141 0.913 40 0.737 181 0.874 0.918 0.0758 133 0.924 47 0.652 180 0.853 0.918 0.0806 140 0.905 38 0.829 178 0.889 0.919 0.0855 145 0.901 40 0.799 185 0.879 0.919 0.0904 152 0.885 42 0.788 194 0.864 0.919 0.0952 151 0.894 41 0.795 192 0.873 0.919 $$ Resolution limits = 46.932 3.200 Number of used reflections = 2799 Percentage observed = 99.8303 Percentage of free reflections = 4.8606 Overall R factor = 0.2761 Free R factor = 0.3848 Overall weighted R factor = 0.2830 Free weighted R factor = 0.3781 Overall correlation coefficient = 0.8118 Free correlation coefficient = 0.6305 DPI based on free R factor = 0.8326 Overall figure of merit = 0.8957 ML based su of positional parameters = 0.6276 ML based su of thermal parameters = 34.2870 ----------------------------------------------------------------------------- Trying gamma equal 2.3412671E-02 Gamma decreased to 1.7767932E-02 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 137 ASP C . - A 138 PRO N . mod.= 1.517 id.= 1.341 dev= -0.176 sig.= 0.016 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 98 UNK C - A 99 UNK CA mod.= 103.32 id.= 121.70 dev= 18.377 sig.= 1.800 A 106 GLY C - A 107 VAL CA mod.= 101.45 id.= 121.70 dev= 20.248 sig.= 1.800 A 107 VAL N - A 107 VAL C mod.= 142.08 id.= 111.20 dev=-30.881 sig.= 2.800 **** Torsion angle outliers **** Torsion angle deviations from the ideal >10.000Sigma will be monitored A 137 ASP CA - A 138 PRO CA mod.= 114.78 id.= 180.00 per.= 1 dev= 65.22 sig.= 5.00 B 34 UNK CA - B 35 UNK CA mod.= 119.89 id.= 180.00 per.= 1 dev= 60.11 sig.= 5.00 B 52 PRO CA - B 53 GLY CA mod.=-123.53 id.= 180.00 per.= 1 dev= -56.47 sig.= 5.00 B 90 SER CA - B 91 GLY CA mod.= -93.13 id.= 180.00 per.= 1 dev= -86.87 sig.= 5.00 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored A 137 ASP OD1 . - A 138 PRO CD . mod.= 1.361 id.= 3.440 dev= -2.08 sig.= 0.20 sym.= 1 0 0 0 WRITTEN OUTPUT MTZ FILE Logical Name: HKLOUT Filename: /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1254 0.061 0.022 Bond angles : refined atoms 1703 4.388 1.960 Torsion angles, period 1. refined 172 16.834 5.000 Torsion angles, period 2. refined 42 42.053 24.048 Torsion angles, period 3. refined 189 22.766 15.000 Torsion angles, period 4. refined 6 19.290 15.000 Chiral centres: refined atoms 208 0.271 0.200 Planar groups: refined atoms 928 0.016 0.020 VDW repulsions: refined atoms 705 0.457 0.200 VDW; torsion: refined atoms 862 0.386 0.200 HBOND: refined atoms 55 0.332 0.200 VDW repulsions; symmetry: refined atoms 33 0.317 0.200 HBOND; symmetry: refined atoms 1 0.162 0.200 M. chain bond B values: refined atoms 893 0.000 1.500 M. chain angle B values: refined atoms 1350 0.000 2.000 S. chain bond B values: refined atoms 414 0.783 3.000 S. chain angle B values: refined atoms 353 1.412 4.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.487, B = -14.084 Partial structure 1: scale = 0.307, B = -0.930 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 11. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 11. v. resln :N:1,6,7,11,12: :Cycle 11. and v. resln :N:1,4,5,9,10: :Cycle 11. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.003 46 96.23 547.8 472.6 0.39 0.48 5 638.5 524.6 0.39 0.46 0.008 70 98.63 815.3 655.6 0.32 0.35 2 478.4 212.3 0.74 0.63 0.013 80 100.00 741.4 688.5 0.27 0.29 9 629.6 515.3 0.29 0.32 0.017 93 100.00 527.7 516.7 0.33 0.32 6 567.3 397.4 0.45 0.45 0.022 102 100.00 509.5 499.1 0.39 0.40 4 699.2 410.2 0.44 0.36 0.027 129 100.00 529.9 523.4 0.36 0.37 2 819.1 533.6 0.35 0.39 0.032 112 98.41 525.1 536.4 0.37 0.37 12 594.4 484.6 0.41 0.39 0.037 125 100.00 672.3 650.6 0.31 0.33 9 715.6 798.5 0.32 0.32 0.042 141 100.00 742.5 731.5 0.26 0.26 5 853.0 631.9 0.26 0.27 0.047 148 100.00 719.9 676.3 0.23 0.24 3 656.2 443.0 0.70 0.65 0.051 159 100.00 722.2 697.8 0.25 0.25 6 874.4 735.8 0.18 0.17 0.056 159 100.00 815.4 738.9 0.25 0.25 4 639.4 632.5 0.34 0.34 0.061 158 100.00 728.9 665.0 0.25 0.25 9 721.8 395.5 0.51 0.53 0.066 167 100.00 646.4 609.9 0.26 0.27 6 705.6 613.2 0.40 0.37 0.071 181 100.00 666.7 612.6 0.26 0.27 5 870.6 813.1 0.18 0.20 0.076 180 100.00 675.9 625.6 0.26 0.26 11 690.5 570.2 0.39 0.39 0.081 178 100.00 649.3 607.9 0.25 0.25 14 517.7 559.3 0.40 0.38 0.085 185 100.00 583.8 589.1 0.26 0.25 8 466.1 358.9 0.60 0.52 0.090 194 100.00 548.6 526.8 0.27 0.26 11 730.7 583.2 0.37 0.34 0.095 192 100.00 576.2 564.4 0.25 0.24 12 418.0 403.7 0.48 0.45 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 11. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 11. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0029 13 0.980 33 0.903 46 0.925 0.915 0.0077 30 0.953 40 0.950 70 0.951 0.915 0.0126 41 0.926 39 0.891 80 0.909 0.915 0.0175 56 0.937 37 0.826 93 0.893 0.915 0.0223 64 0.928 38 0.855 102 0.901 0.916 0.0272 81 0.934 48 0.843 129 0.900 0.916 0.0320 73 0.934 39 0.869 112 0.911 0.916 0.0369 86 0.927 39 0.861 125 0.906 0.916 0.0418 100 0.953 41 0.841 141 0.920 0.916 0.0466 109 0.937 39 0.864 148 0.918 0.916 0.0515 113 0.928 46 0.836 159 0.901 0.916 0.0563 114 0.947 45 0.903 159 0.934 0.916 0.0612 122 0.941 36 0.839 158 0.918 0.916 0.0661 124 0.910 43 0.825 167 0.888 0.916 0.0709 141 0.913 40 0.736 181 0.874 0.916 0.0758 133 0.924 47 0.652 180 0.853 0.916 0.0806 140 0.905 38 0.836 178 0.890 0.916 0.0855 145 0.901 40 0.798 185 0.879 0.916 0.0904 152 0.885 42 0.795 194 0.865 0.916 0.0952 151 0.894 41 0.797 192 0.874 0.916 $$ Resolution limits = 46.932 3.200 Number of used reflections = 2799 Percentage observed = 99.8303 Percentage of free reflections = 4.8606 Overall R factor = 0.2741 Free R factor = 0.3856 Overall weighted R factor = 0.2809 Free weighted R factor = 0.3788 Overall correlation coefficient = 0.8143 Free correlation coefficient = 0.6291 DPI based on free R factor = 0.8343 Overall figure of merit = 0.8958 ML based su of positional parameters = 0.6276 ML based su of thermal parameters = 34.2870 ----------------------------------------------------------------------------- Time in seconds: CPU = 5.42 Elapsed = 5.00 **** Things for loggraph, R factor and others vs cycle **** $TABLE: Rfactor analysis, stats vs cycle : $GRAPHS: vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LLG vs cycle :N:1,5: :Geometry vs cycle:N:1,6,7,8: $$ Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$ $$ 0 0.390 0.441 0.884 943.4 0.050 4.403 0.179 1 0.331 0.405 0.889 279.2 0.065 5.299 0.245 2 0.310 0.393 0.892 56.8 0.061 4.758 0.221 3 0.299 0.386 0.893 -85.2 0.062 4.654 0.229 4 0.292 0.386 0.894 -162.9 0.063 4.614 0.238 5 0.287 0.385 0.895 -222.6 0.063 4.574 0.246 6 0.284 0.383 0.895 -255.3 0.062 4.537 0.253 7 0.280 0.385 0.895 -277.0 0.062 4.500 0.258 8 0.278 0.384 0.895 -297.9 0.062 4.462 0.263 9 0.276 0.385 0.896 -329.6 0.061 4.427 0.267 10 0.274 0.386 0.896 -338.8 0.061 4.388 0.271 $$
Refmac_5.3.0037: End of Refmac_5.3.0037 Times: User: 8.1s System: 0.4s Elapsed: 0:09
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Result:
170 residues were built in 2 chains, the longest having 127 residues. 165 residues were sequenced, after pruning.
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############################################################### ############################################################### ############################################################### ### 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
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Initial | After 10 cycles | |
---|---|---|
R factor | 0.341 | 0.232 |
Rfree | 0.411 | 0.355 |
The following tables were found in the logfile: Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. Fom(<cos(DelPhi)>-acentric, centric, overall v resln |
Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Rfactor analysis, stats vs cycle |
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############################################################### ############################################################### ############################################################### ### 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. v. resln :N:1,6,7,11,12: :Cycle 1. and v. resln :N:1,4,5,9,10: :Cycle 1. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.003 46 96.23 520.9 417.0 0.44 0.50 5 607.2 579.2 0.23 0.29 0.008 70 98.63 775.2 606.5 0.33 0.35 2 454.9 238.8 0.47 0.42 0.013 80 100.00 704.9 626.0 0.25 0.25 9 598.7 471.1 0.42 0.50 0.017 93 100.00 501.7 511.8 0.35 0.34 6 539.4 493.8 0.36 0.40 0.022 102 100.00 484.5 494.7 0.37 0.37 4 664.8 502.7 0.58 0.52 0.027 129 100.00 503.9 482.5 0.39 0.39 2 778.9 488.3 0.40 0.37 0.032 112 98.41 499.3 509.9 0.41 0.40 12 565.2 454.9 0.37 0.34 0.037 125 100.00 639.2 624.2 0.37 0.38 9 680.4 696.5 0.44 0.44 0.042 141 100.00 706.0 706.4 0.29 0.31 5 811.1 613.8 0.31 0.30 0.047 148 100.00 684.6 635.8 0.33 0.34 3 624.0 371.4 0.52 0.44 0.051 159 100.00 686.7 618.5 0.33 0.34 6 831.4 695.0 0.24 0.25 0.056 159 100.00 775.3 677.8 0.31 0.32 4 608.0 516.7 0.50 0.48 0.061 158 100.00 693.1 616.5 0.31 0.31 9 686.3 424.7 0.47 0.42 0.066 167 100.00 614.6 570.8 0.34 0.35 6 670.9 343.4 0.61 0.58 0.071 181 100.00 633.9 553.3 0.32 0.33 5 827.9 622.9 0.35 0.37 0.076 180 100.00 642.7 592.8 0.37 0.36 11 656.6 557.5 0.37 0.37 0.081 178 100.00 617.4 579.4 0.32 0.32 14 492.3 472.1 0.43 0.36 0.085 185 100.00 555.1 521.2 0.36 0.34 8 443.2 294.6 0.41 0.38 0.090 194 100.00 521.7 484.0 0.34 0.34 11 694.8 453.9 0.41 0.37 0.095 192 100.00 547.9 516.6 0.40 0.40 12 397.5 362.9 0.48 0.45 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 1. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 1. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0029 13 0.980 33 0.908 46 0.929 0.913 0.0077 30 0.949 40 0.943 70 0.946 0.910 0.0126 41 0.928 39 0.878 80 0.903 0.908 0.0175 56 0.935 37 0.829 93 0.893 0.907 0.0223 64 0.925 38 0.861 102 0.901 0.905 0.0272 81 0.925 48 0.817 129 0.885 0.904 0.0320 73 0.922 39 0.865 112 0.902 0.902 0.0369 86 0.924 39 0.851 125 0.901 0.901 0.0418 100 0.948 41 0.847 141 0.919 0.900 0.0466 109 0.931 39 0.847 148 0.909 0.899 0.0515 113 0.923 46 0.824 159 0.894 0.898 0.0563 114 0.935 45 0.901 159 0.925 0.898 0.0612 122 0.935 36 0.821 158 0.909 0.897 0.0661 124 0.895 43 0.802 167 0.871 0.896 0.0709 141 0.892 40 0.712 181 0.852 0.895 0.0758 133 0.903 47 0.632 180 0.833 0.894 0.0806 140 0.896 38 0.796 178 0.875 0.894 0.0855 145 0.891 40 0.741 185 0.859 0.893 0.0904 152 0.872 42 0.748 194 0.845 0.892 0.0952 151 0.878 41 0.809 192 0.864 0.891 $$ Resolution limits = 46.932 3.200 Number of used reflections = 2799 Percentage observed = 99.8303 Percentage of free reflections = 4.8606 Overall R factor = 0.3414 Free R factor = 0.4106 Overall weighted R factor = 0.3456 Free weighted R factor = 0.3986 Overall correlation coefficient = 0.7216 Free correlation coefficient = 0.5801 DPI based on free R factor = 0.9064 Overall figure of merit = 0.8842 ML based su of positional parameters = 0.8066 ML based su of thermal parameters = 44.9462 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Convergence reached with no gamma cycles CGMAT cycle number = 2 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1313 0.054 0.022 Bond angles : refined atoms 1777 4.728 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.519, B = -8.761 Partial structure 1: scale = 0.327, B = -10.000 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2820 Free R factor = 0.3768 Overall figure of merit = 0.8916 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Convergence reached with no gamma cycles CGMAT cycle number = 3 weigth matrix 9.9999994E-02 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1313 0.053 0.022 Bond angles : refined atoms 1777 4.533 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.522, B = -8.257 Partial structure 1: scale = 0.327, B = -10.000 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2626 Free R factor = 0.3852 Overall figure of merit = 0.8902 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Convergence reached with no gamma cycles CGMAT cycle number = 4 weigth matrix 9.9999994E-02 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1313 0.056 0.022 Bond angles : refined atoms 1777 4.445 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.527, B = -7.481 Partial structure 1: scale = 0.325, B = -10.000 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2555 Free R factor = 0.3855 Overall figure of merit = 0.8932 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Convergence reached with no gamma cycles CGMAT cycle number = 5 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1313 0.056 0.022 Bond angles : refined atoms 1777 4.208 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.526, B = -8.132 Partial structure 1: scale = 0.326, B = -10.000 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2492 Free R factor = 0.3836 Overall figure of merit = 0.8922 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Convergence reached with no gamma cycles CGMAT cycle number = 6 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1313 0.057 0.022 Bond angles : refined atoms 1777 4.263 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.530, B = -7.742 Partial structure 1: scale = 0.324, B = -10.000 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2444 Free R factor = 0.3721 Overall figure of merit = 0.8947 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Convergence reached with no gamma cycles CGMAT cycle number = 7 weigth matrix 9.9999994E-02 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1313 0.057 0.022 Bond angles : refined atoms 1777 4.136 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.530, B = -7.880 Partial structure 1: scale = 0.326, B = -10.000 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2413 Free R factor = 0.3740 Overall figure of merit = 0.8937 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Convergence reached with no gamma cycles CGMAT cycle number = 8 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1313 0.056 0.022 Bond angles : refined atoms 1777 4.096 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.534, B = -7.419 Partial structure 1: scale = 0.326, B = -10.000 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2382 Free R factor = 0.3597 Overall figure of merit = 0.8966 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Convergence reached with no gamma cycles CGMAT cycle number = 9 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1313 0.056 0.022 Bond angles : refined atoms 1777 4.084 1.960 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.535, B = -7.289 Partial structure 1: scale = 0.327, B = -10.000 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2361 Free R factor = 0.3670 Overall figure of merit = 0.8956 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Convergence reached with no gamma cycles CGMAT cycle number = 10 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 127 PHE CE1 . - A 127 PHE CZ . mod.= 1.775 id.= 1.382 dev= -0.393 sig.= 0.030 A 137 ASP CG . - A 137 ASP OD2 . mod.= 1.574 id.= 1.249 dev= -0.325 sig.= 0.019 A 137 ASP CA . - A 137 ASP C . mod.= 1.797 id.= 1.525 dev= -0.272 sig.= 0.021 B 145 LYS CD . - B 145 LYS CE . mod.= 1.823 id.= 1.520 dev= -0.303 sig.= 0.030 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 106 GLY C - A 107 VAL CA mod.= 102.00 id.= 121.70 dev= 19.700 sig.= 1.800 A 107 VAL N - A 107 VAL C mod.= 141.34 id.= 111.20 dev=-30.136 sig.= 2.800 **** Torsion angle outliers **** Torsion angle deviations from the ideal >10.000Sigma will be monitored A 52 PRO CA - A 53 GLY CA mod.=-126.82 id.= 180.00 per.= 1 dev= -53.18 sig.= 5.00 A 90 SER CA - A 91 GLY CA mod.= -85.37 id.= 180.00 per.= 1 dev= -94.63 sig.= 5.00 B 138 PRO CA - B 139 VAL CA mod.=-117.43 id.= 0.00 per.= 1 dev= 117.43 sig.= 5.00 weigth matrix 0.1000000 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1313 0.054 0.022 Bond angles : refined atoms 1777 3.980 1.960 Torsion angles, period 1. refined 168 16.818 5.000 Torsion angles, period 2. refined 54 39.210 23.889 Torsion angles, period 3. refined 218 23.373 15.000 Torsion angles, period 4. refined 7 24.130 15.000 Chiral centres: refined atoms 207 0.227 0.200 Planar groups: refined atoms 976 0.012 0.020 VDW repulsions: refined atoms 657 0.341 0.200 VDW; torsion: refined atoms 888 0.379 0.200 HBOND: refined atoms 47 0.333 0.200 VDW repulsions; symmetry: refined atoms 38 0.387 0.200 HBOND; symmetry: refined atoms 1 0.188 0.200 M. chain bond B values: refined atoms 870 0.466 1.500 M. chain angle B values: refined atoms 1342 0.601 2.000 S. chain bond B values: refined atoms 501 2.367 3.000 S. chain angle B values: refined atoms 435 3.326 4.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.537, B = -7.030 Partial structure 1: scale = 0.326, B = -10.000 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 10. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 10. v. resln :N:1,6,7,11,12: :Cycle 10. and v. resln :N:1,4,5,9,10: :Cycle 10. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.003 46 96.23 497.7 415.7 0.39 0.43 5 580.1 461.8 0.34 0.41 0.008 70 98.63 740.7 656.9 0.22 0.24 2 434.6 232.5 0.46 0.40 0.013 80 100.00 673.5 617.6 0.22 0.23 9 572.0 461.5 0.33 0.41 0.017 93 100.00 479.4 488.9 0.31 0.31 6 515.4 524.3 0.37 0.36 0.022 102 100.00 462.9 475.3 0.29 0.30 4 635.1 468.6 0.55 0.52 0.027 129 100.00 481.4 475.1 0.33 0.33 2 744.1 609.6 0.18 0.24 0.032 112 98.41 477.0 490.4 0.29 0.29 12 540.0 432.4 0.33 0.30 0.037 125 100.00 610.7 624.6 0.26 0.27 9 650.1 657.4 0.38 0.35 0.042 141 100.00 674.5 671.3 0.19 0.20 5 774.9 595.5 0.23 0.24 0.047 148 100.00 654.0 632.2 0.22 0.23 3 596.1 447.6 0.25 0.18 0.051 159 100.00 656.1 633.8 0.19 0.19 6 794.3 709.9 0.22 0.23 0.056 159 100.00 740.8 694.8 0.20 0.20 4 580.9 603.9 0.39 0.38 0.061 158 100.00 662.2 598.7 0.23 0.24 9 655.7 466.7 0.36 0.38 0.066 167 100.00 587.2 543.2 0.24 0.24 6 641.0 462.7 0.33 0.35 0.071 181 100.00 605.6 558.4 0.22 0.23 5 790.9 825.0 0.37 0.40 0.076 180 100.00 614.0 594.8 0.24 0.24 11 627.3 640.0 0.32 0.29 0.081 178 100.00 589.9 554.9 0.21 0.22 14 470.3 462.2 0.31 0.29 0.085 185 100.00 530.3 520.1 0.23 0.23 8 423.4 406.9 0.58 0.47 0.090 194 100.00 498.4 471.1 0.24 0.23 11 663.8 516.5 0.42 0.39 0.095 192 100.00 523.4 504.1 0.23 0.23 12 379.7 285.4 0.45 0.41 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 10. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 10. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0029 13 0.981 33 0.945 46 0.955 0.939 0.0077 30 0.953 40 0.960 70 0.957 0.934 0.0126 41 0.931 39 0.898 80 0.915 0.931 0.0175 56 0.942 37 0.829 93 0.897 0.929 0.0223 64 0.926 38 0.863 102 0.902 0.927 0.0272 81 0.937 48 0.823 129 0.895 0.925 0.0320 73 0.935 39 0.872 112 0.913 0.923 0.0369 86 0.930 39 0.854 125 0.907 0.921 0.0418 100 0.953 41 0.852 141 0.923 0.920 0.0466 109 0.938 39 0.860 148 0.918 0.918 0.0515 113 0.929 46 0.839 159 0.903 0.917 0.0563 114 0.951 45 0.918 159 0.941 0.915 0.0612 122 0.942 36 0.836 158 0.918 0.914 0.0661 124 0.911 43 0.808 167 0.885 0.913 0.0709 141 0.909 40 0.739 181 0.872 0.912 0.0758 133 0.920 47 0.633 180 0.845 0.911 0.0806 140 0.905 38 0.845 178 0.892 0.910 0.0855 145 0.904 40 0.790 185 0.879 0.908 0.0904 152 0.890 42 0.795 194 0.869 0.907 0.0952 151 0.897 41 0.828 192 0.882 0.906 $$ Resolution limits = 46.932 3.200 Number of used reflections = 2799 Percentage observed = 99.8303 Percentage of free reflections = 4.8606 Overall R factor = 0.2345 Free R factor = 0.3561 Overall weighted R factor = 0.2409 Free weighted R factor = 0.3519 Overall correlation coefficient = 0.8691 Free correlation coefficient = 0.6979 DPI based on free R factor = 0.7862 Overall figure of merit = 0.8974 ML based su of positional parameters = 0.6422 ML based su of thermal parameters = 35.9339 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000E+00 Convergence reached with no gamma cycles **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 90 SER CB . - A 90 SER OG . mod.= 1.630 id.= 1.417 dev= -0.213 sig.= 0.020 A 101 MET SD . - A 101 MET CE . mod.= 1.538 id.= 1.791 dev= 0.253 sig.= 0.025 A 127 PHE CE1 . - A 127 PHE CZ . mod.= 1.914 id.= 1.382 dev= -0.532 sig.= 0.030 A 137 ASP CG . - A 137 ASP OD2 . mod.= 1.447 id.= 1.249 dev= -0.198 sig.= 0.019 B 145 LYS CD . - B 145 LYS CE . mod.= 1.826 id.= 1.520 dev= -0.306 sig.= 0.030 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 106 GLY C - A 107 VAL CA mod.= 102.27 id.= 121.70 dev= 19.431 sig.= 1.800 A 107 VAL N - A 107 VAL C mod.= 140.82 id.= 111.20 dev=-29.618 sig.= 2.800 A 137 ASP N - A 137 ASP C mod.= 139.88 id.= 111.20 dev=-28.678 sig.= 2.800 **** Torsion angle outliers **** Torsion angle deviations from the ideal >10.000Sigma will be monitored A 52 PRO CA - A 53 GLY CA mod.=-127.35 id.= 180.00 per.= 1 dev= -52.65 sig.= 5.00 A 53 GLY CA - A 54 GLY CA mod.=-127.44 id.= 180.00 per.= 1 dev= -52.56 sig.= 5.00 A 90 SER CA - A 91 GLY CA mod.= -92.61 id.= 180.00 per.= 1 dev= -87.39 sig.= 5.00 B 138 PRO CA - B 139 VAL CA mod.=-113.87 id.= 0.00 per.= 1 dev= 113.87 sig.= 5.00 WRITTEN OUTPUT MTZ FILE Logical Name: HKLOUT Filename: /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1313 0.054 0.022 Bond angles : refined atoms 1777 3.918 1.960 Torsion angles, period 1. refined 168 16.352 5.000 Torsion angles, period 2. refined 54 39.244 23.889 Torsion angles, period 3. refined 218 23.553 15.000 Torsion angles, period 4. refined 7 24.443 15.000 Chiral centres: refined atoms 207 0.228 0.200 Planar groups: refined atoms 976 0.012 0.020 VDW repulsions: refined atoms 649 0.338 0.200 VDW; torsion: refined atoms 896 0.375 0.200 HBOND: refined atoms 48 0.330 0.200 VDW repulsions; symmetry: refined atoms 38 0.312 0.200 M. chain bond B values: refined atoms 873 0.476 1.500 M. chain angle B values: refined atoms 1342 0.627 2.000 S. chain bond B values: refined atoms 501 2.370 3.000 S. chain angle B values: refined atoms 435 3.313 4.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.537, B = -7.199 Partial structure 1: scale = 0.329, B = -10.000 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 11. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 11. v. resln :N:1,6,7,11,12: :Cycle 11. and v. resln :N:1,4,5,9,10: :Cycle 11. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.003 46 96.23 497.4 404.9 0.39 0.44 5 579.7 461.5 0.34 0.41 0.008 70 98.63 740.2 655.3 0.21 0.23 2 434.3 237.5 0.45 0.40 0.013 80 100.00 673.1 619.6 0.21 0.22 9 571.6 453.9 0.33 0.41 0.017 93 100.00 479.0 488.2 0.31 0.31 6 515.0 543.2 0.40 0.38 0.022 102 100.00 462.6 474.1 0.29 0.30 4 634.7 463.8 0.54 0.51 0.027 129 100.00 481.1 472.4 0.32 0.32 2 743.6 622.3 0.16 0.21 0.032 112 98.41 476.7 490.4 0.29 0.29 12 539.6 430.8 0.33 0.31 0.037 125 100.00 610.3 626.4 0.25 0.26 9 649.7 671.7 0.37 0.34 0.042 141 100.00 674.1 672.2 0.19 0.20 5 774.4 595.9 0.23 0.24 0.047 148 100.00 653.6 629.8 0.22 0.22 3 595.8 479.1 0.20 0.11 0.051 159 100.00 655.7 635.3 0.19 0.19 6 793.8 710.7 0.22 0.22 0.056 159 100.00 740.3 694.8 0.19 0.20 4 580.5 611.5 0.39 0.37 0.061 158 100.00 661.8 601.3 0.23 0.23 9 655.3 464.5 0.35 0.36 0.066 167 100.00 586.8 545.2 0.23 0.23 6 640.5 454.7 0.34 0.37 0.071 181 100.00 605.2 562.4 0.22 0.22 5 790.4 812.9 0.37 0.40 0.076 180 100.00 613.6 594.0 0.23 0.23 11 626.9 643.7 0.35 0.32 0.081 178 100.00 589.5 560.3 0.21 0.22 14 470.0 463.6 0.28 0.26 0.085 185 100.00 530.0 525.0 0.23 0.23 8 423.1 399.3 0.62 0.50 0.090 194 100.00 498.1 470.1 0.23 0.22 11 663.4 513.3 0.43 0.40 0.095 192 100.00 523.1 509.5 0.23 0.22 12 379.5 298.8 0.42 0.38 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 11. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 11. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0029 13 0.982 33 0.944 46 0.954 0.939 0.0077 30 0.954 40 0.959 70 0.957 0.935 0.0126 41 0.931 39 0.896 80 0.914 0.931 0.0175 56 0.942 37 0.829 93 0.897 0.928 0.0223 64 0.926 38 0.864 102 0.903 0.926 0.0272 81 0.938 48 0.820 129 0.894 0.924 0.0320 73 0.934 39 0.871 112 0.912 0.922 0.0369 86 0.930 39 0.853 125 0.906 0.920 0.0418 100 0.953 41 0.849 141 0.922 0.918 0.0466 109 0.938 39 0.856 148 0.916 0.917 0.0515 113 0.930 46 0.840 159 0.904 0.915 0.0563 114 0.950 45 0.916 159 0.940 0.913 0.0612 122 0.943 36 0.838 158 0.919 0.912 0.0661 124 0.911 43 0.808 167 0.885 0.911 0.0709 141 0.909 40 0.732 181 0.870 0.909 0.0758 133 0.919 47 0.640 180 0.846 0.908 0.0806 140 0.904 38 0.849 178 0.892 0.907 0.0855 145 0.904 40 0.785 185 0.878 0.906 0.0904 152 0.888 42 0.792 194 0.867 0.905 0.0952 151 0.896 41 0.829 192 0.882 0.903 $$ Resolution limits = 46.932 3.200 Number of used reflections = 2799 Percentage observed = 99.8303 Percentage of free reflections = 4.8606 Overall R factor = 0.2317 Free R factor = 0.3549 Overall weighted R factor = 0.2377 Free weighted R factor = 0.3510 Overall correlation coefficient = 0.8723 Free correlation coefficient = 0.6974 DPI based on free R factor = 0.7835 Overall figure of merit = 0.8970 ML based su of positional parameters = 0.6422 ML based su of thermal parameters = 35.9339 ----------------------------------------------------------------------------- Time in seconds: CPU = 5.98 Elapsed = 6.00 **** Things for loggraph, R factor and others vs cycle **** $TABLE: Rfactor analysis, stats vs cycle : $GRAPHS: vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LLG vs cycle :N:1,5: :Geometry vs cycle:N:1,6,7,8: $$ Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$ $$ 0 0.341 0.411 0.884 282.3 0.047 5.127 0.180 1 0.282 0.377 0.892 -418.1 0.054 4.728 0.201 2 0.263 0.385 0.890 -521.1 0.053 4.533 0.221 3 0.256 0.386 0.893 -696.1 0.056 4.445 0.239 4 0.249 0.384 0.892 -690.9 0.056 4.208 0.238 5 0.244 0.372 0.895 -805.9 0.057 4.263 0.240 6 0.241 0.374 0.894 -792.9 0.057 4.136 0.238 7 0.238 0.360 0.897 -934.5 0.056 4.096 0.233 8 0.236 0.367 0.896 -924.5 0.056 4.084 0.232 9 0.234 0.356 0.897 -1025.6 0.054 3.980 0.227 10 0.232 0.355 0.897 -1031.4 0.054 3.918 0.228 $$
Refmac_5.3.0037: End of Refmac_5.3.0037 Times: User: 8.9s System: 0.4s Elapsed: 0:09
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