Summary:
| Initial | After 10 cycles | |
|---|---|---|
| R factor | 0.206 | 0.172 |
| Rfree | 0.178 | 0.229 |
| RMSD Bond Length | 0.030 | 0.022 |
| RMSD Bond Angle | 3.367 | 2.030 |
| RMSD Chiral Centre | 0.248 | 0.131 |
|
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 5.99: Refmac_5.2.0019 version 5.2.0019 : 04/08/05## ############################################################### User: pjx Run date: 25/10/2005 Run time: 15:19:23 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up.
$TEXT:Reference1: $$ comment $$
"Refinement of Macromolecular Structures by the Maximum-Likelihood Method:"
G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
Acta Crystallogr. D53, 240-255
EU Validation contract: BIO2CT-92-0524
$$
$SUMMARY :Reference1: $$ Refmac: $$
:TEXT:Reference1: $$
Data line--- make check NONE
Data line--- make hydrogen YES hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
Data line--- refi type REST resi MLKF meth CGMAT bref ISOT
Data line--- ncyc 10
Data line--- scal type SIMP reso 2.300 36.786 LSSC ANISO EXPE
Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
Data line--- weight MATRIX 0.3
Data line--- monitor MEDIUM torsion 10.0 distance 10.0 angle 10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere 10.0 rbond 10.0 ncsr 10.0
Data line--- labin FP=FTOXD3 SIGFP=SIGFTOXD3 FREE=FreeR_flag
Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM
Data line--- PNAME TOXD
Data line--- DNAME NATIVE
Data line--- RSIZE 80
Data line--- END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /home/pjx/CCP4_REMOTE/ccp4/examples/toxd/toxd.mtz
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib
**** Input and Default parameters# ****
Input coordinate file. Logical name - XYZIN actual file name - /home/pjx/CCP4_REMOTE/ccp4/examples/toxd/toxd.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /tmp/pjx/PROJECT_7_2_pdb_1.tmp
Input reflection file. Logical name - HKLIN actual file name - /home/pjx/CCP4_REMOTE/ccp4/examples/toxd/toxd.mtz
Output reflection file. Logical name - HKLOUT actual file name - /tmp/pjx/PROJECT_7_4_mtz_1.tmp
Cell from mtz : 73.582 38.733 23.189 90.000 90.000 90.000
Space group from mtz: number - 19; name - P 21 21 21
Refinement type : Restrained
**** Makecif parameters ****
Dictionary files for restraints : /home/pjx/CCP4_REMOTE/ccp4/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /home/pjx/CCP4_REMOTE/ccp4/lib/data/monomers/ener_lib.cif
Program will rely on residue and atom names. No checking
If this option is used then monomers should be checked carefully before using
Hydrogens in input coordinate file will be kept
Links between monomers will be checked. Only those links present in the coordinate file will be used
All links to sugar will be analysed and used
For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
Symmetry related links will be analysed and used
Cis peptides will be found and used automatically
Residual : Rice Maximum Likelihood for Fs
**** Least-square scaling parameters ****
Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
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 0.0095
Refinement of individual isotropic Bfactors
Refinement resln : 36.7856 2.3002
Estimated number of reflections : 3829
Free R exclusion - flag equals: 0
Weighting by comparison of trace of matrix
Weighting parameters : 0.3000
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
using free set of reflns with experimental sigmas
Scaling and SigmaA resln: 36.7860 2.3000
Damping factors: 1.0000 1.0000
**** Geometry restraints and weights ****
Sigma:
Bonding distances
Weight = 1.00
Bond angles
Weight = 1.00
Planar groups
WEIGHT= 1.00
Chiral centers
Weight= 1.00
NON-BONDED CONTACTS
Overall weight = 1.00
Sigma for simple VDW = 0.20
Sigma for VDW trhough torsion angle = 0.20
Sigma for HBOND = 0.20
Sigma for metal-ion = 0.20
Sigma for DUMMY and other atom = 0.30
Distance for donor-accepetor = vdw1+vdw2+(-0.30)
Distance for acceptor - H = vdw1+ ( 0.10)
VDW distance through torsion = vdw1+vdw2+(-0.30)
Distance for DUMMY-others = vdw1+vdw2+(-0.70)
TORSION ANGLES
Weight= 1.00
THERMAL FACTORS
Weight= 1.00
Main chain bond (1-2 neighbour) 1.50A**2
Main chain angle (1-3 neighbour) 2.00A**2
Side chain bond 3.00A**2
Side chain angle 4.50A**2
RESTRAINTS AGAINST EXCESSIVE SHIFTS
Positional parameters 0.00A
Thermal parameters 0.00A
Occupancy parameters 0.00
RADIUS OF CONFIDENCE
Positional parameters 0.30A
Thermal parameters 0.03A**2
Occupancy parameters 0.50
Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers 10.000
Angle outliers 10.000
Torsion outliers 10.000
Chiral volume outliers 10.000
Plane outliers 10.000
Non-bonding outliers 10.000
B value outliers 10.000
---------------------------------------------------------------
Input file :/home/pjx/CCP4_REMOTE/ccp4/examples/toxd/toxd.pdb
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 4.7
_lib_update 30/03/05
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 2432
with complete description : 449
NUMBER OF MODIFICATIONS : 46
NUMBER OF LINKS : 64
I am reading libraries. Please wait.
- energy parameters
- monomer"s description (links & mod )
FORMATTED OLD file opened on unit 45
Logical name: ATOMSF, Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/atomsf.lib
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib
Number of atoms : 561
Number of residues : 123
Number of chains : 7
I am reading library. Please wait.
mon_lib.cif
WARNING : link:SS is found dist = 2.008 ideal_dist= 2.031
ch:AA res: 7 CYS at:SG .->AA res: 57 CYS at:SG .
WARNING : link:SS is found dist = 2.073 ideal_dist= 2.031
ch:AA res: 16 CYS at:SG .->AA res: 40 CYS at:SG .
WARNING : link:SS is found dist = 2.011 ideal_dist= 2.031
ch:AA res: 32 CYS at:SG .->AA res: 53 CYS at:SG .
--------------------------------
--- title of input coord file ---
PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-XX
--------------------------------
ATTENTION: atom:CB GLN AA 1 is missing in the structure
ATTENTION: atom:CG GLN AA 1 is missing in the structure
ATTENTION: atom:CD GLN AA 1 is missing in the structure
ATTENTION: atom:OE1 GLN AA 1 is missing in the structure
ATTENTION: atom:NE2 GLN AA 1 is missing in the structure
ATTENTION: atom:CG LYS AA 19 is missing in the structure
ATTENTION: atom:CD LYS AA 19 is missing in the structure
ATTENTION: atom:CE LYS AA 19 is missing in the structure
ATTENTION: atom:NZ LYS AA 19 is missing in the structure
ATTENTION: atom:CD LYS AA 28 is missing in the structure
ATTENTION: atom:CE LYS AA 28 is missing in the structure
ATTENTION: atom:NZ LYS AA 28 is missing in the structure
ATTENTION: atom:CD ARG AA 34 is missing in the structure
ATTENTION: atom:NE ARG AA 34 is missing in the structure
ATTENTION: atom:CZ ARG AA 34 is missing in the structure
ATTENTION: atom:NH1 ARG AA 34 is missing in the structure
ATTENTION: atom:NH2 ARG AA 34 is missing in the structure
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib
Number of chains : 7
Total number of monomers : 123
Number of atoms : 578
Number of missing atoms : 17
Number of rebuilt atoms : 0
Number of unknown atoms : 0
Number of deleted atoms : 0
Number of bonds restraints : 511
Number of angles restraints : 689
Number of torsions restraints : 347
Number of chiralities : 61
Number of planar groups : 88
loop_
_atom_type_symbol
_atom_type_scat_Cromer_Mann_a1
_atom_type_scat_Cromer_Mann_b1
_atom_type_scat_Cromer_Mann_a2
_atom_type_scat_Cromer_Mann_b2
_atom_type_scat_Cromer_Mann_a3
_atom_type_scat_Cromer_Mann_b3
_atom_type_scat_Cromer_Mann_a4
_atom_type_scat_Cromer_Mann_b4
_atom_type_scat_Cromer_Mann_c
N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290
C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156
O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508
S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 0.8669
Number of reflections in file 3235
Number of reflection read 3235
CGMAT cycle number = 1
**** B-value outliers ****
B-value differences > 10.00Sigma will be monitored
A 10 HIS CG - A 10 HIS CA ABS(DELTA)= 21.160 Sigma= 2.000
w_average 0.434987366
GRID VALUES:
0.116666667 Angstrom for D
4.91666651 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 511 0.030 0.021
Bond angles : refined atoms 689 3.367 1.988
Torsion angles, period 1. refined 58 4.372 5.000
Torsion angles, period 2. refined 26 25.097 21.538
Torsion angles, period 3. refined 85 21.041 15.000
Torsion angles, period 4. refined 7 23.300 15.000
Chiral centres: refined atoms 61 0.248 0.200
Planar groups: refined atoms 388 0.016 0.020
VDW repulsions: refined atoms 223 0.219 0.200
VDW; torsion: refined atoms 339 0.319 0.200
HBOND: refined atoms 44 0.197 0.200
VDW repulsions; symmetry: refined atoms 17 0.216 0.200
HBOND; symmetry: refined atoms 9 0.204 0.200
M. chain bond B values: refined atoms 292 1.842 1.500
M. chain angle B values: refined atoms 466 3.399 2.000
S. chain bond B values: refined atoms 219 3.285 3.000
S. chain angle B values: refined atoms 223 5.085 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 21.082, B = -1.436
Partial structure 1: scale = 0.402, B = 90.253
Overall anisotropic scale factors
B11 = -0.89 B22 = 0.62 B33 = 0.27 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.005 51 100.00 170.9 195.3 0.41 0.51 1 276.5 304.1 0.10 0.10
0.015 73 98.73 177.2 183.5 0.35 0.38 5 153.8 180.9 0.33 0.32
0.024 88 98.92 153.5 152.0 0.23 0.23 4 129.3 146.7 0.32 0.30
0.034 102 100.00 190.4 191.8 0.18 0.16 8 168.4 159.4 0.14 0.13
0.043 108 98.31 193.7 181.5 0.17 0.16 8 235.8 240.5 0.09 0.09
0.053 125 100.00 237.8 221.2 0.14 0.14 12 227.4 201.3 0.13 0.13
0.062 120 98.46 229.2 216.7 0.14 0.13 8 333.7 295.4 0.12 0.11
0.071 155 98.76 219.2 206.1 0.16 0.15 4 203.0 199.4 0.12 0.12
0.081 153 100.00 171.1 163.6 0.17 0.16 7 196.3 185.8 0.09 0.09
0.090 150 97.50 168.6 157.6 0.16 0.16 6 148.1 143.2 0.14 0.15
0.100 168 99.45 152.5 145.8 0.19 0.18 14 153.6 136.9 0.26 0.26
0.109 157 98.78 128.0 120.7 0.19 0.17 5 138.6 134.5 0.14 0.12
0.118 190 98.99 115.6 113.2 0.21 0.19 7 136.7 132.1 0.17 0.13
0.128 188 98.47 109.1 104.0 0.23 0.21 5 98.9 119.8 0.31 0.21
0.137 181 98.96 95.4 97.8 0.22 0.18 9 92.5 92.5 0.16 0.15
0.147 193 97.09 97.0 98.2 0.22 0.20 7 120.7 116.0 0.20 0.14
0.156 207 97.30 85.6 90.1 0.24 0.19 9 75.0 80.5 0.37 0.36
0.165 203 95.00 84.5 87.3 0.25 0.21 6 84.1 83.7 0.22 0.17
0.175 205 96.36 70.8 76.7 0.28 0.23 7 55.0 72.9 0.33 0.38
0.184 203 90.91 70.8 80.0 0.31 0.25 7 83.0 92.4 0.39 0.36
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0054 16 0.946 35 0.918 51 0.926 0.991
0.0149 39 0.950 34 0.881 73 0.918 0.981
0.0243 54 0.939 34 0.874 88 0.914 0.974
0.0337 65 0.962 37 0.953 102 0.959 0.968
0.0431 73 0.962 35 0.863 108 0.930 0.963
0.0525 90 0.970 35 0.955 125 0.965 0.958
0.0619 91 0.974 29 0.908 120 0.958 0.954
0.0713 111 0.962 44 0.848 155 0.929 0.950
0.0808 113 0.937 40 0.906 153 0.929 0.946
0.0902 122 0.944 28 0.938 150 0.943 0.943
0.0996 132 0.946 36 0.916 168 0.940 0.940
0.1090 126 0.940 31 0.861 157 0.924 0.937
0.1184 147 0.895 43 0.883 190 0.893 0.934
0.1278 150 0.877 38 0.904 188 0.882 0.931
0.1372 151 0.861 30 0.843 181 0.858 0.928
0.1466 160 0.879 33 0.796 193 0.865 0.925
0.1561 171 0.846 36 0.803 207 0.839 0.923
0.1655 173 0.848 30 0.811 203 0.843 0.920
0.1749 171 0.822 34 0.615 205 0.788 0.918
0.1843 179 0.811 24 0.682 203 0.796 0.915
$$
Resolution limits = 36.786 2.300
Number of used reflections = 3020
Percentage observed = 97.7111
Percentage of free reflections = 4.4001
Overall R factor = 0.2060
Free R factor = 0.1782
Overall weighted R factor = 0.1919
Free weighted R factor = 0.1680
Overall correlation coefficient = 0.9238
Free correlation coefficient = 0.9557
Cruickshanks DPI for coordinate error= 0.4120
DPI based on free R factor = 0.1807
Overall figure of merit = 0.8889
ML based su of positional parameters = 0.1228
ML based su of thermal parameters = 5.3159
-----------------------------------------------------------------------------
Trying gamma equal 0.
Convergence reached with no gamma cycles
CGMAT cycle number = 2
w_average 0.424437284
GRID VALUES:
0.116666667 Angstrom for D
5. Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 511 0.022 0.021
Bond angles : refined atoms 689 2.213 1.988
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 20.926, B = 1.390
Partial structure 1: scale = 0.393, B = 59.181
Overall anisotropic scale factors
B11 = -0.89 B22 = 0.62 B33 = 0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1889
Free R factor = 0.1955
Overall figure of merit = 0.8679
-----------------------------------------------------------------------------
Trying gamma equal 0.
Convergence reached with no gamma cycles
CGMAT cycle number = 3
w_average 0.420279294
GRID VALUES:
0.116666667 Angstrom for D
4.94999981 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 511 0.022 0.021
Bond angles : refined atoms 689 2.060 1.988
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 20.932, B = 1.268
Partial structure 1: scale = 0.388, B = 32.681
Overall anisotropic scale factors
B11 = -0.89 B22 = 0.62 B33 = 0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1805
Free R factor = 0.2036
Overall figure of merit = 0.8565
-----------------------------------------------------------------------------
Trying gamma equal 0.
Convergence reached with no gamma cycles
CGMAT cycle number = 4
w_average 0.416690171
GRID VALUES:
0.116666667 Angstrom for D
4.97619057 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 511 0.022 0.021
Bond angles : refined atoms 689 2.048 1.988
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 20.893, B = 1.124
Partial structure 1: scale = 0.387, B = 32.096
Overall anisotropic scale factors
B11 = -0.89 B22 = 0.62 B33 = 0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1770
Free R factor = 0.2099
Overall figure of merit = 0.8489
-----------------------------------------------------------------------------
Trying gamma equal 0.
Convergence reached with no gamma cycles
CGMAT cycle number = 5
w_average 0.41352284
GRID VALUES:
0.116666667 Angstrom for D
5. Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 511 0.022 0.021
Bond angles : refined atoms 689 2.044 1.988
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 20.868, B = 1.084
Partial structure 1: scale = 0.386, B = 30.312
Overall anisotropic scale factors
B11 = -0.89 B22 = 0.62 B33 = 0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1755
Free R factor = 0.2154
Overall figure of merit = 0.8428
-----------------------------------------------------------------------------
Trying gamma equal 0.
Convergence reached with no gamma cycles
CGMAT cycle number = 6
w_average 0.411703348
GRID VALUES:
0.116666667 Angstrom for D
4.89130449 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 511 0.022 0.021
Bond angles : refined atoms 689 2.044 1.988
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 20.836, B = 1.092
Partial structure 1: scale = 0.386, B = 31.292
Overall anisotropic scale factors
B11 = -0.89 B22 = 0.62 B33 = 0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1743
Free R factor = 0.2207
Overall figure of merit = 0.8388
-----------------------------------------------------------------------------
Trying gamma equal 0.
Convergence reached with no gamma cycles
CGMAT cycle number = 7
w_average 0.410540104
GRID VALUES:
0.116666667 Angstrom for D
4.9130435 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 511 0.022 0.021
Bond angles : refined atoms 689 2.039 1.988
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 20.814, B = 1.092
Partial structure 1: scale = 0.385, B = 30.203
Overall anisotropic scale factors
B11 = -0.89 B22 = 0.62 B33 = 0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1737
Free R factor = 0.2220
Overall figure of merit = 0.8368
-----------------------------------------------------------------------------
Trying gamma equal 0.
Convergence reached with no gamma cycles
CGMAT cycle number = 8
w_average 0.409628153
GRID VALUES:
0.116666667 Angstrom for D
5.06521749 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 511 0.022 0.021
Bond angles : refined atoms 689 2.036 1.988
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 20.789, B = 1.084
Partial structure 1: scale = 0.385, B = 29.634
Overall anisotropic scale factors
B11 = -0.89 B22 = 0.62 B33 = 0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1735
Free R factor = 0.2255
Overall figure of merit = 0.8348
-----------------------------------------------------------------------------
Trying gamma equal 0.
Convergence reached with no gamma cycles
CGMAT cycle number = 9
w_average 0.408848047
GRID VALUES:
0.116666667 Angstrom for D
5.08333349 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 511 0.022 0.021
Bond angles : refined atoms 689 2.030 1.988
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 20.748, B = 1.046
Partial structure 1: scale = 0.384, B = 29.655
Overall anisotropic scale factors
B11 = -0.89 B22 = 0.62 B33 = 0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1733
Free R factor = 0.2272
Overall figure of merit = 0.8331
-----------------------------------------------------------------------------
Trying gamma equal 0.
Convergence reached with no gamma cycles
CGMAT cycle number = 10
w_average 0.408117712
GRID VALUES:
0.116666667 Angstrom for D
4.94000006 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 511 0.022 0.021
Bond angles : refined atoms 689 2.028 1.988
Torsion angles, period 1. refined 58 6.882 5.000
Torsion angles, period 2. refined 26 22.799 21.538
Torsion angles, period 3. refined 85 19.508 15.000
Torsion angles, period 4. refined 7 21.138 15.000
Chiral centres: refined atoms 61 0.130 0.200
Planar groups: refined atoms 388 0.008 0.020
VDW repulsions: refined atoms 186 0.192 0.200
VDW; torsion: refined atoms 329 0.317 0.200
HBOND: refined atoms 38 0.270 0.200
VDW repulsions; symmetry: refined atoms 21 0.227 0.200
HBOND; symmetry: refined atoms 4 0.126 0.200
M. chain bond B values: refined atoms 297 0.975 1.500
M. chain angle B values: refined atoms 466 1.776 2.000
S. chain bond B values: refined atoms 238 3.269 3.000
S. chain angle B values: refined atoms 223 5.338 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 20.738, B = 1.109
Partial structure 1: scale = 0.384, B = 28.364
Overall anisotropic scale factors
B11 = -0.89 B22 = 0.62 B33 = 0.27 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.005 51 100.00 173.8 191.0 0.40 0.47 1 281.1 297.6 0.06 0.06
0.015 73 98.73 180.2 175.1 0.26 0.27 5 156.4 170.0 0.33 0.26
0.024 88 98.92 156.0 156.8 0.18 0.18 4 131.4 145.2 0.16 0.18
0.034 102 100.00 193.6 197.7 0.17 0.16 8 171.2 164.7 0.12 0.12
0.043 108 98.31 196.9 190.2 0.15 0.14 8 239.7 251.2 0.13 0.14
0.053 125 100.00 241.8 229.7 0.12 0.12 12 231.2 199.7 0.19 0.18
0.062 120 98.46 233.0 223.9 0.09 0.09 8 339.3 304.9 0.15 0.15
0.071 155 98.76 222.9 212.5 0.13 0.13 4 206.4 177.7 0.23 0.30
0.081 153 100.00 173.9 168.5 0.13 0.12 7 199.5 207.3 0.15 0.14
0.090 150 97.50 171.4 163.6 0.14 0.13 6 150.6 152.6 0.23 0.27
0.100 168 99.45 155.1 148.0 0.16 0.14 14 156.2 108.3 0.37 0.34
0.109 157 98.78 130.1 121.3 0.17 0.15 5 140.9 138.5 0.25 0.16
0.118 190 98.99 117.6 115.2 0.19 0.17 7 139.0 131.9 0.15 0.13
0.128 188 98.47 111.0 104.7 0.19 0.17 5 100.6 117.6 0.28 0.20
0.137 181 98.96 97.0 95.7 0.20 0.15 9 94.1 105.0 0.36 0.36
0.147 193 97.09 98.6 98.9 0.18 0.15 7 122.7 110.4 0.27 0.20
0.156 207 97.30 87.0 86.6 0.23 0.18 9 76.2 74.9 0.31 0.29
0.165 203 95.00 85.9 87.6 0.22 0.17 6 85.4 91.2 0.34 0.18
0.175 205 96.36 72.0 76.1 0.25 0.18 7 55.9 68.5 0.37 0.39
0.184 203 90.91 72.0 75.6 0.24 0.18 7 84.4 105.3 0.55 0.43
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0054 16 0.905 35 0.875 51 0.884 0.981
0.0149 39 0.889 34 0.868 73 0.879 0.972
0.0243 54 0.912 34 0.847 88 0.887 0.966
0.0337 65 0.924 37 0.879 102 0.908 0.961
0.0431 73 0.942 35 0.820 108 0.902 0.957
0.0525 90 0.964 35 0.899 125 0.946 0.953
0.0619 91 0.950 29 0.875 120 0.931 0.950
0.0713 111 0.938 44 0.825 155 0.906 0.947
0.0808 113 0.894 40 0.879 153 0.890 0.943
0.0902 122 0.918 28 0.851 150 0.905 0.940
0.0996 132 0.912 36 0.862 168 0.901 0.938
0.1090 126 0.885 31 0.777 157 0.864 0.935
0.1184 147 0.835 43 0.839 190 0.836 0.933
0.1278 150 0.804 38 0.859 188 0.815 0.930
0.1372 151 0.782 30 0.773 181 0.781 0.928
0.1466 160 0.820 33 0.669 193 0.794 0.926
0.1561 171 0.752 36 0.703 207 0.743 0.924
0.1655 173 0.776 30 0.773 203 0.776 0.921
0.1749 171 0.751 34 0.514 205 0.711 0.919
0.1843 179 0.723 24 0.469 203 0.693 0.917
$$
Resolution limits = 36.786 2.300
Number of used reflections = 3020
Percentage observed = 97.7111
Percentage of free reflections = 4.4001
Overall R factor = 0.1729
Free R factor = 0.2284
Overall weighted R factor = 0.1588
Free weighted R factor = 0.2017
Overall correlation coefficient = 0.9468
Free correlation coefficient = 0.9201
Cruickshanks DPI for coordinate error= 0.3459
DPI based on free R factor = 0.2316
Overall figure of merit = 0.8315
ML based su of positional parameters = 0.1565
ML based su of thermal parameters = 6.6840
-----------------------------------------------------------------------------
Trying gamma equal 0.
Convergence reached with no gamma cycles
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /tmp/pjx/PROJECT_7_4_mtz_1.tmp
* Title:
Output mtz file from refmac
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 TOXD
NATIVE
NATIVE
73.5820 38.7330 23.1890 90.0000 90.0000 90.0000
0.00000
* Number of Columns = 13
* Number of Reflections = 3233
* Missing value set to NaN in input mtz file
* HISTORY for current MTZ file :
* Column Labels, Types, Ranges [and Dataset IDs] :
H H 0.0000 31.0000 0
K H 0.0000 16.0000 0
L H 0.0000 10.0000 0
FreeR_flag I 0.0000 19.0000 0
FTOXD3 F 8.8496 916.8461 1
SIGFTOXD3 Q 0.8687 19.9385 1
FC F 0.6434 3180.6484 1
PHIC P 0.0000 360.0000 1
FWT F 0.0108 968.5911 1
PHWT P 0.0000 360.0000 1
DELFWT F 0.0000 264.2049 1
PHDELWT P 0.0000 360.0000 1
FOM W 0.0000 1.0000 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
73.5820 38.7330 23.1890 90.0000 90.0000 90.0000
* Resolution Range :
0.00085 0.18900 ( 34.274 - 2.300 A )
* Sort Order :
1 2 3 0 0
* Number of Symmetry Operations = 4
* Number of Primitive Operations = 4
* Space Group = 19 'P 21 21 21'
* Lattice Type = P
* Point Group Name = PG222
* Symmetry Operations :
Symmetry 1 X, Y, Z
1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 2 -X+1/2, -Y, Z+1/2
-1.00 0.00 0.00 0.50
0.00 -1.00 0.00 0.00
0.00 0.00 1.00 0.50
0.00 0.00 0.00 1.00
Symmetry 3 X+1/2, -Y+1/2, -Z
1.00 0.00 0.00 0.50
0.00 -1.00 0.00 0.50
0.00 0.00 -1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 4 -X, Y+1/2, -Z+1/2
-1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.50
0.00 0.00 -1.00 0.50
0.00 0.00 0.00 1.00
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 511 0.022 0.021
Bond angles : refined atoms 689 2.030 1.988
Torsion angles, period 1. refined 58 6.935 5.000
Torsion angles, period 2. refined 26 22.629 21.538
Torsion angles, period 3. refined 85 19.542 15.000
Torsion angles, period 4. refined 7 21.226 15.000
Chiral centres: refined atoms 61 0.131 0.200
Planar groups: refined atoms 388 0.008 0.020
VDW repulsions: refined atoms 186 0.191 0.200
VDW; torsion: refined atoms 329 0.317 0.200
HBOND: refined atoms 38 0.269 0.200
VDW repulsions; symmetry: refined atoms 21 0.227 0.200
HBOND; symmetry: refined atoms 4 0.131 0.200
M. chain bond B values: refined atoms 297 0.953 1.500
M. chain angle B values: refined atoms 466 1.776 2.000
S. chain bond B values: refined atoms 238 3.283 3.000
S. chain angle B values: refined atoms 223 5.354 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 20.726, B = 1.103
Partial structure 1: scale = 0.384, B = 28.186
Overall anisotropic scale factors
B11 = -0.89 B22 = 0.62 B33 = 0.27 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.005 51 100.00 173.9 192.1 0.40 0.47 1 281.3 297.6 0.06 0.06
0.015 73 98.73 180.3 175.0 0.26 0.27 5 156.5 168.9 0.31 0.25
0.024 88 98.92 156.1 156.8 0.18 0.18 4 131.5 145.5 0.18 0.20
0.034 102 100.00 193.7 197.5 0.17 0.16 8 171.3 163.8 0.12 0.12
0.043 108 98.31 197.0 190.8 0.14 0.14 8 239.9 251.5 0.13 0.14
0.053 125 100.00 241.9 229.8 0.12 0.12 12 231.3 199.6 0.19 0.18
0.062 120 98.46 233.1 224.0 0.09 0.09 8 339.5 304.8 0.15 0.15
0.071 155 98.76 223.0 213.0 0.13 0.12 4 206.5 174.9 0.24 0.31
0.081 153 100.00 174.0 168.7 0.13 0.12 7 199.6 208.1 0.15 0.14
0.090 150 97.50 171.5 163.9 0.13 0.13 6 150.7 153.9 0.23 0.27
0.100 168 99.45 155.1 148.1 0.16 0.14 14 156.3 107.7 0.37 0.34
0.109 157 98.78 130.2 121.3 0.17 0.15 5 141.0 138.2 0.25 0.16
0.118 190 98.99 117.6 115.2 0.19 0.17 7 139.0 132.0 0.15 0.13
0.128 188 98.47 111.0 104.8 0.19 0.17 5 100.6 118.6 0.28 0.20
0.137 181 98.96 97.0 95.8 0.20 0.15 9 94.1 105.9 0.37 0.36
0.147 193 97.09 98.7 99.0 0.18 0.16 7 122.8 110.3 0.27 0.20
0.156 207 97.30 87.0 86.6 0.23 0.18 9 76.3 74.5 0.30 0.29
0.165 203 95.00 86.0 87.5 0.21 0.17 6 85.5 91.5 0.34 0.18
0.175 205 96.36 72.0 76.1 0.25 0.18 7 56.0 68.3 0.38 0.40
0.184 203 90.91 72.0 75.5 0.24 0.18 7 84.4 104.5 0.55 0.43
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0054 16 0.902 35 0.877 51 0.885 0.981
0.0149 39 0.886 34 0.865 73 0.876 0.972
0.0243 54 0.910 34 0.847 88 0.886 0.966
0.0337 65 0.923 37 0.877 102 0.906 0.961
0.0431 73 0.942 35 0.820 108 0.903 0.957
0.0525 90 0.964 35 0.900 125 0.946 0.953
0.0619 91 0.949 29 0.879 120 0.932 0.950
0.0713 111 0.938 44 0.824 155 0.905 0.947
0.0808 113 0.893 40 0.880 153 0.890 0.943
0.0902 122 0.918 28 0.863 150 0.907 0.940
0.0996 132 0.911 36 0.860 168 0.900 0.938
0.1090 126 0.884 31 0.778 157 0.863 0.935
0.1184 147 0.833 43 0.838 190 0.834 0.933
0.1278 150 0.802 38 0.860 188 0.814 0.930
0.1372 151 0.781 30 0.776 181 0.780 0.928
0.1466 160 0.819 33 0.669 193 0.793 0.926
0.1561 171 0.751 36 0.702 207 0.742 0.924
0.1655 173 0.775 30 0.772 203 0.775 0.921
0.1749 171 0.749 34 0.515 205 0.711 0.919
0.1843 179 0.722 24 0.462 203 0.691 0.917
$$
Resolution limits = 36.786 2.300
Number of used reflections = 3020
Percentage observed = 97.7111
Percentage of free reflections = 4.4001
Overall R factor = 0.1724
Free R factor = 0.2292
Overall weighted R factor = 0.1585
Free weighted R factor = 0.2024
Overall correlation coefficient = 0.9472
Free correlation coefficient = 0.9190
Cruickshanks DPI for coordinate error= 0.3450
DPI based on free R factor = 0.2325
Overall figure of merit = 0.8308
ML based su of positional parameters = 0.1565
ML based su of thermal parameters = 6.6840
-----------------------------------------------------------------------------
Time in seconds: CPU = 4.90
Elapsed = 0.00
**** 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:
$$
Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$
$$
0 0.206 0.178 0.889 16260.1 0.030 3.367 0.248
1 0.189 0.196 0.868 15382.6 0.022 2.213 0.136
2 0.181 0.204 0.856 15228.2 0.022 2.060 0.122
3 0.177 0.210 0.849 15206.6 0.022 2.048 0.121
4 0.175 0.215 0.843 15211.9 0.022 2.044 0.122
5 0.174 0.221 0.839 15215.6 0.022 2.044 0.124
6 0.174 0.222 0.837 15214.7 0.022 2.039 0.126
7 0.174 0.225 0.835 15220.9 0.022 2.036 0.127
8 0.173 0.227 0.833 15230.7 0.022 2.030 0.128
9 0.173 0.228 0.832 15234.0 0.022 2.028 0.130
10 0.172 0.229 0.831 15233.9 0.022 2.030 0.131
$$
Refmac_5.2.0019: End of Refmac_5.2.0019 Times: User: 6.0s System: 0.4s Elapsed: 0:07
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
CCP4i: Writing final coordinates to /home/pjx/PROJECTS/myProject/toxd_refmac1.pdb
CCP4i: Writing final phases to /home/pjx/PROJECTS/myProject/toxd_refmac1.mtz
Generated for you by baubles 0.0.6 on Thu Feb 14 10:41:22 2008