Resolve output
The output from resolve follows. The data are for the initiation factor 5A test case shown in the example section of the manual.
*******************************************************
* --- Resolve --- *
* *
* Reciprocal-space solvent flattening and *
* Maximum-likelihood density modification *
* *
* *
*******************************************************
(version 1.03 of 03-Jun-2000)
Tom Terwilliger, Los Alamos National Laboratory, "terwilliger@LANL.gov"
>solvent_content 0.60
Fraction of unit cell assumed to be solvent is: 0.6000000
All done with inputs
Weight on obs:
The date today is 03-jun-00. Your license is good until 15-dec-07.
Opening
solve.mtz
on unit 1 with 1 0
User: terwill Logical Name: solve.mtz
Status: READONLY Filename: solve.mtz
HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
* Title:
.
* Number of Columns = 11
* Number of Reflections = 12442
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FP SIGFP PHIB FOM HLA HLB HLC HLD
* Column Types :
H H H F Q P W A A A A
* Cell Dimensions :
113.95 113.95 32.47 90.00 90.00 90.00
* Resolution Range :
0.00262 0.22672 ( 19.537 - 2.100 A )
* There is no sort order recorded in the MTZ header
* Space group = I4 (number 79)
Opened mtz file
solve.mtz
* Input Program Labels :
H K L FP PHIB FOM HLA HLB HLC HLD
* Input File Labels :
H K L FP SIGFP PHIB FOM HLA HLB HLC HLD
* Lookup Table : the number indicates the input column no.
* Array element n corresponds to the nth program label
0 0 0 4 6 7 8 9 10 11
lookup = 0 0 0 4 6
7 8 9 10 11
FP PHIB FOM taken from columns 4 6 7
Total of 12442 reflections read from file
Adding F000 term (0.0) to this list
Closed mtz file
Space group is 79
FORMATTED OLD file opened on unit 11
Logical name: SYMOP, Full name: /usr/local/lib/resolve/symop.lib
Centric Zone 1 Reflections of Type hk0
Cycles of mask generation: 5
Sub-cycles per mask cycle: 10
Expected I corrected for centering by factor of 2
Results of wilson scaling:
Scale on I = 1.89
B-value = 9.75
Scaling data with value of 1.89
Total of 12442 reflections with 0.05 < s < 0.48 used.
Mask cycle 1
New Wang averaging radius = 4.00
fraction protein= 0.4000000
rms of this map is 9.4361752E-02 avg = 7.6590821E-02
Mean +/- SD of density in protein region : 0.00 +/- 0.39
Mean +/- SD of density in solvent region : 0.00 +/- 0.19
fraction protein= 0.4000000
rms of this map is 7.5199082E-02 avg = 6.4762838E-02
Minor cycle 1
Plot of Observed (o) and model (x)
electron density distributions for protein region
where the model distribution is given by,
p_model(beta*(rho+offset)) = p_ideal(rho)
and then convoluted with a gaussian with width of sigma
where sigma, offset and beta are given below under
"Error estimate."
NOTE: the mean for the protein region should be
greater than the solvent region, but the most
probable protein density is less than the mean
of the solvent
0.04..................................................
. . .
. . .
. xxxx . .
. oxxooxxo .
. x o xo .
. xx .xx .
p(rho) . ox . xx .
. xx . xxo .
. xx . xoo .
. xo . xxxoo .
. oo . xxx .
. xx . xxxx .
. xo . xxxxx .
. xxxo . xxxxxxxo .
0.0 xxo............................................xxx
-2 -1 0 1 2 3
normalized rho (0 = mean of solvent region)
-------------------------------------------------------------------------------
Plot of Observed (o) and model (x)
electron density distributions for solvent region
where the model distribution is given by,
p_model(beta*(rho+offset)) = p_ideal(rho)
and then convoluted with a gaussian with width of sigma
where sigma, offset and beta are given below under
"Error estimate."
0.06..................................................
. . .
. . .
. xxxx .
. xo. xx .
. xx . x .
. x . x .
p(rho) . x . oxo .
. x . x .
. x . x .
. x . x .
. x . x .
. x . o .
. xx . xx .
. xxo . oxx .
0.0 xxxxxxxxxx......................xxxxxxxxxxxxxxxxxx
-2 -1 0 1 2 3
normalized rho (0 = mean of solvent region)
-------------------------------------------------------------------------------
Error estimate for map on this cycle
The estimated error in this map is 0.18 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.39 and 0.19 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 0.83, offset is -0.14 and sigma is a random variable with rms value of 0.18
Mean starting figure of merit this cycle
Overall Centric Acentric
0.78 0.57 0.80
Mean normalized structure factor changes this cycle
Centric Acentric
0.33 0.24
New figure of merit () of phasing based on:
(1) experimental phase information, and
(2) likelihood of the resulting map
These are the 2 sources of phase information used in resolve. The phase
information from them should be correlated and the phase information from
the map should increase during maximum- likelihood density modification.
Correlation between experimental and map phase information is measured by
, the mean cosine of the phase difference.
Acentric reflections only:
------ Figure of merit ------ Correlation
DMIN Obs map Fc Total obs-map obs-fc map-fc N
ALL: 0.72 0.35 0.00 0.79 0.50 0.00 0.00 11337
6.0 0.81 0.62 0.00 0.91 0.62 0.00 0.00 431
3.8 0.73 0.66 0.00 0.90 0.51 0.00 0.00 1473
3.0 0.75 0.53 0.00 0.86 0.55 0.00 0.00 1892
2.6 0.76 0.33 0.00 0.83 0.53 0.00 0.00 1931
2.3 0.72 0.22 0.00 0.76 0.49 0.00 0.00 3455
2.1 0.63 0.15 0.00 0.66 0.43 0.00 0.00 2155
Centric reflections only:
------ Figure of merit ------ Correlation
DMIN Obs map Fc Total obs-map obs-fc map-fc N
ALL: 0.54 0.38 0.00 0.71 0.34 0.00 0.00 1105
6.0 0.63 0.52 0.00 0.83 0.41 0.00 0.00 125
3.8 0.58 0.53 0.00 0.80 0.33 0.00 0.00 218
3.0 0.54 0.45 0.00 0.76 0.20 0.00 0.00 194
2.6 0.53 0.35 0.00 0.71 0.39 0.00 0.00 174
2.3 0.51 0.23 0.00 0.62 0.39 0.00 0.00 250
2.1 0.43 0.19 0.00 0.53 0.38 0.00 0.00 144
All reflections:
------ Figure of merit ------ Correlation
DMIN Obs map Fc Total obs-map obs-fc map-fc N
ALL: 0.70 0.35 0.00 0.79 0.49 0.00 0.00 12442
6.0 0.77 0.60 0.00 0.89 0.57 0.00 0.00 556
3.8 0.71 0.65 0.00 0.89 0.49 0.00 0.00 1691
3.0 0.73 0.53 0.00 0.85 0.51 0.00 0.00 2086
2.6 0.74 0.34 0.00 0.82 0.52 0.00 0.00 2105
2.3 0.71 0.22 0.00 0.75 0.48 0.00 0.00 3705
2.1 0.62 0.15 0.00 0.65 0.43 0.00 0.00 2299
Phase change at end of this cycle:
vs resolution for acent, cent, all
DMIN -----acent--------- ---------cent---------------all----------
N N N
0.0 0.83 0.84 11337. 0.77 0.82 1105. 0.82 0.84 12442.
6.0 0.85 0.86 431. 0.70 0.78 125. 0.82 0.84 556.
3.8 0.77 0.78 1473. 0.73 0.77 218. 0.76 0.78 1691.
3.0 0.81 0.83 1892. 0.69 0.75 194. 0.80 0.82 2086.
2.6 0.82 0.83 1931. 0.80 0.85 174. 0.81 0.83 2105.
2.3 0.84 0.87 3455. 0.85 0.91 250. 0.85 0.87 3705.
2.1 0.86 0.89 2155. 0.81 0.87 144. 0.86 0.89 2299.
End of first cycle
____________________________________________________________
Minor cycle 2
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.50 and 0.15 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.09, offset is -0.20 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.79 0.71 0.79
Mean normalized structure factor changes this cycle
Centric Acentric
0.08 0.11
Minor cycle 3
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.53 and 0.13 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.22 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.82 0.78 0.82
Mean normalized structure factor changes this cycle
Centric Acentric
0.03 0.03
Minor cycle 4
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.53 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.22 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.82 0.79 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.01 0.01
Minor cycle 5
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.53 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.17, offset is -0.22 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.82 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.01 0.00
Minor cycle 6
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.53 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.22 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.01 0.00
Minor cycle 7
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.53 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.17, offset is -0.22 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 8
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.53 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.22 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 9
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.53 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.17, offset is -0.22 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 10
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.53 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.22 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Mask cycle 2
New Wang averaging radius = 4.00
fraction protein= 0.4000000
rms of this map is 0.1590082 avg = 0.1050666
Mean +/- SD of density in protein region : 0.00 +/- 0.54
Mean +/- SD of density in solvent region : 0.00 +/- 0.12
fraction protein= 0.4000000
rms of this map is 5.4312378E-02 avg = 4.1890603E-02
Minor cycle 1
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.17, offset is -0.22 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.02 0.01
Minor cycle 2
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.24 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.01 0.00
Minor cycle 3
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.24 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 4
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.24 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 5
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 6
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.24 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 7
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 8
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 9
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 10
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Mask cycle 3
New Wang averaging radius = 4.00
fraction protein= 0.4000000
rms of this map is 0.1592118 avg = 0.1054954
Mean +/- SD of density in protein region : 0.00 +/- 0.54
Mean +/- SD of density in solvent region : 0.00 +/- 0.12
fraction protein= 0.4000000
rms of this map is 5.4026034E-02 avg = 4.1681550E-02
Minor cycle 1
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.01 0.00
Minor cycle 2
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 3
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 4
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 5
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 6
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 7
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 8
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 9
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 10
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Mask cycle 4
New Wang averaging radius = 4.00
fraction protein= 0.4000000
rms of this map is 0.1591863 avg = 0.1055615
Mean +/- SD of density in protein region : 0.00 +/- 0.54
Mean +/- SD of density in solvent region : 0.00 +/- 0.12
fraction protein= 0.4000000
rms of this map is 5.4176159E-02 avg = 4.1793596E-02
Minor cycle 1
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 2
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 3
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 4
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 5
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 6
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 7
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 8
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 9
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 10
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Mask cycle 5
New Wang averaging radius = 4.00
fraction protein= 0.4000000
rms of this map is 0.1591644 avg = 0.1055716
Mean +/- SD of density in protein region : 0.00 +/- 0.54
Mean +/- SD of density in solvent region : 0.00 +/- 0.12
fraction protein= 0.4000000
rms of this map is 5.4171968E-02 avg = 4.1796260E-02
Minor cycle 1
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 2
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 3
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 4
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 5
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 6
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 7
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 8
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 9
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.16, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
Minor cycle 10
____________________________________________________________
Final cycle
Plot of Observed (o) and model (x)
electron density distributions for protein region
where the model distribution is given by,
p_model(beta*(rho+offset)) = p_ideal(rho)
and then convoluted with a gaussian with width of sigma
where sigma, offset and beta are given below under
"Error estimate."
NOTE: the mean for the protein region should be
greater than the solvent region, but the most
probable protein density is less than the mean
of the solvent
0.03..................................................
. . .
. . .
. xxxxx . .
. oxo oooxxo . .
. xo o oxx . .
. x oxo .
p(rho) . x xo .
. oxx .xx .
. x . xxoo .
. x . xxxo .
. ox . xxxxxx .
. xxo . ooxxxxxxxx .
xxoo . oxxxxxxoo.
oo . o xxxo
0.0 o................................................x
-2 -1 0 1 2 3
normalized rho (0 = mean of solvent region)
-------------------------------------------------------------------------------
Plot of Observed (o) and model (x)
electron density distributions for solvent region
where the model distribution is given by,
p_model(beta*(rho+offset)) = p_ideal(rho)
and then convoluted with a gaussian with width of sigma
where sigma, offset and beta are given below under
"Error estimate."
0.10..................................................
. . .
. . .
. ooo .
. .o .
. o. o .
. o xxo .
p(rho) . ox. x .
. x . x .
. x . x .
. xx . xx .
. xo . o x .
. xo . oxx .
. xo . oxx .
. xxxoo . oxxx .
0.0 xxxxxxxxxxxooo.............ooxxxxxxxxxxxxxxxxxxxxx
-2 -1 0 1 2 3
normalized rho (0 = mean of solvent region)
-------------------------------------------------------------------------------
Error estimate for map on this cycle
The estimated error in this map is 0.13 based on an analysis of the electron
density distributions in the protein and solvent regions with rms
values of 0.54 and 0.12 respectively.
The value of the scale factor beta relating idealized density distributions
P_ideal(rho) to observed ones is:
obs_rho = beta * (ideal_rho + offset) + sigma
where beta = 1.15, offset is -0.25 and sigma is a random variable with rms value of 0.13
Mean starting figure of merit this cycle
Overall Centric Acentric
0.83 0.80 0.83
Mean normalized structure factor changes this cycle
Centric Acentric
0.00 0.00
New figure of merit () of phasing based on:
(1) experimental phase information, and
(2) likelihood of the resulting map
These are the 2 sources of phase information used in resolve. The phase
information from them should be correlated and the phase information from
the map should increase during maximum- likelihood density modification.
Correlation between experimental and map phase information is measured by
, the mean cosine of the phase difference.
Acentric reflections only:
------ Figure of merit ------ Correlation
DMIN Obs map Fc Total obs-map obs-fc map-fc N
ALL: 0.72 0.50 0.00 0.83 0.58 0.00 0.00 11337
6.0 0.81 0.77 0.00 0.94 0.70 0.00 0.00 431
3.8 0.73 0.81 0.00 0.94 0.64 0.00 0.00 1473
3.0 0.75 0.72 0.00 0.91 0.63 0.00 0.00 1892
2.6 0.76 0.51 0.00 0.86 0.60 0.00 0.00 1931
2.3 0.72 0.37 0.00 0.79 0.55 0.00 0.00 3455
2.1 0.63 0.25 0.00 0.69 0.47 0.00 0.00 2155
Centric reflections only:
------ Figure of merit ------ Correlation
DMIN Obs map Fc Total obs-map obs-fc map-fc N
ALL: 0.54 0.58 0.00 0.80 0.46 0.00 0.00 1105
6.0 0.63 0.71 0.00 0.92 0.52 0.00 0.00 125
3.8 0.58 0.74 0.00 0.89 0.45 0.00 0.00 218
3.0 0.54 0.69 0.00 0.87 0.43 0.00 0.00 194
2.6 0.53 0.55 0.00 0.79 0.47 0.00 0.00 174
2.3 0.51 0.44 0.00 0.71 0.50 0.00 0.00 250
2.1 0.43 0.36 0.00 0.61 0.39 0.00 0.00 144
All reflections:
------ Figure of merit ------ Correlation
DMIN Obs map Fc Total obs-map obs-fc map-fc N
ALL: 0.70 0.51 0.00 0.83 0.57 0.00 0.00 12442
6.0 0.77 0.76 0.00 0.93 0.66 0.00 0.00 556
3.8 0.71 0.80 0.00 0.93 0.62 0.00 0.00 1691
3.0 0.73 0.71 0.00 0.91 0.61 0.00 0.00 2086
2.6 0.74 0.52 0.00 0.86 0.59 0.00 0.00 2105
2.3 0.71 0.37 0.00 0.79 0.55 0.00 0.00 3705
2.1 0.62 0.26 0.00 0.69 0.47 0.00 0.00 2299
Phase change at end of this cycle:
vs resolution for acent, cent, all
DMIN -----acent--------- ---------cent---------------all----------
N N N
0.0 0.82 0.83 11337. 0.73 0.75 1105. 0.81 0.82 12442.
6.0 0.83 0.84 431. 0.74 0.75 125. 0.81 0.82 556.
3.8 0.77 0.77 1473. 0.67 0.69 218. 0.75 0.76 1691.
3.0 0.80 0.81 1892. 0.67 0.70 194. 0.79 0.80 2086.
2.6 0.81 0.82 1931. 0.77 0.79 174. 0.81 0.82 2105.
2.3 0.83 0.85 3455. 0.79 0.84 250. 0.83 0.85 3705.
2.1 0.84 0.87 2155. 0.75 0.77 144. 0.83 0.86 2299.
All done .. writing out new phases
mtz_write: write out mtz file
Opening mtz file for output:
resolve.mtz
(Q)QOPEN allocated # 1
User: terwill Logical Name: resolve.mtz
Status: UNKNOWN Filename: resolve.mtz
Writing column labels to mtz file
HEADER INFORMATION FOR OUTPUT MTZ FILE ON INDEX 3
* Title:
* Number of Columns = 6
* Number of Reflections = 12441
* Missing value set to NaN in output mtz file
* Column Labels :
H K L FP PHIM FOMM
* Column Types :
H H H F P W
* Cell Dimensions :
113.95 113.95 32.47 90.00 90.00 90.00
* Resolution Range :
0.00262 0.22672 ( 19.542 - 2.100 A )
* There is no sort order recorded in the MTZ header
* Space group = I4 (number 79)
Total of 12441 reflections written to file.