Summary:
| Initial | After 25 cycles | |
|---|---|---|
| R factor | 0.1807 | 0.1590 |
| Rfree | 0.2006 | 0.1848 |
| RMSD Bond Length | 0.0 | 0.0207 |
| RMSD Bond Angle | 0.0 | 2.098 |
| RMSD Chiral Centre | 0.0 | 0.141 |
Result:
| Initial | Final | |
|---|---|---|
| R factor | 0.1807 | 0.1590 |
| R free | 0.2006 | 0.1848 |
| Rms BondLength | 0.0219 | 0.0207 |
| Rms BondAngle | 2.1456 | 2.0978 |
| Rms ChirVolume | 0.1332 | 0.1414 |
|
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 26. Rfactor analysis, F distribution v resln Cycle 26. 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 Cycle 26. Rfactor analysis, F distribution v resln Cycle 26. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Rfactor analysis, stats vs cycle |
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Current view: full logfile [Show logfile summary] [Hide logfile]
############################################################### ############################################################### ############################################################### ### CCP4 6.3: Refmac_5.7.0032 version 5.7.0032 : 05/09/12## ############################################################### User: Administrator Run date: 10/ 5/2013 Run time: 20:39:14 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up.
$TEXT:Reference1: $$ Main reference $$
"REFMAC5 for the refinement of macromolecular crystal structures:"
G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011)
Acta Crystallogr. D67, 355-367
$$
$SUMMARY :Reference1: $$ Refmac: $$
:TEXT:Reference1: $$
$TEXT:Reference2: $$ Secondary reference $$
"Refinement of Macromolecular Structures by the Maximum-Likelihood Method:"
G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
Acta Crystallogr. D53, 240-255
EU Validation contract: BIO2CT-92-0524
$$
$SUMMARY :Reference2: $$ Refmac: $$
:TEXT:Reference2: $$
Data line--- make check NONE
Data line--- make hydrogen ALL 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--- refi tlsc 10
Data line--- ncyc 15
Data line--- scal type BULK LSSC ANISO EXPE
Data line--- solvent YES
Data line--- weight AUTO
Data line--- monitor MEDIUM torsion 10.0 distance 10.0 angle 10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere 10.0 rbond 10.0 ncsr 10.0
Data line--- labin FP=F SIGFP=SIGF FREE=FreeR_flag
Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM
Data line--- temp 0.8
Data line--- tlso addu
Data line--- PNAME lizozim
Data line--- DNAME 1
Data line--- RSIZE 80
Data line--- END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: C:/SOLVE_REFINE/lizozim/mr-refine-build\lizozim-xds-p43212.mtz
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: C:\CCP4\6.3\lib\data\syminfo.lib
**** Input and Default parameters# ****
Input coordinate file. Logical name - XYZIN actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\r31-coot-1.pdb
Output coordinate file. Logical name - XYZOUT actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\r42.pdb
Input reflection file. Logical name - HKLIN actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\lizozim-xds-p43212.mtz
Output reflection file. Logical name - HKLOUT actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\r42.mtz
Cell from mtz : 78.713 78.713 36.840 90.000 90.000 90.000
Space group from mtz: number - 96; name - P 43 21 2
Refinement type : Restrained
**** Makecif parameters ****
Dictionary files for restraints : C:\CCP4\6.3\lib\data\monomers\mon*cif
Parameters for new entry and VDW: C:\CCP4\6.3\lib\data\monomers\ener_lib.cif
Program will rely on residue and atom names. No checking
If this option is used then monomers should be checked carefully before using
Hydrogens will be restored in their riding positions
Links between monomers will be checked. Only those links present in the coordinate file will be used
All links to sugar will be analysed and used
For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
Symmetry related links will be analysed and used
Cis peptides will be found and used automatically
Residual : Rice Maximum Likelihood for Fs
**** Least-square scaling parameters ****
Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Bulk solvent based on Babinet"s principle
Constant bulk solvent in non protein region
Probe radii for non-ions 1.200
Probe radii for ions 0.800
Shrinkage of the mask by 0.800
**** Map sharpening parameters and methods ****
No map sharpening will be performed
Method of minimisation : Sparse Matrix
Experimental sigmas used for weighting
Number of Bins and width: 20 0.0268
Refinement of individual isotropic Bfactors
Refinement resln : 55.6587 1.3660
Estimated number of reflections : 31789
Free R exclusion - flag equals: 0
Auto weighting. An attempt
Refinement cycles : 15
Scaling type :
Bulk solvent using using Babinet principle
Estimation of D/Sigma in resolution bins
using free set of reflns with experimental sigmas
using free set of reflns with experimental sigmas
Scaling and SigmaA resln: 55.6587 1.3660
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= 0.80
Main chain bond (1-2 neighbour) 1.5A**2
Main chain angle (1-3 neighbour) 2.0A**2
Side chain bond 3.0A**2
Side chain angle 4.5A**2
RESTRAINTS AGAINST EXCESSIVE SHIFTS
Positional parameters 0.00A
Thermal parameters 0.00A
Occupancy parameters 0.00
RADIUS OF CONFIDENCE
Positional parameters 0.00A
Thermal parameters 0.00A**2
Occupancy parameters 0.00
Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers 10.000
Angle outliers 10.000
Torsion outliers 10.000
Chiral volume outliers 10.000
Plane outliers 10.000
Non-bonding outliers 10.000
B value outliers 10.000
---------------------------------------------------------------
Input file :C:/SOLVE_REFINE/lizozim/mr-refine-build\r31-coot-1.pdb
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 5.39
_lib_update 06/11/12
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 11462
with complete description : 11462
NUMBER OF MODIFICATIONS : 53
NUMBER OF LINKS : 66
I am reading libraries. Please wait.
- energy parameters
- monomer"s description (links & mod )
FORMATTED OLD file opened on unit 45
Logical name: ATOMSF, Filename: C:\CCP4\6.3\lib\data\atomsf.lib
Number of atoms : 1123
Number of residues : 241
Number of chains : 4
I am reading library. Please wait.
mon_lib.cif
WARNING : link:SS is found dist = 2.038 ideal_dist= 2.031
ch:AA res: 6 CYS at:SG .->AA res: 127 CYS at:SG .
WARNING : link:SS is found dist = 2.072 ideal_dist= 2.031
ch:AA res: 30 CYS at:SG .->AA res: 115 CYS at:SG .
INFO: link is found (not be used) dist= 2.424 ideal_dist= 2.275
ch:AA res: 35 GLU at:OE1 .->ch:BB res: 1 NA at:NA .
INFO: link is found (not be used) dist= 2.327 ideal_dist= 2.240
ch:AA res: 60 SER at:O .->ch:DD res: 1 NA at:NA .
WARNING : link:SS is found dist = 2.033 ideal_dist= 2.031
ch:AA res: 64 CYS at:SG .->AA res: 80 CYS at:SG .
INFO: link is found (not be used) dist= 2.387 ideal_dist= 2.240
ch:AA res: 64 CYS at:O .->ch:DD res: 1 NA at:NA .
INFO: link is found (not be used) dist= 2.515 ideal_dist= 2.434
ch:AA res: 72 SER at:OG .->ch:DD res: 1 NA at:NA .
INFO: link is found (not be used) dist= 2.419 ideal_dist= 2.240
ch:AA res: 73 ARG at:O .->ch:DD res: 1 NA at:NA .
WARNING : link:SS is found dist = 2.034 ideal_dist= 2.031
ch:AA res: 76 CYS at:SG .->AA res: 94 CYS at:SG .
--------------------------------
--- title of input coord file ---
PDB_code:2ZIL
PDB_name:HYDROLASE
PDB_date:18-FEB-08
--------------------------------
ATTENTION: atom:CD GLN 121 AA is missing in the structure
ATTENTION: atom:OE1 GLN 121 AA is missing in the structure
ATTENTION: atom:NE2 GLN 121 AA is missing in the structure
Number of chains : 4
Total number of monomers : 241
Number of atoms : 2331
Number of missing atoms : 3
Number of rebuilt atoms : 983
Number of unknown atoms : 0
Number of deleted atoms : 0
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
H 0.4930 10.5109 0.3229 26.1257 0.1402 3.1424 0.0408 57.7997 0.0030
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
NA 4.7626 3.2850 3.1736 8.8422 1.2674 0.3136 1.1128 129.4240 0.6760
Number of distances : 0
Number of angles : 0
Number of torsions : 0
Number of planes : 0
Number of chirals : 0
Number of intervals : 0
--------------------------------------------------------------------------------
---------------------------------------
Standard External All
Bonds: 1999 0 1999
Angles: 3588 0 3588
Chirals: 146 0 146
Planes: 329 0 329
Torsions: 833 0 833
---------------------------------------
**** Info from mtz file ****
FreeR flag 0
Number of "free" reflections 1280
Number of all reflections 25101
--------------------------------------------------------------------------------
Number of reflections in file 25120
Number of reflections read 25101
Data line--- TLS chain A
Data line--- RANGE 'A 1.' 'A 129.' ALL
###### TLS Group Definitions ######
Group: 1: No. of pieces: 1
Chain: A Span: 1 129
Calculating TLS origin of group 1 from centroid of group.
TLS origin for group 1 0.82065988 20.340693 8.8515692
Initial TLS parameters
TLS group 1: chain A
T tensor ( 1) = 0.000 0.000 0.000 0.000 0.000 0.000
L tensor ( 1) = 0.000 0.000 0.000 0.000 0.000 0.000
S tensor ( 1) = 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
***TLS refinement cycle*** 1
fast hessian tabulation
-----------------------------------------------------------------------------
Overall : scale = 0.921, B = -0.175
Babinet"s bulk solvent: scale = 0.180, B = 153.590
Partial structure 1: scale = 0.426, B = 31.826
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.014 319 95.97 346.7 335.5 0.22 0.30 14 226.8 241.4 0.20 0.25
0.040 535 100.00 363.1 383.5 0.20 0.27 34 385.4 421.8 0.21 0.33
0.067 672 100.00 443.8 421.3 0.18 0.24 32 378.9 380.2 0.18 0.23
0.094 779 99.75 376.4 350.6 0.19 0.23 31 387.4 347.6 0.20 0.22
0.121 879 100.00 279.5 273.7 0.19 0.24 43 286.5 278.0 0.18 0.24
0.148 958 100.00 235.7 242.4 0.19 0.22 42 212.6 211.6 0.22 0.26
0.174 1040 100.00 222.7 223.6 0.17 0.19 38 235.4 248.0 0.15 0.17
0.201 1096 100.00 207.0 199.6 0.17 0.18 65 197.6 195.7 0.19 0.21
0.228 1185 100.00 189.2 185.0 0.16 0.18 56 206.3 196.7 0.16 0.17
0.255 1205 100.00 164.6 159.1 0.17 0.18 82 171.9 170.9 0.21 0.22
0.281 1298 100.00 142.0 138.2 0.18 0.18 59 140.5 139.1 0.20 0.21
0.308 1337 100.00 123.5 122.1 0.18 0.18 76 126.0 122.7 0.22 0.22
0.335 1403 100.00 111.7 109.0 0.18 0.17 88 105.0 104.3 0.24 0.23
0.362 1434 100.00 104.9 100.1 0.17 0.16 74 109.0 100.3 0.20 0.19
0.388 1507 100.00 98.7 95.3 0.17 0.16 76 94.6 93.4 0.22 0.20
0.415 1532 100.00 89.4 86.0 0.17 0.16 97 87.2 80.1 0.21 0.19
0.442 1579 100.00 84.1 80.6 0.17 0.16 92 85.5 80.2 0.20 0.20
0.469 1633 100.00 79.0 75.4 0.17 0.16 109 73.8 72.0 0.23 0.20
0.495 1576 93.50 69.6 67.9 0.19 0.17 79 75.0 72.0 0.23 0.19
0.522 1250 72.50 67.5 66.1 0.18 0.16 63 67.4 63.0 0.22 0.20
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0137 179 0.910 140 0.839 319 0.879 0.963
0.0405 376 0.925 159 0.828 535 0.896 0.975
0.0672 518 0.938 154 0.827 672 0.913 0.984
0.0940 623 0.924 156 0.856 779 0.911 0.991
0.1208 716 0.873 163 0.771 879 0.854 0.992
0.1475 800 0.894 158 0.761 958 0.872 0.963
0.1743 883 0.920 157 0.800 1040 0.902 0.953
0.2010 934 0.923 162 0.860 1096 0.913 0.977
0.2278 1022 0.925 163 0.852 1185 0.915 0.987
0.2546 1048 0.904 157 0.829 1205 0.894 0.981
0.2813 1136 0.883 162 0.800 1298 0.873 0.969
0.3081 1176 0.884 161 0.774 1337 0.871 0.964
0.3349 1243 0.879 160 0.811 1403 0.871 0.970
0.3616 1269 0.884 165 0.745 1434 0.868 0.982
0.3884 1347 0.882 160 0.844 1507 0.878 0.984
0.4151 1380 0.890 152 0.779 1532 0.879 0.981
0.4419 1421 0.890 158 0.822 1579 0.883 0.987
0.4687 1477 0.883 156 0.832 1633 0.878 0.982
0.4954 1447 0.858 131 0.741 1578 0.849 0.966
0.5222 1161 0.879 87 0.805 1248 0.874 0.963
$$
Resolution limits = 19.098 1.366
Number of used reflections = 23217
Percentage observed = 97.4781
Percentage of free reflections = 5.1089
Overall R factor = 0.1807
Free R factor = 0.2006
Overall weighted R factor = 0.1920
Free weighted R factor = 0.2151
Overall weighted R2 factor = 0.2558
Free weighted R2 factor = 0.2848
Overall correlation coefficient = 0.9544
Free correlation coefficient = 0.9435
Cruickshanks DPI for coordinate error= 0.0557
DPI based on free R factor = 0.0619
Overall figure of merit = 0.8814
ML based su of positional parameters = 0.0366
ML based su of thermal parameters = 1.7499
-----------------------------------------------------------------------------
TLS group 1: chain A
T tensor ( 1) = 0.001 0.003 0.005 -0.001 -0.000 -0.000
L tensor ( 1) = 0.120 0.115 0.075 0.079 0.019 0.008
S tensor ( 1) = 0.014 -0.005 -0.003 -0.006 -0.019 -0.006 -0.000 -0.007
***TLS refinement cycle*** 2
fast hessian tabulation
-----------------------------------------------------------------------------
Overall : scale = 0.923, B = -0.630
Babinet"s bulk solvent: scale = 0.182, B = 153.597
Partial structure 1: scale = 0.426, B = 32.476
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1787
Free R factor = 0.1980
Overall figure of merit = 0.8844
-----------------------------------------------------------------------------
TLS group 1: chain A
T tensor ( 1) = 0.002 0.005 0.008 -0.002 -0.000 -0.001
L tensor ( 1) = 0.197 0.188 0.121 0.130 0.029 0.012
S tensor ( 1) = 0.023 -0.008 -0.004 -0.010 -0.030 -0.011 -0.001 -0.010
***TLS refinement cycle*** 3
fast hessian tabulation
-----------------------------------------------------------------------------
Overall : scale = 0.924, B = -0.864
Babinet"s bulk solvent: scale = 0.184, B = 153.593
Partial structure 1: scale = 0.426, B = 32.483
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1778
Free R factor = 0.1969
Overall figure of merit = 0.8856
-----------------------------------------------------------------------------
TLS group 1: chain A
T tensor ( 1) = 0.002 0.006 0.010 -0.002 -0.000 -0.001
L tensor ( 1) = 0.249 0.237 0.151 0.166 0.035 0.013
S tensor ( 1) = 0.028 -0.011 -0.005 -0.013 -0.038 -0.013 -0.001 -0.013
***TLS refinement cycle*** 4
fast hessian tabulation
-----------------------------------------------------------------------------
Overall : scale = 0.925, B = -0.994
Babinet"s bulk solvent: scale = 0.185, B = 153.588
Partial structure 1: scale = 0.426, B = 32.518
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1774
Free R factor = 0.1964
Overall figure of merit = 0.8861
-----------------------------------------------------------------------------
TLS group 1: chain A
T tensor ( 1) = 0.003 0.007 0.011 -0.003 -0.000 -0.002
L tensor ( 1) = 0.283 0.270 0.171 0.191 0.038 0.013
S tensor ( 1) = 0.032 -0.012 -0.005 -0.015 -0.043 -0.015 -0.001 -0.014
***TLS refinement cycle*** 5
fast hessian tabulation
-----------------------------------------------------------------------------
Overall : scale = 0.925, B = -1.094
Babinet"s bulk solvent: scale = 0.185, B = 153.583
Partial structure 1: scale = 0.426, B = 32.583
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1771
Free R factor = 0.1961
Overall figure of merit = 0.8864
-----------------------------------------------------------------------------
TLS group 1: chain A
T tensor ( 1) = 0.003 0.008 0.012 -0.003 -0.000 -0.002
L tensor ( 1) = 0.307 0.294 0.183 0.209 0.040 0.013
S tensor ( 1) = 0.035 -0.014 -0.006 -0.016 -0.046 -0.017 -0.001 -0.015
***TLS refinement cycle*** 6
fast hessian tabulation
-----------------------------------------------------------------------------
Overall : scale = 0.926, B = -1.172
Babinet"s bulk solvent: scale = 0.186, B = 153.578
Partial structure 1: scale = 0.426, B = 32.647
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1770
Free R factor = 0.1959
Overall figure of merit = 0.8867
-----------------------------------------------------------------------------
TLS group 1: chain A
T tensor ( 1) = 0.003 0.008 0.013 -0.004 -0.000 -0.001
L tensor ( 1) = 0.324 0.311 0.192 0.222 0.041 0.012
S tensor ( 1) = 0.037 -0.014 -0.006 -0.017 -0.049 -0.018 -0.001 -0.016
***TLS refinement cycle*** 7
fast hessian tabulation
-----------------------------------------------------------------------------
Overall : scale = 0.926, B = -1.231
Babinet"s bulk solvent: scale = 0.186, B = 153.573
Partial structure 1: scale = 0.426, B = 32.717
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1769
Free R factor = 0.1957
Overall figure of merit = 0.8869
-----------------------------------------------------------------------------
TLS group 1: chain A
T tensor ( 1) = 0.004 0.009 0.013 -0.004 -0.001 -0.001
L tensor ( 1) = 0.336 0.323 0.198 0.232 0.042 0.011
S tensor ( 1) = 0.038 -0.015 -0.006 -0.018 -0.050 -0.018 -0.001 -0.017
***TLS refinement cycle*** 8
fast hessian tabulation
-----------------------------------------------------------------------------
Overall : scale = 0.926, B = -1.277
Babinet"s bulk solvent: scale = 0.187, B = 153.568
Partial structure 1: scale = 0.426, B = 32.808
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1768
Free R factor = 0.1956
Overall figure of merit = 0.8870
-----------------------------------------------------------------------------
TLS group 1: chain A
T tensor ( 1) = 0.004 0.010 0.014 -0.004 -0.001 -0.001
L tensor ( 1) = 0.345 0.332 0.202 0.239 0.042 0.010
S tensor ( 1) = 0.039 -0.015 -0.006 -0.018 -0.051 -0.019 -0.000 -0.017
***TLS refinement cycle*** 9
fast hessian tabulation
-----------------------------------------------------------------------------
Overall : scale = 0.926, B = -1.311
Babinet"s bulk solvent: scale = 0.187, B = 153.561
Partial structure 1: scale = 0.426, B = 32.840
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1768
Free R factor = 0.1954
Overall figure of merit = 0.8871
-----------------------------------------------------------------------------
TLS group 1: chain A
T tensor ( 1) = 0.004 0.010 0.014 -0.004 -0.001 -0.001
L tensor ( 1) = 0.351 0.339 0.205 0.245 0.042 0.009
S tensor ( 1) = 0.040 -0.016 -0.006 -0.019 -0.052 -0.019 -0.000 -0.017
***TLS refinement cycle*** 10
fast hessian tabulation
-----------------------------------------------------------------------------
Overall : scale = 0.927, B = -1.338
Babinet"s bulk solvent: scale = 0.187, B = 153.554
Partial structure 1: scale = 0.426, B = 32.850
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.014 319 95.97 614.2 594.9 0.22 0.30 14 394.5 420.1 0.20 0.25
0.040 535 100.00 513.7 542.3 0.20 0.27 34 542.8 591.5 0.20 0.32
0.067 672 100.00 572.4 544.0 0.18 0.23 32 524.1 525.8 0.18 0.24
0.094 779 99.75 468.0 436.3 0.19 0.23 31 497.5 447.5 0.21 0.23
0.121 879 100.00 341.1 334.2 0.19 0.23 43 322.3 313.3 0.18 0.23
0.148 958 100.00 280.6 288.2 0.19 0.22 42 261.1 258.5 0.21 0.24
0.174 1040 100.00 260.8 262.1 0.17 0.19 38 277.9 292.7 0.14 0.17
0.201 1096 100.00 241.4 233.0 0.16 0.18 65 232.1 229.1 0.19 0.21
0.228 1185 100.00 218.2 213.1 0.16 0.17 56 229.8 218.5 0.15 0.16
0.255 1205 100.00 188.2 181.5 0.16 0.17 82 184.4 182.2 0.20 0.21
0.281 1298 100.00 161.3 157.3 0.17 0.17 59 155.5 154.7 0.20 0.20
0.308 1337 100.00 139.6 138.7 0.18 0.17 76 136.0 131.5 0.20 0.21
0.335 1403 100.00 125.4 122.4 0.17 0.17 88 119.4 119.0 0.22 0.22
0.362 1434 100.00 117.8 112.6 0.17 0.16 74 114.6 107.0 0.19 0.18
0.388 1507 100.00 109.8 106.0 0.17 0.16 76 105.1 105.9 0.22 0.20
0.415 1532 100.00 98.7 95.1 0.16 0.15 97 98.9 91.0 0.20 0.19
0.442 1579 100.00 92.9 89.2 0.17 0.15 92 94.2 88.7 0.20 0.19
0.469 1633 100.00 86.9 83.2 0.17 0.15 109 86.9 84.6 0.22 0.20
0.495 1576 93.50 75.3 73.8 0.18 0.16 79 78.6 76.6 0.22 0.18
0.522 1250 72.50 72.3 71.2 0.17 0.15 63 69.2 63.2 0.22 0.20
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0137 179 0.912 140 0.841 319 0.881 0.963
0.0405 376 0.926 159 0.828 535 0.897 0.975
0.0672 518 0.938 154 0.827 672 0.913 0.984
0.0940 623 0.924 156 0.854 779 0.910 0.991
0.1208 716 0.870 163 0.780 879 0.854 0.992
0.1475 800 0.893 158 0.761 958 0.871 0.963
0.1743 883 0.921 157 0.800 1040 0.903 0.953
0.2010 934 0.926 162 0.864 1096 0.917 0.977
0.2278 1022 0.929 163 0.862 1185 0.920 0.987
0.2546 1048 0.909 157 0.823 1205 0.898 0.981
0.2813 1136 0.891 162 0.813 1298 0.881 0.969
0.3081 1176 0.893 161 0.787 1337 0.880 0.964
0.3349 1243 0.893 160 0.830 1403 0.885 0.970
0.3616 1269 0.897 165 0.760 1434 0.881 0.982
0.3884 1347 0.892 160 0.846 1507 0.887 0.984
0.4151 1380 0.898 152 0.794 1532 0.887 0.981
0.4419 1421 0.896 158 0.820 1579 0.888 0.987
0.4687 1477 0.890 156 0.834 1633 0.885 0.982
0.4954 1447 0.868 131 0.746 1578 0.858 0.966
0.5222 1161 0.879 87 0.823 1248 0.875 0.963
$$
Resolution limits = 19.098 1.366
Number of used reflections = 23217
Percentage observed = 97.4781
Percentage of free reflections = 5.1089
Overall R factor = 0.1767
Free R factor = 0.1954
Overall weighted R factor = 0.1876
Free weighted R factor = 0.2094
Overall weighted R2 factor = 0.2515
Free weighted R2 factor = 0.2783
Overall correlation coefficient = 0.9559
Free correlation coefficient = 0.9459
Cruickshanks DPI for coordinate error= 0.0545
DPI based on free R factor = 0.0603
Overall figure of merit = 0.8872
ML based su of positional parameters = 0.0354
ML based su of thermal parameters = 1.6608
-----------------------------------------------------------------------------
TLS group 1: chain A
T tensor ( 1) = 0.004 0.010 0.014 -0.005 -0.001 -0.001
L tensor ( 1) = 0.356 0.344 0.207 0.249 0.042 0.009
S tensor ( 1) = 0.041 -0.016 -0.006 -0.019 -0.053 -0.020 -0.000 -0.017
CGMAT cycle number = 1
Atom (C 104 O)"s total occupancy (occ*multipl) > 1.0. Changing it
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 120 VAL C . - A 121 GLN N . mod.= 1.178 id.= 1.329 dev= 0.151 sig.= 0.014
**** VDW outliers ****
VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored
A 6 CYS HB3 . - A 14 ARG HH22B mod.= 0.955 id.= 2.400 dev= -1.45 sig.= 0.20 sym.= 6 0 0 1 type = 7
Limits of asymmetric unit : 1.00 1.00 0.13
Grid spacing to be used : 192 192 96
Maximuum H,K,L : 58 58 27
Minimum acceptable grid spacing: 128 128 60
Limits of asymmetric unit : 1.00 1.00 0.13
Grid spacing to be used : 192 192 96
Maximuum H,K,L : 58 58 27
Minimum acceptable grid spacing: 128 128 60
fast hessian tabulation
Weight matrix 3.4578958
Actual weight 10.000000 is applied to the X-ray term
Norm of X_ray positional gradient 100.
Norm of Geom. positional gradient 69.1
Norm of X_ray B-factor gradient 257.
Norm of Geom. B-factor gradient 136.
Product of X_ray and Geom posit. gradients -0.123E+08
Cosine of angle between them -0.284
Product of X_ray and Geom B-fact gradients 0.231E+07
Cosine of angle between them 0.032
Residuals: XRAY= 0.1104E+07 GEOM= 7166. TOTAL= 0.1111E+07
function value 1110801.1
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.022 0.019
Bond distances: others 962 0.000 0.020
Bond angles : refined atoms 1408 2.146 1.903
Bond angles : others 2180 3.837 3.007
Torsion angles, period 1. refined 132 6.482 5.000
Torsion angles, period 2. refined 51 36.614 22.745
Torsion angles, period 3. refined 169 11.939 15.000
Torsion angles, period 3. others 8 49.109 15.000
Torsion angles, period 4. refined 12 21.082 15.000
Chiral centres: refined atoms 146 0.133 0.200
Planar groups: refined atoms 1225 0.012 0.020
Planar groups: others 277 0.023 0.020
VDW repulsions: refined_atoms 317 0.262 0.200
VDW repulsions.others 851 0.233 0.200
VDW; torsion: refined_atoms 523 0.186 0.200
VDW; torsion.others 533 0.106 0.200
HBOND: refined_atoms 17 0.144 0.200
Metal-ion: refined_atoms 4 0.150 0.200
VDW repulsions: symmetry: refined_atoms 23 0.301 0.200
VDW repulsions: symmetry: others 34 0.422 0.200
HBOND: symmetry: refined_atoms 1 0.175 0.200
M. chain bond B values: refined atoms 519 1.203 0.914
M. chain bond B values: others 518 1.161 0.911
M. chain angle B values: refined atoms 648 1.742 1.373
M. chain angle B values: others 649 1.746 1.376
S. chain bond B values: refined atoms 518 2.100 1.130
S. chain bond B values: others 518 2.079 1.128
S. chain angle B values: refined atoms 758 3.003 1.615
S. chain angle B values: others 758 3.003 1.613
Long range B values: refined atoms 1315 4.992 8.334
Long range B values: others 1276 4.739 7.993
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.927, B = -1.351
Babinet"s bulk solvent: scale = 0.189, B = 153.554
Partial structure 1: scale = 0.426, B = 33.291
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.014 319 95.97 613.7 593.0 0.22 0.30 14 394.2 424.4 0.20 0.26
0.040 535 100.00 513.2 541.8 0.20 0.27 34 542.4 593.6 0.21 0.33
0.067 672 100.00 571.9 543.7 0.18 0.23 32 523.6 527.6 0.18 0.24
0.094 779 99.75 467.5 435.6 0.19 0.23 31 497.0 446.1 0.21 0.23
0.121 879 100.00 340.8 333.9 0.19 0.23 43 322.0 313.7 0.18 0.24
0.148 958 100.00 280.4 288.2 0.19 0.22 42 260.9 257.9 0.21 0.24
0.174 1040 100.00 260.6 261.9 0.17 0.19 38 277.6 292.2 0.14 0.17
0.201 1096 100.00 241.2 232.8 0.16 0.18 65 231.9 228.7 0.19 0.21
0.228 1185 100.00 218.0 212.9 0.16 0.17 56 229.5 218.8 0.15 0.16
0.255 1205 100.00 188.0 181.4 0.16 0.17 82 184.2 182.0 0.20 0.21
0.281 1298 100.00 161.2 157.1 0.17 0.17 59 155.4 154.5 0.20 0.20
0.308 1337 100.00 139.5 138.6 0.18 0.17 76 135.8 131.3 0.20 0.21
0.335 1403 100.00 125.3 122.2 0.17 0.17 88 119.3 119.0 0.22 0.22
0.362 1434 100.00 117.7 112.5 0.17 0.16 74 114.5 107.0 0.19 0.18
0.388 1507 100.00 109.7 105.9 0.17 0.16 76 105.0 105.9 0.22 0.20
0.415 1532 100.00 98.6 95.0 0.16 0.15 97 98.8 90.9 0.20 0.19
0.442 1579 100.00 92.8 89.1 0.17 0.15 92 94.1 88.6 0.20 0.19
0.469 1633 100.00 86.8 83.1 0.17 0.15 109 86.8 84.5 0.22 0.20
0.495 1576 93.50 75.3 73.7 0.18 0.16 79 78.5 76.5 0.22 0.18
0.522 1250 72.50 72.2 71.1 0.17 0.15 63 69.1 63.1 0.22 0.20
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0137 179 0.910 140 0.837 319 0.878 0.963
0.0405 376 0.925 159 0.827 535 0.896 0.975
0.0672 518 0.938 154 0.831 672 0.913 0.984
0.0940 623 0.924 156 0.850 779 0.909 0.991
0.1208 716 0.869 163 0.778 879 0.852 0.992
0.1475 800 0.892 158 0.763 958 0.871 0.963
0.1743 883 0.921 157 0.801 1040 0.903 0.953
0.2010 934 0.926 162 0.863 1096 0.916 0.977
0.2278 1022 0.930 163 0.862 1185 0.921 0.987
0.2546 1048 0.910 157 0.823 1205 0.898 0.981
0.2813 1136 0.891 162 0.812 1298 0.881 0.969
0.3081 1176 0.893 161 0.788 1337 0.880 0.964
0.3349 1243 0.893 160 0.831 1403 0.886 0.970
0.3616 1269 0.898 165 0.760 1434 0.882 0.982
0.3884 1347 0.892 160 0.847 1507 0.887 0.984
0.4151 1380 0.898 152 0.794 1532 0.887 0.981
0.4419 1421 0.896 158 0.820 1579 0.888 0.987
0.4687 1477 0.890 156 0.834 1633 0.885 0.982
0.4954 1447 0.868 131 0.746 1578 0.857 0.966
0.5222 1161 0.879 87 0.823 1248 0.875 0.963
$$
Resolution limits = 19.098 1.366
Number of used reflections = 23217
Percentage observed = 97.4781
Percentage of free reflections = 5.1089
Overall R factor = 0.1765
Free R factor = 0.1955
Overall weighted R factor = 0.1874
Free weighted R factor = 0.2095
Overall weighted R2 factor = 0.2511
Free weighted R2 factor = 0.2790
Overall correlation coefficient = 0.9560
Free correlation coefficient = 0.9458
Cruickshanks DPI for coordinate error= 0.0606
DPI based on free R factor = 0.0603
Overall figure of merit = 0.8872
ML based su of positional parameters = 0.0354
ML based su of thermal parameters = 1.6604
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000
Trying gamma equal 5.00000007E-02
Gamma decreased to 3.99999991E-02
fvalues 112483.31 7166.0430 1105907.0 1131999.1
CGMAT cycle number = 2
fast hessian tabulation
Weight matrix 3.8690114
Actual weight 10.000000 is applied to the X-ray term
function value 1096807.8
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.021 0.019
Bond distances: others 962 0.001 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.925, B = -0.720
Babinet"s bulk solvent: scale = 0.180, B = 153.534
Partial structure 1: scale = 0.427, B = 32.143
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1675
Free R factor = 0.1904
Overall figure of merit = 0.8936
-----------------------------------------------------------------------------
Trying gamma equal 3.99999991E-02
Gamma decreased to 3.09090894E-02
fvalues 109870.97 5734.7017 1089699.4 1104444.4
CGMAT cycle number = 3
fast hessian tabulation
Weight matrix 4.3409519
Actual weight 10.000000 is applied to the X-ray term
function value 1086855.4
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.022 0.019
Bond distances: others 962 0.005 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.923, B = -0.021
Babinet"s bulk solvent: scale = 0.173, B = 153.519
Partial structure 1: scale = 0.427, B = 31.120
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1612
Free R factor = 0.1868
Overall figure of merit = 0.8994
-----------------------------------------------------------------------------
Trying gamma equal 3.09090894E-02
Gamma decreased to 2.26446260E-02
fvalues 108117.51 5685.4990 1084878.0 1086860.6
CGMAT cycle number = 4
fast hessian tabulation
Weight matrix 4.0741229
Actual weight 9.0909090 is applied to the X-ray term
function value 986273.88
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.023 0.019
Bond distances: others 962 0.006 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.921, B = -0.027
Babinet"s bulk solvent: scale = 0.171, B = 153.514
Partial structure 1: scale = 0.427, B = 30.796
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1595
Free R factor = 0.1855
Overall figure of merit = 0.9011
-----------------------------------------------------------------------------
Trying gamma equal 2.26446260E-02
Gamma decreased to 1.51314782E-02
fvalues 107863.41 5713.8003 985832.88 986290.19
CGMAT cycle number = 5
fast hessian tabulation
Weight matrix 3.7343411
Actual weight 8.2644625 is applied to the X-ray term
function value 896603.69
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.023 0.019
Bond distances: others 962 0.004 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.921, B = -0.023
Babinet"s bulk solvent: scale = 0.170, B = 153.514
Partial structure 1: scale = 0.428, B = 30.799
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1592
Free R factor = 0.1851
Overall figure of merit = 0.9016
-----------------------------------------------------------------------------
Trying gamma equal 1.51314782E-02
Gamma decreased to 8.30134377E-03
fvalues 107810.36 5622.4238 896335.19 896617.06
CGMAT cycle number = 6
fast hessian tabulation
Weight matrix 3.7626138
Actual weight 8.2644625 is applied to the X-ray term
function value 896256.81
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.022 0.019
Bond distances: others 962 0.003 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.920, B = -0.021
Babinet"s bulk solvent: scale = 0.168, B = 153.514
Partial structure 1: scale = 0.428, B = 30.806
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1591
Free R factor = 0.1847
Overall figure of merit = 0.9020
-----------------------------------------------------------------------------
Trying gamma equal 8.30134377E-03
Gamma decreased to 2.09213095E-03
fvalues 107783.25 5501.7769 896065.56 896272.38
CGMAT cycle number = 7
fast hessian tabulation
Weight matrix 3.7739828
Actual weight 8.2644625 is applied to the X-ray term
function value 896069.06
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.022 0.019
Bond distances: others 962 0.003 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.920, B = -0.019
Babinet"s bulk solvent: scale = 0.168, B = 153.515
Partial structure 1: scale = 0.428, B = 30.856
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1589
Free R factor = 0.1848
Overall figure of merit = 0.9022
-----------------------------------------------------------------------------
Trying gamma equal 2.09213095E-03
Gamma decreased to 0.0000000
fvalues 107768.05 5434.8384 895961.13 896079.81
CGMAT cycle number = 8
fast hessian tabulation
Weight matrix 3.7790251
Actual weight 8.2644625 is applied to the X-ray term
function value 895972.56
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.022 0.019
Bond distances: others 962 0.004 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.920, B = -0.016
Babinet"s bulk solvent: scale = 0.166, B = 153.512
Partial structure 1: scale = 0.428, B = 30.633
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1588
Free R factor = 0.1849
Overall figure of merit = 0.9023
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000
Trying gamma equal 2.56579034E-02
Gamma decreased to 2.05263235E-02
fvalues 107760.64 5396.1538 895861.56 895979.94
CGMAT cycle number = 9
fast hessian tabulation
Weight matrix 3.7851777
Actual weight 8.2644625 is applied to the X-ray term
function value 895881.06
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.022 0.019
Bond distances: others 962 0.003 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.919, B = -0.013
Babinet"s bulk solvent: scale = 0.166, B = 153.512
Partial structure 1: scale = 0.429, B = 30.631
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1588
Free R factor = 0.1849
Overall figure of merit = 0.9024
-----------------------------------------------------------------------------
Trying gamma equal 2.05263235E-02
Gamma decreased to 1.58612505E-02
fvalues 107754.01 5361.7007 895809.13 895890.63
CGMAT cycle number = 10
fast hessian tabulation
Weight matrix 3.7950871
Actual weight 8.2644625 is applied to the X-ray term
function value 895778.31
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.022 0.019
Bond distances: others 962 0.003 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.919, B = -0.009
Babinet"s bulk solvent: scale = 0.166, B = 153.509
Partial structure 1: scale = 0.428, B = 30.431
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1587
Free R factor = 0.1848
Overall figure of merit = 0.9026
-----------------------------------------------------------------------------
Trying gamma equal 1.58612505E-02
Gamma decreased to 1.16202747E-02
fvalues 107743.30 5341.6475 895728.06 895782.06
CGMAT cycle number = 11
fast hessian tabulation
Weight matrix 3.7967482
Actual weight 8.2644625 is applied to the X-ray term
function value 895754.69
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.022 0.019
Bond distances: others 962 0.003 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.919, B = -0.007
Babinet"s bulk solvent: scale = 0.165, B = 153.510
Partial structure 1: scale = 0.428, B = 30.462
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1587
Free R factor = 0.1848
Overall figure of merit = 0.9026
-----------------------------------------------------------------------------
Trying gamma equal 1.16202747E-02
Gamma decreased to 7.76484236E-03
fvalues 107741.63 5331.6147 895730.00 895758.25
CGMAT cycle number = 12
fast hessian tabulation
Weight matrix 3.8064208
Actual weight 8.2644625 is applied to the X-ray term
function value 895718.50
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.022 0.019
Bond distances: others 962 0.003 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.919, B = -0.004
Babinet"s bulk solvent: scale = 0.165, B = 153.509
Partial structure 1: scale = 0.428, B = 30.440
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1587
Free R factor = 0.1848
Overall figure of merit = 0.9027
-----------------------------------------------------------------------------
Trying gamma equal 7.76484236E-03
Gamma decreased to 4.25990392E-03
fvalues 107737.39 5328.1738 895690.88 895719.81
CGMAT cycle number = 13
fast hessian tabulation
Weight matrix 3.4584599
Actual weight 7.5131474 is applied to the X-ray term
function value 814790.94
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.022 0.019
Bond distances: others 962 0.003 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.919, B = -0.007
Babinet"s bulk solvent: scale = 0.165, B = 153.509
Partial structure 1: scale = 0.428, B = 30.437
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1587
Free R factor = 0.1848
Overall figure of merit = 0.9027
-----------------------------------------------------------------------------
Trying gamma equal 4.25990392E-03
Gamma decreased to 1.07359642E-03
fvalues 107740.73 5322.1357 814814.06 814794.13
fvalues 107740.73 5322.1357 814792.31 814794.13
CGMAT cycle number = 14
fast hessian tabulation
Weight matrix 3.1466434
Actual weight 6.8301339 is applied to the X-ray term
function value 741202.50
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.022 0.019
Bond distances: others 962 0.004 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.919, B = -0.008
Babinet"s bulk solvent: scale = 0.164, B = 153.509
Partial structure 1: scale = 0.428, B = 30.417
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1587
Free R factor = 0.1848
Overall figure of merit = 0.9027
-----------------------------------------------------------------------------
Trying gamma equal 1.07359642E-03
Gamma decreased to 0.0000000
fvalues 107746.27 5287.5947 741191.63 741209.06
CGMAT cycle number = 15
fast hessian tabulation
Weight matrix 3.1434772
Actual weight 6.8301339 is applied to the X-ray term
function value 741246.50
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.021 0.019
Bond distances: others 962 0.004 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.918, B = -0.010
Babinet"s bulk solvent: scale = 0.164, B = 153.509
Partial structure 1: scale = 0.428, B = 30.420
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1589
Free R factor = 0.1848
Overall figure of merit = 0.9027
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000
Trying gamma equal 1.31665589E-02
Gamma decreased to 1.05332471E-02
fvalues 107771.84 5154.5078 741226.50 741250.63
Limits of asymmetric unit : 1.00 1.00 0.13
Grid spacing to be used : 192 192 96
Maximuum H,K,L : 58 58 27
Minimum acceptable grid spacing: 128 128 60
Limits of asymmetric unit : 1.00 1.00 0.13
Grid spacing to be used : 192 192 96
Maximuum H,K,L : 58 58 27
Minimum acceptable grid spacing: 128 128 60
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: C:/SOLVE_REFINE/lizozim/mr-refine-build\r42.mtz
Norm of X_ray positional gradient 0.00
Norm of Geom. positional gradient 0.00
Norm of X_ray B-factor gradient 0.00
Norm of Geom. B-factor gradient 0.00
Product of X_ray and Geom posit. gradients 0.00
Cosine of angle between them 0.000
Product of X_ray and Geom B-fact gradients 0.00
Cosine of angle between them 0.000
Residuals: XRAY= 0.7362E+06 GEOM= 5063. TOTAL= 0.7413E+06
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1037 0.021 0.019
Bond distances: others 962 0.003 0.020
Bond angles : refined atoms 1408 2.098 1.903
Bond angles : others 2180 0.995 3.007
Torsion angles, period 1. refined 132 6.359 5.000
Torsion angles, period 2. refined 51 36.414 22.745
Torsion angles, period 3. refined 169 12.215 15.000
Torsion angles, period 3. others 8 4.152 15.000
Torsion angles, period 4. refined 12 23.914 15.000
Chiral centres: refined atoms 146 0.141 0.200
Planar groups: refined atoms 1225 0.011 0.020
Planar groups: others 277 0.001 0.020
VDW repulsions: refined_atoms 312 0.266 0.200
VDW repulsions.others 890 0.176 0.200
VDW; torsion: refined_atoms 522 0.187 0.200
VDW; torsion.others 581 0.087 0.200
HBOND: refined_atoms 17 0.143 0.200
Metal-ion: refined_atoms 4 0.138 0.200
VDW repulsions: symmetry: refined_atoms 18 0.258 0.200
VDW repulsions: symmetry: others 26 0.143 0.200
HBOND: symmetry: refined_atoms 2 0.098 0.200
M. chain bond B values: refined atoms 519 1.087 0.745
M. chain bond B values: others 518 1.051 0.742
M. chain angle B values: refined atoms 648 1.584 1.120
M. chain angle B values: others 649 1.586 1.123
S. chain bond B values: refined atoms 518 2.157 0.954
S. chain bond B values: others 518 2.156 0.953
S. chain angle B values: refined atoms 758 2.937 1.358
S. chain angle B values: others 758 2.933 1.357
Long range B values: refined atoms 1306 4.040 6.869
Long range B values: others 1267 3.926 6.556
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.918, B = -0.008
Babinet"s bulk solvent: scale = 0.163, B = 153.509
Partial structure 1: scale = 0.429, B = 30.446
Overall anisotropic scale factors
B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
**** Things for loggraph, R factor and others ****
$TABLE: Cycle 26. Rfactor analysis, F distribution v resln :
$GRAPHS:Cycle 26. v. resln :N:1,6,7,11,12:
:Cycle 26. and v. resln :N:1,4,5,9,10:
:Cycle 26. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.014 319 95.97 619.9 599.5 0.21 0.30 14 398.2 435.1 0.20 0.25
0.040 535 100.00 518.4 545.8 0.19 0.26 34 547.8 590.4 0.20 0.32
0.067 672 100.00 577.6 550.8 0.17 0.22 32 528.9 530.0 0.19 0.23
0.094 779 99.75 472.2 441.8 0.18 0.22 31 502.0 441.3 0.21 0.23
0.121 879 100.00 344.3 338.3 0.18 0.22 43 325.2 314.1 0.18 0.23
0.148 958 100.00 283.2 290.8 0.18 0.20 42 263.5 257.8 0.20 0.23
0.174 1040 100.00 263.2 266.2 0.16 0.18 38 280.4 296.5 0.15 0.19
0.201 1096 100.00 243.7 237.2 0.15 0.17 65 234.3 233.4 0.18 0.19
0.228 1185 100.00 220.2 216.3 0.14 0.16 56 231.9 218.4 0.15 0.16
0.255 1205 100.00 189.9 185.3 0.15 0.15 82 186.1 185.1 0.20 0.21
0.281 1298 100.00 162.8 160.1 0.15 0.15 59 156.9 156.5 0.19 0.20
0.308 1337 100.00 140.9 141.0 0.15 0.15 76 137.2 136.3 0.18 0.18
0.335 1403 100.00 126.5 124.3 0.15 0.14 88 120.5 119.1 0.21 0.20
0.362 1434 100.00 118.9 114.8 0.14 0.13 74 115.6 108.3 0.17 0.17
0.388 1507 100.00 110.8 107.4 0.14 0.13 76 106.1 104.3 0.18 0.16
0.415 1532 100.00 99.6 95.7 0.13 0.12 97 99.8 92.3 0.17 0.16
0.442 1579 100.00 93.8 90.0 0.13 0.12 92 95.0 89.1 0.16 0.16
0.469 1633 100.00 87.7 84.3 0.13 0.12 109 87.7 83.5 0.18 0.16
0.495 1576 93.50 76.0 74.7 0.15 0.13 79 79.3 76.1 0.20 0.17
0.522 1250 72.50 72.9 71.8 0.14 0.12 63 69.8 63.7 0.21 0.18
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 26. Fom(-acentric, centric, overall v resln:
$GRAPHS:Cycle 26. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0137 179 0.909 140 0.829 319 0.874 0.968
0.0405 376 0.926 159 0.824 535 0.895 0.979
0.0672 518 0.939 154 0.836 672 0.915 0.986
0.0940 623 0.926 156 0.856 779 0.912 0.992
0.1208 716 0.876 163 0.783 879 0.859 0.992
0.1475 800 0.899 158 0.766 958 0.877 0.963
0.1743 883 0.926 157 0.801 1040 0.907 0.951
0.2010 934 0.927 162 0.844 1096 0.914 0.973
0.2278 1022 0.934 163 0.868 1185 0.925 0.985
0.2546 1048 0.912 157 0.853 1205 0.905 0.981
0.2813 1136 0.890 162 0.817 1298 0.881 0.969
0.3081 1176 0.909 161 0.818 1337 0.898 0.964
0.3349 1243 0.911 160 0.844 1403 0.903 0.970
0.3616 1269 0.904 165 0.775 1434 0.889 0.984
0.3884 1347 0.917 160 0.881 1507 0.913 0.991
0.4151 1380 0.924 152 0.828 1532 0.914 0.993
0.4419 1421 0.930 158 0.854 1579 0.923 1.005
0.4687 1477 0.919 156 0.874 1633 0.915 0.992
0.4954 1447 0.902 131 0.791 1578 0.893 0.977
0.5222 1161 0.905 87 0.854 1248 0.902 0.971
$$
Resolution limits = 19.098 1.366
Number of used reflections = 23217
Percentage observed = 97.4781
Percentage of free reflections = 5.1089
Overall R factor = 0.1590
Free R factor = 0.1848
Overall weighted R factor = 0.1683
Free weighted R factor = 0.1966
Overall weighted R2 factor = 0.2339
Free weighted R2 factor = 0.2657
Overall correlation coefficient = 0.9615
Free correlation coefficient = 0.9493
Cruickshanks DPI for coordinate error= 0.0546
DPI based on free R factor = 0.0570
Overall figure of merit = 0.9027
ML based su of positional parameters = 0.0307
ML based su of thermal parameters = 1.4015
-----------------------------------------------------------------------------
Time in seconds: CPU = 0.00
Elapsed = 114.00
**** 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:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$
$$
0 0.1807 0.2006 0.881 111196. 6077.7 0.0 0.0 0.0 0.0 0.0
1 0.1787 0.1980 0.884 110791. 6056.0 0.0 0.0 0.0 0.0 0.0
2 0.1778 0.1969 0.886 110612. 6046.1 0.0 0.0 0.0 0.0 0.0
3 0.1774 0.1964 0.886 110529. 6041.3 0.0 0.0 0.0 0.0 0.0
4 0.1771 0.1961 0.886 110482. 6038.3 0.0 0.0 0.0 0.0 0.0
5 0.1770 0.1959 0.887 110449. 6036.0 0.0 0.0 0.0 0.0 0.0
6 0.1769 0.1957 0.887 110429. 6034.5 0.0 0.0 0.0 0.0 0.0
7 0.1768 0.1956 0.887 110416. 6033.4 0.0 0.0 0.0 0.0 0.0
8 0.1768 0.1954 0.887 110405. 6032.4 0.0 0.0 0.0 0.0 0.0
9 0.1767 0.1954 0.887 110399. 6031.9 0.0 0.0 0.0 0.0 0.0
10 0.1765 0.1955 0.887 110364. 6031.4 0.0219 1.149 2.146 1.094 0.133
11 0.1675 0.1904 0.894 109107. 5982.5 0.0212 1.095 2.107 1.075 0.134
12 0.1612 0.1868 0.899 108117. 5941.2 0.0224 1.149 2.157 1.105 0.140
13 0.1595 0.1855 0.901 107862. 5930.0 0.0230 1.181 2.204 1.133 0.144
14 0.1592 0.1851 0.902 107809. 5926.9 0.0228 1.169 2.199 1.130 0.144
15 0.1591 0.1847 0.902 107781. 5924.5 0.0223 1.144 2.180 1.120 0.144
16 0.1589 0.1848 0.902 107767. 5923.9 0.0221 1.131 2.169 1.114 0.144
17 0.1588 0.1849 0.902 107760. 5923.6 0.0220 1.124 2.163 1.111 0.144
18 0.1588 0.1849 0.902 107753. 5923.5 0.0219 1.121 2.160 1.110 0.144
19 0.1587 0.1848 0.903 107743. 5922.6 0.0219 1.119 2.159 1.109 0.144
20 0.1587 0.1848 0.903 107741. 5922.8 0.0219 1.119 2.158 1.109 0.145
21 0.1587 0.1848 0.903 107737. 5922.6 0.0219 1.120 2.159 1.109 0.145
22 0.1587 0.1848 0.903 107740. 5923.4 0.0219 1.120 2.160 1.110 0.145
23 0.1587 0.1848 0.903 107745. 5923.1 0.0217 1.111 2.151 1.105 0.145
24 0.1589 0.1848 0.903 107771. 5924.0 0.0210 1.077 2.118 1.086 0.143
25 0.1590 0.1848 0.903 107785. 5924.4 0.0207 1.057 2.098 1.075 0.141
$$
$TEXT:Result: $$ Final results $$
Initial Final
R factor 0.1807 0.1590
R free 0.2006 0.1848
Rms BondLength 0.0219 0.0207
Rms BondAngle 2.1456 2.0978
Rms ChirVolume 0.1332 0.1414
$$
Refmac_5.7.0032: End of Refmac_5.7.0032 Times: User: 0.0s System: 0.0s Elapsed: 2:07
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
CCP4i: Writing final coordinates (XYZOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r42.pdb
CCP4i: Writing final phases (HKLOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r42.mtz
CCP4i: Writing final TLS (TLSOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r42.tls
Generated for you by baubles 0.0.8 on Fri May 10 20:41:21 2013