Summary:
| Initial | After 10 cycles | |
|---|---|---|
| R factor | 0.2920 | 0.2701 |
| Rfree | 0.3766 | 0.3563 |
| RMSD Bond Length | 0.0380 | 0.0180 |
| RMSD Bond Angle | 2.814 | 1.855 |
| RMSD Chiral Centre | 0.407 | 0.129 |
Result:
| Restraint type | N restraints | Rms Delta | Av(Sigma) |
|---|---|---|---|
| Bond distances: refined atoms | 1514 | 0.018 | 0.022 |
| Bond angles : refined atoms | 2042 | 1.855 | 1.954 |
| Torsion angles, period 1. refined | 179 | 8.482 | 5.000 |
| Torsion angles, period 2. refined | 84 | 40.479 | 23.810 |
| Torsion angles, period 3. refined | 268 | 20.052 | 15.000 |
| Torsion angles, period 4. refined | 16 | 16.374 | 15.000 |
| Chiral centres: refined atoms | 216 | 0.129 | 0.200 |
| Planar groups: refined atoms | 1171 | 0.009 | 0.021 |
| VDW repulsions: refined_atoms | 670 | 0.245 | 0.200 |
| VDW; torsion: refined_atoms | 1007 | 0.322 | 0.200 |
| HBOND: refined_atoms | 37 | 0.172 | 0.200 |
| VDW repulsions: symmetry: refined_atoms | 58 | 0.198 | 0.200 |
| HBOND: symmetry: refined_atoms | 5 | 0.339 | 0.200 |
| M. chain bond B values: refined atoms | 903 | 1.076 | 1.500 |
| M. chain angle B values: refined atoms | 1459 | 1.895 | 2.000 |
| S. chain bond B values: refined atoms | 611 | 2.670 | 3.000 |
| S. chain angle B values: refined atoms | 583 | 3.993 | 4.500 |
The following warnings were issued:
|
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 |
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
############################################################### ############################################################### ############################################################### ### CCP4 6.0: Refmac_5.4.0065 version 5.4.0065 : 12/02/07## ############################################################### User: ccp4 Run date: 6/ 2/2008 Run time: 14:00:21 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 ssbridg
e 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 ---> blim 2.0 200.0
Data line --->
scal type SIMP reso 2.193 60.412 LSSC ANISO EXPE
Data line ---> solvent YES VDWProb 1.2 IONProb 0.8 RSHRink 0.8
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_ip SIGFP=SIGF_ip FREE=FreeR_flag
Data line --->
labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM
Data line ---> PNAME gp2
Data line ---> DNAME fsfsfs
Data line ---> RSIZE 80
Data line ---> END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /y/people/ccp4/projects/buccaneer/oleg/v1.mtz
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/syminfo.lib
**** Input and Default parameters# ****
Input coordinate file. Logical name - XYZIN actual file name - /y/people/ccp4/projects/buccaneer/oleg/v1-phic_pirate1_buccaneer3a-coot-3.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /tmp/ccp4/buccaneer_286_2_pdb_1.tmp
Input reflection file. Logical name - HKLIN actual file name - /y/people/ccp4/projects/buccaneer/oleg/v1.mtz
Output reflection file. Logical name - HKLOUT actual file name - /tmp/ccp4/buccaneer_286_3_mtz_1.tmp
Cell from mtz : 69.795 69.795 72.458 90.000 90.000 120.000
Space group from mtz: number - 154; name - P 32 2 1
Refinement type : Restrained
**** Makecif parameters ****
Dictionary files for restraints : /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/ener_lib.cif
Program will rely on residue and atom names. No checking
If this option is used then monomers should be checked carefully before using
Hydrogens in input coordinate file will be kept
Links between monomers will be checked. Only those links present in the coordinate file will be used
All links to sugar will be analysed and used
For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
Symmetry related links will be analysed and used
Cis peptides will be found and used automatically
Residual : 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 1.200
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 0.0104
Refinement of individual isotropic Bfactors
Refinement resln : 60.4122 2.1931
Estimated number of reflections : 16247
Free R exclusion - flag equals: 0
Auto weighting. An attempt
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: 60.4120 2.1930
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) 1.5A**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 0.30A
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 :/y/people/ccp4/projects/buccaneer/oleg/v1-phic_pirate1_buccaneer3a
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 4.13
_lib_update 18/01/08
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 2436
with complete description : 455
NUMBER OF MODIFICATIONS : 47
NUMBER OF LINKS : 64
I am reading libraries. Please wait.
- energy parameters
- monomer"s description (links & mod )
FORMATTED OLD file opened on unit 45
Logical name: ATOMSF, Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/atomsf.lib
Number of atoms : 1519
Number of residues : 191
Number of chains : 2
I am reading library. Please wait.
mon_lib.cif
$TEXT:Warning: $$ comment $$
WARNING : CIS peptide bond (not be used) angle = 2.35
ch:AA res: 174 ASP --> 175 LYS
$$
--------------------------------
--- title of input coord file ---
PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-9-
--------------------------------
ATTENTION: atom:CB UNK 206 AA is missing in the structure
ATTENTION: atom:O TRP 211 AA is missing in the structure
Number of chains : 2
Total number of monomers : 191
Number of atoms : 1521
Number of missing atoms : 2
Number of rebuilt atoms : 0
Number of unknown atoms : 0
Number of deleted atoms : 0
Number of bonds restraints : 1514
Number of angles restraints : 2042
Number of torsions restraints : 1036
Number of chiralities : 216
Number of planar groups : 271
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
We are here
Bonds before and after 1514 1514
Angles before and after 2042 2042
Chirals before and after 216 216
planes before and after 271 271
Torsions before and after 1036 1036
Number of reflections in file 10792
Number of reflection read 10714
CGMAT cycle number = 1
Starting restraints
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 170 ASP C . - A 171 TYR N . mod.= 0.927 id.= 1.329 dev= 0.402 sig.= 0.014
A 171 TYR C . - A 171 TYR O . mod.= 0.000 id.= 1.231 dev= 1.231 sig.= 0.020
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 28 PRO CB - A 28 PRO C mod.= 89.41 id.= 110.10 dev= 20.687 sig.= 1.900
A 74 LYS N - A 74 LYS CB mod.= 86.77 id.= 110.50 dev= 23.729 sig.= 1.700
A 171 TYR CA - A 171 TYR O mod.= 90.00 id.= 120.80 dev= 30.800 sig.= 1.700
A 171 TYR O - A 172 GLN N mod.= 90.00 id.= 123.00 dev= 33.000 sig.= 1.600
A 171 TYR CA - A 172 GLN N mod.= 93.31 id.= 116.20 dev= 22.890 sig.= 2.000
A 182 ARG CB - A 182 ARG C mod.= 84.34 id.= 110.10 dev= 25.757 sig.= 1.900
A 183 LEU N - A 183 LEU CB mod.= 90.62 id.= 110.50 dev= 19.875 sig.= 1.700
A 200 ARG CB - A 200 ARG C mod.= 83.67 id.= 110.10 dev= 26.434 sig.= 1.900
A 201 ASP N - A 201 ASP CB mod.= 137.55 id.= 110.50 dev=-27.045 sig.= 1.700
**** Chiral volume outliers ****
Chiral volume deviations from the ideal >10.000Sigma will be monitored
A 29 PHE CA mod.= -0.29 id.= -2.50 dev= -2.215 sig.= 0.200
A 49 ASN CA mod.= 2.19 id.= -2.47 dev= -4.656 sig.= 0.200
**** B-value outliers ****
B-value differences > 10.00Sigma will be monitored
A 171 TYR N - A 170 ASP CA ABS(DELTA)= 28.320 Sigma= 2.000
A 171 TYR N - A 170 ASP C ABS(DELTA)= 29.880 Sigma= 1.500
A 171 TYR CA - A 170 ASP C ABS(DELTA)= 29.880 Sigma= 2.000
A 171 TYR N - A 170 ASP O ABS(DELTA)= 29.860 Sigma= 2.000
A 172 GLN O - A 172 GLN CA ABS(DELTA)= 44.240 Sigma= 2.000
A 173 THR N - A 172 GLN CA ABS(DELTA)= 47.360 Sigma= 2.000
A 172 GLN O - A 172 GLN C ABS(DELTA)= 44.240 Sigma= 1.500
A 173 THR N - A 172 GLN C ABS(DELTA)= 47.360 Sigma= 1.500
A 173 THR CA - A 172 GLN C ABS(DELTA)= 49.750 Sigma= 2.000
weigth matrix 2.2369964E-04
Before reporting
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1514 0.038 0.022
Bond angles : refined atoms 2042 2.814 1.954
Torsion angles, period 1. refined 179 9.251 5.000
Torsion angles, period 2. refined 84 39.204 23.810
Torsion angles, period 3. refined 268 19.726 15.000
Torsion angles, period 4. refined 16 16.242 15.000
Chiral centres: refined atoms 216 0.407 0.200
Planar groups: refined atoms 1171 0.007 0.021
VDW repulsions: refined_atoms 684 0.288 0.200
VDW; torsion: refined_atoms 1013 0.332 0.200
HBOND: refined_atoms 37 0.254 0.200
VDW repulsions: symmetry: refined_atoms 53 0.377 0.200
HBOND: symmetry: refined_atoms 5 0.351 0.200
M. chain bond B values: refined atoms 903 2.588 1.500
M. chain angle B values: refined atoms 1459 3.090 2.000
S. chain bond B values: refined atoms 611 2.368 3.000
S. chain angle B values: refined atoms 583 3.525 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.786, B = 3.320
Partial structure 1: scale = 0.349, B = 23.054
Overall anisotropic scale factors
B11 = 1.10 B22 = 1.10 B33 = -1.65 B12 = 0.55 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 $$
$$
0.005 134 92.76 413.5 389.7 0.27 0.50 7 447.0 330.0 0.37 0.38
0.016 230 100.00 349.4 342.9 0.25 0.40 10 384.9 342.1 0.17 0.21
0.026 291 100.00 252.1 250.7 0.31 0.43 10 225.4 213.6 0.49 0.80
0.036 336 99.72 273.1 274.3 0.27 0.36 15 272.6 247.3 0.38 0.64
0.047 365 100.00 303.0 285.9 0.23 0.30 18 305.0 247.6 0.35 0.41
0.057 414 100.00 292.2 266.6 0.25 0.33 13 414.7 363.7 0.24 0.42
0.067 451 100.00 251.6 230.4 0.25 0.30 25 275.0 227.5 0.35 0.45
0.078 470 100.00 210.1 183.2 0.28 0.35 19 178.1 138.0 0.41 0.49
0.088 494 100.00 164.2 150.8 0.31 0.36 28 180.7 179.8 0.35 0.41
0.098 536 100.00 130.2 122.3 0.33 0.38 31 136.2 103.9 0.40 0.46
0.109 537 100.00 114.5 105.5 0.32 0.36 29 109.8 86.1 0.38 0.39
0.119 581 99.84 86.6 84.3 0.35 0.37 33 87.9 92.5 0.49 0.50
0.129 600 100.00 75.5 72.9 0.36 0.36 24 78.9 73.9 0.49 0.49
0.139 616 99.69 61.9 61.2 0.37 0.35 37 51.2 59.0 0.59 0.54
0.150 636 99.26 54.9 54.5 0.34 0.34 34 50.7 57.6 0.45 0.41
0.160 641 98.53 49.5 50.1 0.34 0.32 31 48.6 49.8 0.44 0.39
0.170 654 96.67 43.0 43.7 0.36 0.32 42 45.7 53.0 0.48 0.42
0.181 669 92.38 39.3 39.2 0.34 0.31 22 34.1 38.0 0.44 0.38
0.191 636 90.65 33.4 34.0 0.37 0.33 33 31.6 30.0 0.50 0.47
0.201 627 84.12 31.4 31.1 0.34 0.29 30 35.1 37.4 0.33 0.24
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 1. Fom(-acentric, centric, overall v resln:
$GRAPHS:Cycle 1. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0054 78 0.682 56 0.525 134 0.616 0.980
0.0157 163 0.692 67 0.496 230 0.635 0.970
0.0260 224 0.560 67 0.564 291 0.561 0.959
0.0364 267 0.703 69 0.548 336 0.671 0.948
0.0467 301 0.753 64 0.716 365 0.747 0.937
0.0570 348 0.767 66 0.690 414 0.755 0.926
0.0673 383 0.772 68 0.733 451 0.766 0.915
0.0776 403 0.727 67 0.622 470 0.712 0.905
0.0879 434 0.708 60 0.666 494 0.703 0.894
0.0982 463 0.700 73 0.518 536 0.675 0.884
0.1085 472 0.693 65 0.557 537 0.677 0.874
0.1188 511 0.636 70 0.598 581 0.631 0.864
0.1292 535 0.642 65 0.538 600 0.630 0.854
0.1395 559 0.608 57 0.507 616 0.599 0.844
0.1498 569 0.621 67 0.544 636 0.613 0.834
0.1601 578 0.638 63 0.601 641 0.634 0.825
0.1704 603 0.637 51 0.612 654 0.635 0.816
0.1807 625 0.671 44 0.604 669 0.666 0.806
0.1910 592 0.665 44 0.611 636 0.661 0.797
0.2013 589 0.702 38 0.689 627 0.701 0.788
$$
Resolution limits = 60.412 2.201
Number of used reflections = 9918
Percentage observed = 97.1623
Percentage of free reflections = 4.7171
Overall R factor = 0.2920
Free R factor = 0.3766
Overall weighted R factor = 0.3475
Free weighted R factor = 0.4525
Overall correlation coefficient = 0.9112
Free correlation coefficient = 0.8639
Cruickshanks DPI for coordinate error= 0.4046
DPI based on free R factor = 0.3296
Overall figure of merit = 0.6641
ML based su of positional parameters = 0.2870
ML based su of thermal parameters = 10.9532
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Trying gamma equal 5.0000001E-02
Gamma decreased to 3.9999999E-02
average, maximum and rms 4.9283175E-04 0.3419545 3.7318300E-02
average, maximum and rms B shifts 2.658017 20.56914 2.108098
CGMAT cycle number = 2
Starting restraints
weigth matrix 5.1245122E-04
Before reporting
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1514 0.036 0.022
Bond angles : refined atoms 2042 2.001 1.954
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.789, B = 0.288
Partial structure 1: scale = 0.351, B = 26.836
Overall anisotropic scale factors
B11 = 1.10 B22 = 1.10 B33 = -1.65 B12 = 0.55 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2807
Free R factor = 0.3642
Overall figure of merit = 0.6837
-----------------------------------------------------------------------------
Trying gamma equal 3.9999999E-02
Gamma decreased to 3.0909089E-02
average, maximum and rms -2.8158716E-04 0.2924476 2.0419937E-02
average, maximum and rms B shifts 0.1588902 10.96816 1.107507
CGMAT cycle number = 3
Starting restraints
weigth matrix 4.5648916E-04
Before reporting
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1514 0.036 0.022
Bond angles : refined atoms 2042 1.921 1.954
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.790, B = -0.030
Partial structure 1: scale = 0.350, B = 27.055
Overall anisotropic scale factors
B11 = 1.10 B22 = 1.10 B33 = -1.65 B12 = 0.55 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2761
Free R factor = 0.3589
Overall figure of merit = 0.6927
-----------------------------------------------------------------------------
Trying gamma equal 3.0909089E-02
Gamma decreased to 2.2644626E-02
average, maximum and rms -4.0951351E-04 0.2375915 1.5768522E-02
average, maximum and rms B shifts -3.8357090E-02 9.031544 0.8933601
CGMAT cycle number = 4
Starting restraints
weigth matrix 5.9690105E-04
Before reporting
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1514 0.036 0.022
Bond angles : refined atoms 2042 1.911 1.954
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.789, B = -0.158
Partial structure 1: scale = 0.350, B = 27.634
Overall anisotropic scale factors
B11 = 1.10 B22 = 1.10 B33 = -1.65 B12 = 0.55 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2741
Free R factor = 0.3560
Overall figure of merit = 0.6986
-----------------------------------------------------------------------------
Trying gamma equal 2.2644626E-02
Gamma decreased to 1.5131478E-02
average, maximum and rms -5.5713055E-04 0.1857136 1.4150417E-02
average, maximum and rms B shifts -0.1234790 6.658434 0.6994349
CGMAT cycle number = 5
Starting restraints
weigth matrix 8.0769148E-04
Before reporting
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1514 0.036 0.022
Bond angles : refined atoms 2042 1.908 1.954
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.788, B = -0.102
Partial structure 1: scale = 0.349, B = 27.647
Overall anisotropic scale factors
B11 = 1.10 B22 = 1.10 B33 = -1.65 B12 = 0.55 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2730
Free R factor = 0.3543
Overall figure of merit = 0.7012
-----------------------------------------------------------------------------
Trying gamma equal 1.5131478E-02
Gamma decreased to 8.3013438E-03
average, maximum and rms -6.5700186E-04 0.1836041 1.3638957E-02
average, maximum and rms B shifts -7.8261055E-02 5.588721 0.5268544
CGMAT cycle number = 6
Starting restraints
weigth matrix 1.5111472E-03
Before reporting
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1514 0.036 0.022
Bond angles : refined atoms 2042 1.897 1.954
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.788, B = -0.089
Partial structure 1: scale = 0.349, B = 27.930
Overall anisotropic scale factors
B11 = 1.10 B22 = 1.10 B33 = -1.65 B12 = 0.55 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2722
Free R factor = 0.3540
Overall figure of merit = 0.7060
-----------------------------------------------------------------------------
Trying gamma equal 8.3013438E-03
Gamma decreased to 2.0921309E-03
average, maximum and rms -7.1817444E-04 0.2031246 1.3585337E-02
average, maximum and rms B shifts -3.1476162E-02 3.818484 0.3863178
CGMAT cycle number = 7
Starting restraints
weigth matrix 5.8069970E-03
Before reporting
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1514 0.036 0.022
Bond angles : refined atoms 2042 1.900 1.954
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.788, B = -0.062
Partial structure 1: scale = 0.349, B = 27.874
Overall anisotropic scale factors
B11 = 1.10 B22 = 1.10 B33 = -1.65 B12 = 0.55 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2717
Free R factor = 0.3541
Overall figure of merit = 0.7069
-----------------------------------------------------------------------------
Trying gamma equal 2.0921309E-03
Gamma decreased to 0.0000000E+00
average, maximum and rms -7.5822714E-04 0.2308955 1.3668665E-02
average, maximum and rms B shifts -2.2930350E-02 2.567143 0.2701696
CGMAT cycle number = 8
Starting restraints
weigth matrix 0.1138975
Before reporting
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1514 0.035 0.022
Bond angles : refined atoms 2042 1.888 1.954
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.788, B = -0.024
Partial structure 1: scale = 0.349, B = 27.873
Overall anisotropic scale factors
B11 = 1.10 B22 = 1.10 B33 = -1.65 B12 = 0.55 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2711
Free R factor = 0.3549
Overall figure of merit = 0.7102
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Gamma decreased to 0.0000000E+00
average, maximum and rms -5.6689919E-04 0.5951940 2.0209249E-02
average, maximum and rms B shifts 2.7340256E-02 1.562113 0.2008526
CGMAT cycle number = 9
Starting restraints
weigth matrix 0.1239944
Before reporting
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1514 0.019 0.022
Bond angles : refined atoms 2042 1.965 1.954
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.789, B = -0.041
Partial structure 1: scale = 0.349, B = 28.129
Overall anisotropic scale factors
B11 = 1.10 B22 = 1.10 B33 = -1.65 B12 = 0.55 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2710
Free R factor = 0.3548
Overall figure of merit = 0.7114
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Gamma decreased to 0.0000000E+00
average, maximum and rms -7.3918171E-04 0.3196759 1.4909632E-02
average, maximum and rms B shifts -6.7073233E-02 1.427452 0.1570524
<4
CGMAT cycle number = 10
**** Torsion angle outliers ****
Torsion angle deviations from the ideal >10.000Sigma will be monitored
A 174 ASP CA - A 175 LYS CA mod.= 88.41 id.= 180.00 per.= 1 dev= 91.59 sig.= 5.00
weigth matrix 0.1263151
Before reporting
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1514 0.018 0.022
Bond angles : refined atoms 2042 1.871 1.954
Torsion angles, period 1. refined 179 8.494 5.000
Torsion angles, period 2. refined 84 40.503 23.810
Torsion angles, period 3. refined 268 19.979 15.000
Torsion angles, period 4. refined 16 16.068 15.000
Chiral centres: refined atoms 216 0.131 0.200
Planar groups: refined atoms 1171 0.010 0.021
VDW repulsions: refined_atoms 668 0.247 0.200
VDW; torsion: refined_atoms 1007 0.321 0.200
HBOND: refined_atoms 37 0.185 0.200
VDW repulsions: symmetry: refined_atoms 59 0.200 0.200
HBOND: symmetry: refined_atoms 5 0.341 0.200
M. chain bond B values: refined atoms 903 1.072 1.500
M. chain angle B values: refined atoms 1459 1.891 2.000
S. chain bond B values: refined atoms 611 2.654 3.000
S. chain angle B values: refined atoms 583 3.973 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.790, B = 0.035
Partial structure 1: scale = 0.348, B = 27.807
Overall anisotropic scale factors
B11 = 1.10 B22 = 1.10 B33 = -1.65 B12 = 0.55 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 $$
$$
0.005 134 92.76 411.4 387.7 0.26 0.49 7 444.8 311.8 0.39 0.37
0.016 230 100.00 347.6 343.7 0.25 0.41 10 383.0 372.1 0.16 0.26
0.026 291 100.00 250.8 248.8 0.31 0.42 10 224.3 215.5 0.44 0.72
0.036 336 99.72 271.7 269.4 0.25 0.33 15 271.3 257.3 0.35 0.59
0.047 365 100.00 301.5 283.3 0.22 0.28 18 303.5 243.7 0.39 0.47
0.057 414 100.00 290.7 268.2 0.23 0.31 13 412.6 357.9 0.29 0.46
0.067 451 100.00 250.3 230.7 0.23 0.29 25 273.7 220.4 0.32 0.46
0.078 470 100.00 209.1 186.7 0.27 0.33 19 177.2 138.3 0.37 0.47
0.088 494 100.00 163.4 150.0 0.29 0.34 28 179.8 181.7 0.37 0.40
0.098 536 100.00 129.6 124.0 0.31 0.35 31 135.5 107.4 0.36 0.41
0.109 537 100.00 113.9 107.4 0.30 0.33 29 109.2 90.1 0.35 0.35
0.119 581 99.84 86.2 83.9 0.32 0.33 33 87.5 93.2 0.46 0.44
0.129 600 100.00 75.1 73.9 0.33 0.33 24 78.5 77.5 0.42 0.43
0.139 616 99.69 61.6 61.2 0.32 0.32 37 51.0 57.4 0.56 0.50
0.150 636 99.26 54.6 55.4 0.30 0.30 34 50.4 56.2 0.41 0.37
0.160 641 98.53 49.3 50.8 0.29 0.28 31 48.4 52.0 0.36 0.33
0.170 654 96.67 42.7 44.1 0.30 0.27 42 45.4 49.8 0.36 0.32
0.181 669 92.38 39.1 40.1 0.28 0.24 22 34.0 36.0 0.27 0.22
0.191 636 90.65 33.2 33.5 0.29 0.25 33 31.5 29.2 0.42 0.40
0.201 627 84.12 31.2 31.8 0.25 0.21 30 34.9 36.6 0.24 0.19
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 10. Fom(-acentric, centric, overall v resln:
$GRAPHS:Cycle 10. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0054 78 0.634 56 0.482 134 0.570 0.945
0.0157 163 0.657 67 0.462 230 0.600 0.941
0.0260 224 0.524 67 0.538 291 0.527 0.937
0.0364 267 0.678 69 0.530 336 0.648 0.932
0.0467 301 0.738 64 0.696 365 0.730 0.928
0.0570 348 0.763 66 0.700 414 0.753 0.924
0.0673 383 0.775 68 0.734 451 0.768 0.920
0.0776 403 0.736 67 0.673 470 0.727 0.916
0.0879 434 0.723 60 0.682 494 0.718 0.912
0.0982 463 0.733 73 0.532 536 0.706 0.908
0.1085 472 0.735 65 0.601 537 0.718 0.903
0.1188 511 0.681 70 0.599 581 0.671 0.899
0.1292 535 0.705 65 0.622 600 0.696 0.895
0.1395 559 0.675 57 0.588 616 0.667 0.891
0.1498 569 0.699 67 0.608 636 0.689 0.887
0.1601 578 0.724 63 0.711 641 0.723 0.883
0.1704 603 0.731 51 0.695 654 0.728 0.879
0.1807 625 0.770 44 0.725 669 0.767 0.875
0.1910 592 0.755 44 0.728 636 0.753 0.871
0.2013 589 0.812 38 0.843 627 0.814 0.867
$$
Resolution limits = 60.412 2.201
Number of used reflections = 9918
Percentage observed = 97.1623
Percentage of free reflections = 4.7171
Overall R factor = 0.2706
Free R factor = 0.3557
Overall weighted R factor = 0.3181
Free weighted R factor = 0.4151
Overall correlation coefficient = 0.9205
Free correlation coefficient = 0.8647
Cruickshanks DPI for coordinate error= 0.3749
DPI based on free R factor = 0.3113
Overall figure of merit = 0.7128
ML based su of positional parameters = 0.2224
ML based su of thermal parameters = 8.2325
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Gamma decreased to 0.0000000E+00
average, maximum and rms -7.0030265E-04 0.3393906 1.3038892E-02
average, maximum and rms B shifts 5.3676289E-02 1.224760 0.1411436
Starting restraints
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /tmp/ccp4/buccaneer_286_3_mtz_1.tmp
-------------------------------------------------------------------------------
$TEXT: Result: $$ $$
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1514 0.018 0.022
Bond angles : refined atoms 2042 1.855 1.954
Torsion angles, period 1. refined 179 8.482 5.000
Torsion angles, period 2. refined 84 40.479 23.810
Torsion angles, period 3. refined 268 20.052 15.000
Torsion angles, period 4. refined 16 16.374 15.000
Chiral centres: refined atoms 216 0.129 0.200
Planar groups: refined atoms 1171 0.009 0.021
VDW repulsions: refined_atoms 670 0.245 0.200
VDW; torsion: refined_atoms 1007 0.322 0.200
HBOND: refined_atoms 37 0.172 0.200
VDW repulsions: symmetry: refined_atoms 58 0.198 0.200
HBOND: symmetry: refined_atoms 5 0.339 0.200
M. chain bond B values: refined atoms 903 1.076 1.500
M. chain angle B values: refined atoms 1459 1.895 2.000
S. chain bond B values: refined atoms 611 2.670 3.000
S. chain angle B values: refined atoms 583 3.993 4.500
$$
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.790, B = -0.016
Partial structure 1: scale = 0.349, B = 27.654
Overall anisotropic scale factors
B11 = 1.10 B22 = 1.10 B33 = -1.65 B12 = 0.55 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.005 134 92.76 411.3 388.1 0.26 0.49 7 444.6 314.3 0.38 0.36
0.016 230 100.00 347.5 343.5 0.25 0.40 10 382.8 371.4 0.16 0.26
0.026 291 100.00 250.7 248.9 0.31 0.42 10 224.2 213.6 0.43 0.70
0.036 336 99.72 271.6 268.9 0.25 0.33 15 271.2 258.4 0.36 0.59
0.047 365 100.00 301.4 283.3 0.22 0.28 18 303.4 243.2 0.40 0.48
0.057 414 100.00 290.6 268.2 0.23 0.31 13 412.4 357.9 0.29 0.47
0.067 451 100.00 250.2 230.5 0.23 0.29 25 273.6 219.3 0.33 0.47
0.078 470 100.00 209.0 186.9 0.27 0.33 19 177.1 138.5 0.38 0.47
0.088 494 100.00 163.3 150.0 0.29 0.34 28 179.7 180.9 0.37 0.41
0.098 536 100.00 129.5 124.1 0.31 0.35 31 135.5 107.8 0.36 0.41
0.109 537 100.00 113.9 107.5 0.30 0.33 29 109.2 89.7 0.35 0.35
0.119 581 99.84 86.1 83.9 0.32 0.33 33 87.5 93.4 0.45 0.44
0.129 600 100.00 75.1 73.9 0.33 0.33 24 78.5 77.4 0.42 0.44
0.139 616 99.69 61.6 61.2 0.32 0.32 37 51.0 57.4 0.57 0.50
0.150 636 99.26 54.6 55.4 0.30 0.29 34 50.4 56.2 0.40 0.36
0.160 641 98.53 49.3 50.7 0.29 0.28 31 48.3 51.8 0.35 0.32
0.170 654 96.67 42.7 44.1 0.30 0.27 42 45.4 49.5 0.36 0.32
0.181 669 92.38 39.1 40.0 0.27 0.24 22 34.0 36.0 0.26 0.21
0.191 636 90.65 33.2 33.5 0.28 0.25 33 31.5 29.3 0.41 0.38
0.201 627 84.12 31.2 31.8 0.25 0.21 30 34.9 36.5 0.24 0.20
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0054 78 0.631 56 0.480 134 0.568 0.943
0.0157 163 0.655 67 0.459 230 0.598 0.939
0.0260 224 0.522 67 0.536 291 0.525 0.935
0.0364 267 0.676 69 0.527 336 0.645 0.931
0.0467 301 0.736 64 0.697 365 0.729 0.927
0.0570 348 0.763 66 0.700 414 0.753 0.924
0.0673 383 0.774 68 0.731 451 0.767 0.920
0.0776 403 0.736 67 0.674 470 0.727 0.916
0.0879 434 0.724 60 0.683 494 0.719 0.912
0.0982 463 0.734 73 0.535 536 0.707 0.908
0.1085 472 0.735 65 0.603 537 0.719 0.904
0.1188 511 0.682 70 0.601 581 0.673 0.901
0.1292 535 0.706 65 0.624 600 0.697 0.897
0.1395 559 0.677 57 0.591 616 0.669 0.893
0.1498 569 0.701 67 0.609 636 0.692 0.889
0.1601 578 0.726 63 0.715 641 0.725 0.886
0.1704 603 0.734 51 0.700 654 0.731 0.882
0.1807 625 0.773 44 0.727 669 0.770 0.878
0.1910 592 0.758 44 0.730 636 0.756 0.875
0.2013 589 0.815 38 0.847 627 0.817 0.871
$$
Resolution limits = 60.412 2.201
Number of used reflections = 9918
Percentage observed = 97.1623
Percentage of free reflections = 4.7171
Overall R factor = 0.2701
Free R factor = 0.3563
Overall weighted R factor = 0.3174
Free weighted R factor = 0.4152
Overall correlation coefficient = 0.9208
Free correlation coefficient = 0.8643
Cruickshanks DPI for coordinate error= 0.3741
DPI based on free R factor = 0.3118
Overall figure of merit = 0.7139
ML based su of positional parameters = 0.2224
ML based su of thermal parameters = 8.2325
-----------------------------------------------------------------------------
Time in seconds: CPU = 20.67
Elapsed = 20.00
**** 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:
$$
Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$
$$
0 0.2920 0.3766 0.664 49212. 2491.6 0.0380 1.916 2.814 1.406 0.407
1 0.2807 0.3642 0.684 48766. 2476.6 0.0357 1.736 2.001 0.925 0.281
2 0.2761 0.3589 0.693 48589. 2470.4 0.0358 1.732 1.921 0.875 0.237
3 0.2741 0.3560 0.699 48507. 2466.9 0.0359 1.736 1.911 0.873 0.208
4 0.2730 0.3543 0.701 48453. 2463.6 0.0360 1.739 1.908 0.875 0.185
5 0.2722 0.3540 0.706 48413. 2461.9 0.0360 1.738 1.897 0.873 0.168
6 0.2717 0.3541 0.707 48379. 2459.6 0.0362 1.743 1.900 0.876 0.157
7 0.2711 0.3549 0.710 48338. 2457.9 0.0348 1.670 1.888 0.873 0.146
8 0.2710 0.3548 0.711 48297. 2455.6 0.0193 0.840 1.965 0.934 0.137
9 0.2706 0.3557 0.713 48269. 2454.3 0.0180 0.755 1.871 0.867 0.131
10 0.2701 0.3563 0.714 48242. 2453.3 0.0180 0.757 1.855 0.857 0.129
$$
Refmac_5.4.0065: End of Refmac_5.4.0065 Times: User: 23.8s System: 1.4s Elapsed: 0:25
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CCP4i: Writing final coordinates (XYZOUT) to /y/people/ccp4/projects/buccaneer/v1-phic_pirate1_buccaneer3a-coot-3_refmac1.pdb
CCP4i: Writing final phases (HKLOUT) to /y/people/ccp4/projects/buccaneer/v1_refmac2.mtz
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