The structure factors that I downloaded from the PDB for my
little MR project contains both reflections behind the beam stop
and reflections of higher resolution than even the original authors
would use. When setting up the MR I entered the more restrictive
resolution limits into the Wizard and Phaser appears to have obeyed.
As near as I can tell from the log files, however, Resolve is
using all the data in the rebuild. I am including a copy of the
log file from the "best" refinement. I would prefer that only
data between 30 and 2.2A were used but it is clear that the
refinement is, at least, monitoring the fit to all the data. I
am presuming that the program is refining against the same data
it is monitoring.
I would like to suggest that either the log file be clearer
about the resolution limits it is actually refining to, or the
plumbing that passes the resolution limits from the AutoMR wizard
to the AutoBuild wizard be checked.
Dale Tronrud
P.S. That's all my problems... For now. The project I'm working
on is cursed and brings out the worst in all the software I have
used.
AutoBuild_run_3_/TEMP0/LIG_EDITED_EDITED_edit_model.pdb
Monomer Library directory:
"/usr/local/phenix-1.3b-rc6/ext_ref_files/mon_lib"
Total number of atoms: 6255
Number of models: 1
Model: 0
Number of conformers: 1
Conformer: " "
Number of atoms: 6255
Number of chains: 4
Number of residues, atoms: 352, 2697
Classifications: {'peptide': 352}
Modifications used: {'COO': 1}
Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
Link IDs: {'PTRANS': 16, 'TRANS': 333, 'PCIS': 2}
Chain breaks: 8
Unresolved non-hydrogen bonds: 41
Unresolved non-hydrogen angles: 50
Unresolved non-hydrogen dihedrals: 32
Unresolved non-hydrogen chiralities: 3
Planarities with less than four sites: {'GLN:plan1': 2, 'GLN:plan2': 2, 'GLN%COO:plan2': 1, 'GLN%COO:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2}
Unresolved non-hydrogen planarities: 26
Number of residues, atoms: 352, 2694
Classifications: {'peptide': 352}
Modifications used: {'COO': 1}
Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10}
Link IDs: {'PTRANS': 17, 'TRANS': 333, 'PCIS': 1}
Chain breaks: 5
Unresolved non-hydrogen bonds: 44
Unresolved non-hydrogen angles: 54
Unresolved non-hydrogen dihedrals: 34
Unresolved non-hydrogen chiralities: 2
Planarities with less than four sites: {'GLN:plan1': 2, 'GLN:plan2': 2, 'GLN%COO:plan2': 1, 'GLN%COO:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2}
Unresolved non-hydrogen planarities: 34
Number of residues, atoms: 7, 432
Unusual residues: {'BCL': 7}
Classifications: {'undetermined': 7}
Link IDs: {None: 6}
Unresolved non-hydrogen bonds: 57
Unresolved non-hydrogen angles: 146
Unresolved non-hydrogen dihedrals: 8
Unresolved non-hydrogen chiralities: 12
Number of residues, atoms: 7, 432
Unusual residues: {'BCL': 7}
Classifications: {'undetermined': 7}
Link IDs: {None: 6}
Unresolved non-hydrogen bonds: 57
Unresolved non-hydrogen angles: 146
Unresolved non-hydrogen dihedrals: 8
Unresolved non-hydrogen chiralities: 12
Time building chain proxies: 8.94, per 1000 atoms: 1.43
================================== X-ray data =================================
F-obs:
AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP
R-free flags:
AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FreeR_flag
Miller array info: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP
Observation type: xray.amplitude
Type of data: double, size=38159
Type of sigmas: double, size=38159
Number of Miller indices: 38159
Anomalous flag: False
Unit cell: (169.1, 169.1, 169.1, 90, 90, 90)
Space group: P 43 3 2 (No. 212)
Systematic absences: 0
Centric reflections: 4505
Resolution range: 75.6238 2.14896
Completeness in resolution range: 0.839637
Completeness with d_max=infinity: 0.8396
Number of F-obs in resolution range: 38159
Number of F-obs <= 0: 0
Refinement resolution range: d_max = 75.6238
d_min = 2.1490
Miller array info: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FreeR_flag
Observation type: None
Type of data: int, size=38159
Type of sigmas: None
Number of Miller indices: 38159
Anomalous flag: False
Unit cell: (169.1, 169.1, 169.1, 90, 90, 90)
Space group: P 43 3 2 (No. 212)
Systematic absences: 0
Centric reflections: 4505
Resolution range: 75.6238 2.14896
Completeness in resolution range: 0.839637
Completeness with d_max=infinity: 0.8396
Test (R-free flags) flag value: 0
Number of work/free reflections by resolution:
work free %free
bin 1: 75.6707 - 4.6295 [4755/4893] 4536 219 4.6%
bin 2: 4.6295 - 3.6746 [4493/4607] 4248 245 5.5%
bin 3: 3.6746 - 3.2101 [4414/4577] 4178 236 5.3%
bin 4: 3.2101 - 2.9166 [4232/4498] 4007 225 5.3%
bin 5: 2.9166 - 2.7075 [4221/4533] 4026 195 4.6%
bin 6: 2.7075 - 2.5479 [4005/4483] 3792 213 5.3%
bin 7: 2.5479 - 2.4203 [3811/4480] 3637 174 4.6%
bin 8: 2.4203 - 2.3149 [3223/4472] 3066 157 4.9%
bin 9: 2.3149 - 2.2258 [2846/4459] 2702 144 5.1%
bin 10: 2.2258 - 2.1490 [2159/4445] 2042 117 5.4%
overall 36234 1925 5.0%
No array of experimental phases found.
========================== Anomalous scatterer groups =========================
All atoms refined with f_prime=0 and f_double_prime=0.
========================== Set up restraints manager ==========================
Number of disulfides: simple=0, symmetry=0
Time building geometry restraints manager: 0.40 seconds
Histogram of bond lengths:
1.12 - 1.26: 957
1.26 - 1.40: 1621
1.40 - 1.55: 3702
1.55 - 1.69: 131
1.69 - 1.83: 23
Bond restraints sorted by residual:
atom i - atom j ideal model delta weight residual
" O1A BCL B 6 " - " CGA BCL B 6 " 1.212 1.117 0.095 2.50e+03 2.25e+01
" O1A BCL D 6 " - " CGA BCL D 6 " 1.212 1.118 0.094 2.50e+03 2.22e+01
" C15 BCL D 6 " - " C16 BCL D 6 " 1.540 1.459 0.081 2.50e+03 1.63e+01
" C15 BCL B 6 " - " C16 BCL B 6 " 1.540 1.460 0.080 2.50e+03 1.60e+01
" N PRO A 188 " - " CD PRO A 188 " 1.473 1.418 0.055 5.10e+03 1.56e+01
... (remaining 6429 not shown)
Histogram of nonbonded interaction distances:
1.49 - 2.17: 9
2.17 - 2.85: 1981
2.85 - 3.53: 8408
3.53 - 4.22: 16251
4.22 - 4.90: 27426
Nonbonded interactions sorted by model distance:
atom i - atom j model vdw sym.op. j
" OG SER A 24 " - " C GLY C 23 " 1.486 3.270
" OG SER A 24 " - " N SER C 24 " 1.747 3.120
" OH TYR A 330 " - " OE1 GLN C 333 " 1.870 3.040 x-1/4,-z-1/4,y+1/4
" C ASN A 121 " - " N LEU A 122 " 1.941 3.350 x+1,y+1,z+1
" OG SER A 24 " - " O GLY C 23 " 1.956 3.040
... (remaining 54070 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 22.73: 1959
22.73 - 45.46: 198
45.46 - 68.20: 68
68.20 - 90.93: 27
90.93 - 113.66: 1
Dihedral angle restraints sorted by residual:
" CA ALA C 327 "
" C ALA C 327 "
" N PRO C 328 "
" CA PRO C 328 "
ideal model delta periodicty weight residual
180.00 -66.34 -113.66 1 4.00e-02 5.17e+02
" C2B BCL D 7 "
" C3B BCL D 7 "
" CAB BCL D 7 "
" OBB BCL D 7 "
ideal model delta periodicty weight residual
0.00 147.16 32.84 2 4.00e-02 4.31e+01
" C2B BCL B 7 "
" C3B BCL B 7 "
" CAB BCL B 7 "
" OBB BCL B 7 "
ideal model delta periodicty weight residual
0.00 147.20 32.80 2 4.00e-02 4.30e+01
... (remaining 2250 not shown)
==================== Fixing bad ADP in input model (if any) ===================
============================== Scattering factors =============================
----------X-ray scattering dictionary----------
Number of scattering types: 4
Type Number sf(0) Gaussians
S 14 15.96 2
O 1076 7.97 2
N 1007 6.97 2
C 4158 5.97 2
sf(0) = scattering factor at diffraction angle 0.
====================== Modifying start model if requested =====================
atom_attributes_list is modified in-place to define missing element types when possible.
==================== Fixing bad ADP in input model (if any) ===================
================== Extract refinement strategy and selections =================
individual_sites = True
rigid_body = False
individual_adp = True
group_adp = False
tls = False
individual_occupancies = False
group_occupancies = False
group_anomalous = False
size = 6255
n_use = 6255
n_use_u_iso = 6255
n_use_u_aniso = 0
n_grad_site = 0
n_grad_u_iso = 0
n_grad_u_aniso = 0
n_grad_occupancy = 0
n_grad_fp = 0
n_grad_fdp = 0
n_anisotropic_flag = 0
total number of scatterers = 6255
==================== Process input NCS or/and find new NCS ====================
NCS groups found in parameter file: 0
Automatic NCS search:
Chains in this PDB file: ['A', 'C']
GROUPS BASED ON QUICK COMPARISON: []
Looking for invariant domains for ...: ['A', 'C'] [[[9, 366]], [[9, 366]]]
Updated/new NCS groups:
refinement.ncs.restraint_group {
reference = chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )
selection = chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )
}
----------Building NCS restraints----------
NCS restraint group 1:
NCS operator 1:
Reference selection: "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
Other selection: "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
Number of atom pairs: 2603
Rotation={{-0.999509, -0.0190423, 0.0248896},
{0.0243783, 0.0266261, 0.999348},
{-0.0196926, 0.999464, -0.0261488}}
Translation={{38.5072}, {-44.0643}, {42.3394}}
Histogram of differences:
0.001760 - 0.701888: 2552
0.701888 - 1.402017: 14
1.402017 - 2.102145: 22
2.102145 - 2.802274: 6
2.802274 - 3.502402: 4
3.502402 - 4.202531: 5
RMS difference with respect to the reference: 0.312576
=================== Write initial parameters into .eff file ===================
============================ Non-default parameters ===========================
A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.
#phil __ON__
refinement {
input {
pdb {
file_name = "/usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/LIG_EDITED_EDITED_edit_model.pdb"
}
xray_data {
file_name = "AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz"
labels = "FP,SIGFP"
high_resolution = 2.2
r_free_flags {
file_name = "AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz"
label = "FreeR_flag"
test_flag_value = 0
}
}
monomers {
file_name = "/usr/users/dale/geometry/chromophores/bcl_tnt.cif"
}
}
output {
prefix = "AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3"
serial = 1
write_eff_file = False
write_geo_file = False
write_def_file = False
export_final_f_model = *mtz cns
write_maps = False
}
main {
ordered_solvent = True
ncs = True
use_experimental_phases = False
random_seed = 516344
}
ncs {
special_position_warnings_only = True
restraint_group {
reference = "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
selection = "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
}
}
ordered_solvent {
low_resolution = 3
}
mask {
ignore_zero_occupancy_atoms = False
}
}
#phil __OFF__
============================= ml refinement start =============================
----------structure factors based statistics (before refinement)----------
----------X-ray data----------
|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
| |
| r_work= 0.3243 r_free= 0.3131 ksol= 0.00 Bsol= 0.00 scale= 1.698 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 |
| |
| maximum likelihood estimate for coordinate error: 0.40 A |
| x-ray target function (ml) for work reflections: 7.754289 |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
| Bin Resolution Compl. No. Refl. R-factors Targets |
|number range work test work test work test|
| 1: 75.6707 - 5.1788 0.97 3272 159 0.4168 0.3905 8.6988 8.5536|
| 2: 5.1788 - 4.1106 0.98 3112 155 0.2200 0.2341 8.4215 8.4968|
| 3: 4.1106 - 3.5910 0.97 3000 188 0.2279 0.2321 8.1284 8.1202|
| 4: 3.5910 - 3.2627 0.97 2977 168 0.2388 0.2465 7.9459 8.0053|
| 5: 3.2627 - 3.0288 0.95 2930 152 0.2747 0.2878 7.8061 7.8021|
| 6: 3.0288 - 2.8502 0.93 2844 159 0.2741 0.2804 7.6418 7.6974|
| 7: 2.8502 - 2.7075 0.93 2860 139 0.2757 0.3123 7.5349 7.6274|
| 8: 2.7075 - 2.5896 0.89 2705 156 0.2878 0.3340 7.453 7.4977|
| 9: 2.5896 - 2.4899 0.89 2715 135 0.2982 0.3356 7.3586 7.5621|
| 10: 2.4899 - 2.4040 0.81 2488 115 0.3089 0.3543 7.3181 7.3706|
| 11: 2.4040 - 2.3288 0.72 2176 109 0.3142 0.3613 7.3041 7.3373|
| 12: 2.3288 - 2.2623 0.67 2018 110 0.3096 0.3293 7.3086 7.3357|
| 13: 2.2623 - 2.2027 0.58 1742 104 0.3370 0.3823 7.3303 7.508|
| 14: 2.2027 - 2.1490 0.46 1395 76 0.3749 0.3710 7.4161 7.4587|
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
| |
| Bin Resolution No. Refl. FOM Phase Scale Alpha Beta |
| # range work test error factor |
| 1: 75.6707 - 5.1788 3272 159 0.64 39.15 1.16 1.12 4689001.73|
| 2: 5.1788 - 4.1106 3112 155 0.79 26.44 2.03 1.66 3059064.97|
| 3: 4.1106 - 3.5910 3000 188 0.82 24.63 2.13 1.94 1936112.07|
| 4: 3.5910 - 3.2627 2977 168 0.81 25.88 2.18 2.02 1377840.11|
| 5: 3.2627 - 3.0288 2930 152 0.78 28.52 2.16 2.01 1065329.57|
| 6: 3.0288 - 2.8502 2844 159 0.76 30.45 2.06 1.97 856549.95|
| 7: 2.8502 - 2.7075 2860 139 0.77 30.05 2.04 1.88 690049.30|
| 8: 2.7075 - 2.5896 2705 156 0.75 31.56 1.99 1.78 594991.98|
| 9: 2.5896 - 2.4899 2715 135 0.72 34.01 1.90 1.74 528160.82|
| 10: 2.4899 - 2.4040 2488 115 0.71 35.26 1.94 1.68 488836.19|
| 11: 2.4040 - 2.3288 2176 109 0.72 34.25 1.95 1.68 443633.67|
| 12: 2.3288 - 2.2623 2018 110 0.73 33.21 1.92 1.64 434086.87|
| 13: 2.2623 - 2.2027 1742 104 0.67 39.14 2.01 1.62 524747.84|
| 14: 2.2027 - 2.1490 1395 76 0.56 47.31 2.05 1.54 720558.54|
|alpha: min = 1.12 max = 2.02 mean = 1.74|
|beta: min = 434086.87 max = 4689001.73 mean = 1388851.17|
|figures of merit: min = 0.00 max = 1.00 mean = 0.74|
|phase err.(work): min = 0.00 max = 89.94 mean = 31.97|
|phase err.(test): min = 0.00 max = 89.63 mean = 32.13|
|-----------------------------------------------------------------------------|
============================== Outliers rejection =============================
basic_wilson_outliers = 0
extreme_wilson_outliers = 2
beamstop_shadow_outliers = 6
total = 8
====================== Target weights (before refinement) =====================
|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc |
| wxc = 12.037420 wxc_scale = 0.500 wc = 1.000 |
| angle between x-ray and geometry gradient vectors: 96.336 (deg) |
| |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu |
| wxc = 0.231372 wxc_scale = 1.000 wc = 1.000 |
| angle between Xray and ADP gradient vectors: 93.656 (deg) |
|-----------------------------------------------------------------------------|
----------Initial model statistics (before refinement)----------
|-Geometry statistics: start--------------------------------------------------|
| Histogram of deviations from ideal values for |
| Bonds | Angles | Nonbonded contacts |
| 0.000 - 0.009: 4797 | 0.000 - 2.504: 7924 | 1.486 - 1.828: 2 |
| 0.009 - 0.019: 1097 | 2.504 - 5.009: 655 | 1.828 - 2.169: 7 |
| 0.019 - 0.028: 284 | 5.009 - 7.513: 145 | 2.169 - 2.511: 30 |
| 0.028 - 0.038: 144 | 7.513 - 10.018: 40 | 2.511 - 2.852: 1951 |
| 0.038 - 0.047: 61 | 10.018 - 12.522: 8 | 2.852 - 3.193: 3550 |
| 0.047 - 0.057: 31 | 12.522 - 15.026: 4 | 3.193 - 3.535: 4858 |
| 0.057 - 0.066: 13 | 15.026 - 17.531: 2 | 3.535 - 3.876: 8239 |
| 0.066 - 0.076: 3 | 17.531 - 20.035: 0 | 3.876 - 4.217: 8012 |
| 0.076 - 0.085: 2 | 20.035 - 22.539: 0 | 4.217 - 4.559: 11917 |
| 0.085 - 0.095: 2 | 22.539 - 25.044: 1 | 4.559 - 4.900: 15509 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
| Type | Count | Deviation from ideal | Targets | Target (sum) |
| | | rmsd max min | | |
| bond | 6434 | 0.012 0.095 0.000 | 0.323 | |
| angle | 8779 | 1.693 25.044 0.000 | 0.420 | |
| chirality | 905 | 0.089 0.406 0.000 | 0.199 | 0.156 |
| planarity | 977 | 0.007 0.154 0.000 | 0.242 | |
| dihedral | 2253 | 17.723 113.659 0.001 | 1.614 | |
| nonbonded | 6434 | 4.142 4.900 1.486 | 0.255 | |
|-----------------------------------------------------------------------------|
|-ADP statistics (Wilson B = 25.121)------------------------------------------|
| Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max |
| type |iso aniso | min max mean | min max mean |
| - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - |
| all : 6255 0 7.67 118.66 27.52 None None None |
| all(noH): 6255 0 7.67 118.66 27.52 None None None |
| Sol. : 0 0 None None None None None None |
| Mac. : 6255 0 7.67 118.66 27.52 None None None |
| Hyd. : 0 0 None None None None None None |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Distribution of isotropic (or equivalent) ADP for non-H atoms: |
| Bin# value range #atoms | Bin# value range #atoms |
| 0: 7.670 - 18.769: 1649 | 5: 63.165 - 74.264: 119 |
| 1: 18.769 - 29.868: 2973 | 6: 74.264 - 85.363: 80 |
| 2: 29.868 - 40.967: 840 | 7: 85.363 - 96.462: 50 |
| 3: 40.967 - 52.066: 296 | 8: 96.462 - 107.561: 28 |
| 4: 52.066 - 63.165: 198 | 9: 107.561 - 118.660: 22 |
| =>continue=> |
|-----------------------------------------------------------------------------|
|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1 = 0 |
|-----------------------------------------------------------------------------|
*********************** REFINEMENT MACRO_CYCLE 1 OF 3 *************************
|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
| |
| r_work= 0.3243 r_free= 0.3131 ksol= 0.00 Bsol= 0.00 scale= 1.698 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 |
| |
| maximum likelihood estimate for coordinate error: 0.40 A |
| x-ray target function (ml) for work reflections: 7.754289 |
|-----------------------------------------------------------------------------|
====================== bulk solvent modeling and scaling ======================
|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
| |
| r_work= 0.2582 r_free= 0.2742 ksol= 0.35 Bsol= 50.00 scale= 2.164 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,2.32,2.32,0.00,0.00,-0.00); trace/3= 2.32 |
| |
| maximum likelihood estimate for coordinate error: 0.39 A |
| x-ray target function (ml) for work reflections: 7.690252 |
|-----------------------------------------------------------------------------|
========================== Target weights: x-ray data =========================
|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc |
| wxc = 10.750300 wxc_scale = 0.500 wc = 1.000 |
| angle between x-ray and geometry gradient vectors: 96.207 (deg) |
| |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu |
| wxc = 0.205411 wxc_scale = 1.000 wc = 1.000 |
| angle between Xray and ADP gradient vectors: 94.015 (deg) |
|-----------------------------------------------------------------------------|
================================ xyz refinement ===============================
|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2582 final r-factor (work) = 0.2348 |
| start r-factor (free) = 0.2742 final r-factor (free) = 0.2713 |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem |
| 42.5209 = 10.75 * 0.50 * 7.7632 + 1.00 * 0.7926 |
| |
| T_final = wxc * wxc_scale * Exray + wc * Echem |
| 41.1803 = 10.75 * 0.50 * 7.6326 + 1.00 * 0.1541 |
|-----------------------------------------------------------------------------|
| number of iterations = 25 | number of function evaluations = 26 |
|-----------------------------------------------------------------------------|
================================ ADP refinement ===============================
----------Individual ADP refinement----------
|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2348 final r-factor (work) = 0.2216 |
| start r-factor (free) = 0.2713 final r-factor (free) = 0.2676 |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp |
| 1.5745 = 0.21 * 1.00 * 7.6326 + 1.00 * 0.0067 |
| |
| T_final = wxu * wxu_scale * Exray + wu * Eadp |
| 1.5631 = 0.21 * 1.00 * 7.5874 + 1.00 * 0.0045 |
|-----------------------------------------------------------------------------|
| number of iterations = 23 | number of function evaluations = 24 |
|-----------------------------------------------------------------------------|
|-ADP statistics (Wilson B = 25.121)------------------------------------------|
| Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max |
| type |iso aniso | min max mean | min max mean |
| - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - |
| all : 6255 0 0.00 117.10 26.33 None None None |
| all(noH): 6255 0 0.00 117.10 26.33 None None None |
| Sol. : 0 0 None None None None None None |
| Mac. : 6255 0 0.00 117.10 26.33 None None None |
| Hyd. : 0 0 None None None None None None |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Distribution of isotropic (or equivalent) ADP for non-H atoms: |
| Bin# value range #atoms | Bin# value range #atoms |
| 0: 0.000 - 11.710: 203 | 5: 58.550 - 70.260: 136 |
| 1: 11.710 - 23.420: 3284 | 6: 70.260 - 81.969: 72 |
| 2: 23.420 - 35.130: 1811 | 7: 81.969 - 93.679: 42 |
| 3: 35.130 - 46.840: 395 | 8: 93.679 - 105.389: 25 |
| 4: 46.840 - 58.550: 266 | 9: 105.389 - 117.099: 21 |
| =>continue=> |
|-----------------------------------------------------------------------------|
*********************** REFINEMENT MACRO_CYCLE 2 OF 3 *************************
|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
| |
| r_work= 0.2216 r_free= 0.2676 ksol= 0.35 Bsol= 50.00 scale= 2.155 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,2.32,2.32,0.00,0.00,-0.00); trace/3= 2.32 |
| |
| maximum likelihood estimate for coordinate error: 0.37 A |
| x-ray target function (ml) for work reflections: 7.578854 |
|-----------------------------------------------------------------------------|
================== ordered solvent: location/analysis/update ==================
Start model:
number = 0
b_iso_min = None (limit = 1.00)
b_iso_max = None (limit = 50.00)
b_iso_mean = None
occupancy_min = None (limit = 0.10)
occupancy_max = None (limit = 1.20)
dist_sol_mol_min = None (limit = 1.80)
dist_sol_mol_max = None (limit = 6.00)
Peak search:
maximum allowed number of peaks: 6250
number of peaks from mFobs-DFmodel map: 449
number of peaks from 2mFobs-DFmodel map: 2500
number of peaks after clustering: 392
Filter by distance & map next to the model:
mapped sites are within: 0.520 - 5.987
number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 291 from: 392
mapped sites are within: 1.816 - 5.987
Peak filtering (peak - peak close contact elimination):
peaks rejected: 0
total number of peaks selected: 291
Final model:
number = 291
b_iso_min = 26.33 (limit = 1.00)
b_iso_max = 26.33 (limit = 50.00)
b_iso_mean = 26.33
occupancy_min = 1.00 (limit = 0.10)
occupancy_max = 1.00 (limit = 1.20)
dist_sol_mol_min = 1.82 (limit = 1.80)
dist_sol_mol_max = 5.99 (limit = 6.00)
====================== bulk solvent modeling and scaling ======================
|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
| |
| r_work= 0.2037 r_free= 0.2379 ksol= 0.34 Bsol= 50.00 scale= 2.123 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.43,2.43,0.00,0.00,-0.00); trace/3= 2.43 |
| |
| maximum likelihood estimate for coordinate error: 0.32 A |
| x-ray target function (ml) for work reflections: 7.486761 |
|-----------------------------------------------------------------------------|
========================== Target weights: x-ray data =========================
|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc |
| wxc = 6.888030 wxc_scale = 0.500 wc = 1.000 |
| angle between x-ray and geometry gradient vectors: 121.803 (deg) |
| |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu |
| wxc = 0.171233 wxc_scale = 1.000 wc = 1.000 |
| angle between Xray and ADP gradient vectors: 117.753 (deg) |
|-----------------------------------------------------------------------------|
================================ xyz refinement ===============================
|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2037 final r-factor (work) = 0.1944 |
| start r-factor (free) = 0.2379 final r-factor (free) = 0.2423 |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem |
| 26.1593 = 6.89 * 0.50 * 7.5465 + 1.00 * 0.1690 |
| |
| T_final = wxc * wxc_scale * Exray + wc * Echem |
| 25.8504 = 6.89 * 0.50 * 7.4673 + 1.00 * 0.1330 |
|-----------------------------------------------------------------------------|
| number of iterations = 25 | number of function evaluations = 27 |
|-----------------------------------------------------------------------------|
================================ ADP refinement ===============================
----------Individual ADP refinement----------
|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1944 final r-factor (work) = 0.1882 |
| start r-factor (free) = 0.2423 final r-factor (free) = 0.2396 |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp |
| 1.2834 = 0.17 * 1.00 * 7.4673 + 1.00 * 0.0047 |
| |
| T_final = wxu * wxu_scale * Exray + wu * Eadp |
| 1.2813 = 0.17 * 1.00 * 7.4563 + 1.00 * 0.0045 |
|-----------------------------------------------------------------------------|
| number of iterations = 18 | number of function evaluations = 19 |
|-----------------------------------------------------------------------------|
|-ADP statistics (Wilson B = 25.121)------------------------------------------|
| Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max |
| type |iso aniso | min max mean | min max mean |
| - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - |
| all : 6546 0 2.33 119.19 25.98 None None None |
| all(noH): 6546 0 2.33 119.19 25.98 None None None |
| Sol. : 291 0 3.23 59.44 29.93 None None None |
| Mac. : 6255 0 2.33 119.19 25.79 None None None |
| Hyd. : 0 0 None None None None None None |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Distribution of isotropic (or equivalent) ADP for non-H atoms: |
| Bin# value range #atoms | Bin# value range #atoms |
| 0: 2.330 - 14.016: 627 | 5: 60.762 - 72.449: 124 |
| 1: 14.016 - 25.703: 3737 | 6: 72.449 - 84.135: 75 |
| 2: 25.703 - 37.389: 1297 | 7: 84.135 - 95.822: 35 |
| 3: 37.389 - 49.076: 396 | 8: 95.822 - 107.508: 18 |
| 4: 49.076 - 60.762: 219 | 9: 107.508 - 119.195: 18 |
| =>continue=> |
|-----------------------------------------------------------------------------|
*********************** REFINEMENT MACRO_CYCLE 3 OF 3 *************************
|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
| |
| r_work= 0.1882 r_free= 0.2396 ksol= 0.34 Bsol= 50.00 scale= 2.114 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.43,2.43,0.00,0.00,-0.00); trace/3= 2.43 |
| |
| maximum likelihood estimate for coordinate error: 0.33 A |
| x-ray target function (ml) for work reflections: 7.449879 |
|-----------------------------------------------------------------------------|
================== ordered solvent: location/analysis/update ==================
Start model:
number = 291
b_iso_min = 3.23 (limit = 1.00)
b_iso_max = 59.44 (limit = 50.00)
b_iso_mean = 29.93
occupancy_min = 1.00 (limit = 0.10)
occupancy_max = 1.00 (limit = 1.20)
dist_sol_mol_min = 2.06 (limit = 1.80)
dist_sol_mol_max = 5.96 (limit = 6.00)
Peak search:
maximum allowed number of peaks: 6250
number of peaks from mFobs-DFmodel map: 420
number of peaks from 2mFobs-DFmodel map: 2405
number of peaks after clustering: 300
Filter by distance & map next to the model:
mapped sites are within: 0.214 - 5.940
number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 118 from: 300
mapped sites are within: 1.802 - 5.940
Peak filtering (peak - peak close contact elimination):
peaks rejected: 0
total number of peaks selected: 118
Final model:
number = 398
b_iso_min = 3.23 (limit = 1.00)
b_iso_max = 49.81 (limit = 50.00)
b_iso_mean = 28.22
occupancy_min = 1.00 (limit = 0.10)
occupancy_max = 1.00 (limit = 1.20)
dist_sol_mol_min = 1.80 (limit = 1.80)
dist_sol_mol_max = 5.96 (limit = 6.00)
====================== bulk solvent modeling and scaling ======================
|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
| |
| r_work= 0.1875 r_free= 0.2312 ksol= 0.33 Bsol= 50.00 scale= 2.126 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,3.18,3.18,0.00,0.00,-0.00); trace/3= 3.18 |
| |
| maximum likelihood estimate for coordinate error: 0.31 A |
| x-ray target function (ml) for work reflections: 7.433926 |
|-----------------------------------------------------------------------------|
========================== Target weights: x-ray data =========================
|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc |
| wxc = 4.792070 wxc_scale = 0.500 wc = 1.000 |
| angle between x-ray and geometry gradient vectors: 137.678 (deg) |
| |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu |
| wxc = 0.173077 wxc_scale = 1.000 wc = 1.000 |
| angle between Xray and ADP gradient vectors: 129.742 (deg) |
|-----------------------------------------------------------------------------|
================================ xyz refinement ===============================
|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1875 final r-factor (work) = 0.1857 |
| start r-factor (free) = 0.2312 final r-factor (free) = 0.2341 |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem |
| 18.0062 = 4.79 * 0.50 * 7.4550 + 1.00 * 0.1437 |
| |
| T_final = wxc * wxc_scale * Exray + wc * Echem |
| 17.9146 = 4.79 * 0.50 * 7.4304 + 1.00 * 0.1110 |
|-----------------------------------------------------------------------------|
| number of iterations = 25 | number of function evaluations = 27 |
|-----------------------------------------------------------------------------|
================================ ADP refinement ===============================
----------Individual ADP refinement----------
|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1857 final r-factor (work) = 0.1818 |
| start r-factor (free) = 0.2341 final r-factor (free) = 0.2331 |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp |
| 1.2906 = 0.17 * 1.00 * 7.4304 + 1.00 * 0.0046 |
| |
| T_final = wxu * wxu_scale * Exray + wu * Eadp |
| 1.2897 = 0.17 * 1.00 * 7.4228 + 1.00 * 0.0050 |
|-----------------------------------------------------------------------------|
| number of iterations = 9 | number of function evaluations = 9 |
|-----------------------------------------------------------------------------|
|-ADP statistics (Wilson B = 25.121)------------------------------------------|
| Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max |
| type |iso aniso | min max mean | min max mean |
| - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - |
| all : 6653 0 0.00 118.91 25.71 None None None |
| all(noH): 6653 0 0.00 118.91 25.71 None None None |
| Sol. : 398 0 0.00 55.54 31.76 None None None |
| Mac. : 6255 0 2.01 118.91 25.32 None None None |
| Hyd. : 0 0 None None None None None None |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Distribution of isotropic (or equivalent) ADP for non-H atoms: |
| Bin# value range #atoms | Bin# value range #atoms |
| 0: 0.000 - 11.891: 364 | 5: 59.455 - 71.345: 131 |
| 1: 11.891 - 23.782: 3643 | 6: 71.345 - 83.236: 75 |
| 2: 23.782 - 35.673: 1625 | 7: 83.236 - 95.127: 43 |
| 3: 35.673 - 47.564: 492 | 8: 95.127 - 107.018: 20 |
| 4: 47.564 - 59.455: 243 | 9: 107.018 - 118.909: 17 |
| =>continue=> |
|-----------------------------------------------------------------------------|
======================= ordered solvent: final clean up =======================
Start model:
number = 398
b_iso_min = 0.00 (limit = 1.00)
b_iso_max = 55.54 (limit = 50.00)
b_iso_mean = 31.76
occupancy_min = 1.00 (limit = 0.10)
occupancy_max = 1.00 (limit = 1.20)
dist_sol_mol_min = 2.05 (limit = 1.80)
dist_sol_mol_max = 5.96 (limit = 6.00)
Final model:
number = 388
b_iso_min = 3.51 (limit = 1.00)
b_iso_max = 49.97 (limit = 50.00)
b_iso_mean = 31.36
occupancy_min = 1.00 (limit = 0.10)
occupancy_max = 1.00 (limit = 1.20)
dist_sol_mol_min = 2.05 (limit = 1.80)
dist_sol_mol_max = 5.96 (limit = 6.00)
----------X-ray data----------
|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
| |
| r_work= 0.1831 r_free= 0.2329 ksol= 0.33 Bsol= 50.00 scale= 2.114 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,3.18,3.18,0.00,0.00,-0.00); trace/3= 3.18 |
| |
| maximum likelihood estimate for coordinate error: 0.32 A |
| x-ray target function (ml) for work reflections: 7.422958 |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
| Bin Resolution Compl. No. Refl. R-factors Targets |
|number range work test work test work test|
| 1: 75.6707 - 5.1788 0.97 3272 159 0.2130 0.2552 8.1276 8.228|
| 2: 5.1788 - 4.1106 0.98 3112 155 0.1356 0.1644 7.8761 8.0672|
| 3: 4.1106 - 3.5910 0.97 3000 188 0.1468 0.1750 7.7387 7.8215|
| 4: 3.5910 - 3.2627 0.97 2977 168 0.1558 0.1979 7.5865 7.8088|
| 5: 3.2627 - 3.0288 0.95 2930 152 0.1709 0.2266 7.4557 7.5858|
| 6: 3.0288 - 2.8502 0.93 2844 159 0.1755 0.2362 7.2991 7.4461|
| 7: 2.8502 - 2.7075 0.93 2860 139 0.1762 0.2620 7.2285 7.4876|
| 8: 2.7075 - 2.5896 0.89 2705 156 0.1910 0.2717 7.1596 7.3038|
| 9: 2.5896 - 2.4899 0.89 2715 135 0.2060 0.2556 7.0999 7.3902|
| 10: 2.4899 - 2.4040 0.81 2488 115 0.2115 0.3023 7.0774 7.2784|
| 11: 2.4040 - 2.3288 0.72 2176 109 0.2299 0.3153 7.0902 7.1912|
| 12: 2.3288 - 2.2623 0.67 2018 110 0.2312 0.2806 7.1132 7.2823|
| 13: 2.2623 - 2.2027 0.58 1742 104 0.2705 0.3734 7.181 7.532|
| 14: 2.2027 - 2.1490 0.46 1395 76 0.3164 0.3752 7.339 7.432|
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
| |
| Bin Resolution No. Refl. FOM Phase Scale Alpha Beta |
| # range work test error factor |
| 1: 75.6707 - 5.1788 3272 159 0.84 21.52 2.03 1.91 1706271.76|
| 2: 5.1788 - 4.1106 3112 155 0.92 13.72 2.19 2.12 1119490.86|
| 3: 4.1106 - 3.5910 3000 188 0.90 16.33 2.16 2.10 948218.23|
| 4: 3.5910 - 3.2627 2977 168 0.88 18.25 2.15 2.06 723060.91|
| 5: 3.2627 - 3.0288 2930 152 0.86 20.64 2.12 2.04 602696.08|
| 6: 3.0288 - 2.8502 2844 159 0.85 21.95 2.09 2.03 469088.14|
| 7: 2.8502 - 2.7075 2860 139 0.84 22.75 2.07 2.01 423879.11|
| 8: 2.7075 - 2.5896 2705 156 0.83 23.91 2.02 1.89 364459.47|
| 9: 2.5896 - 2.4899 2715 135 0.80 26.95 1.96 1.80 333699.76|
| 10: 2.4899 - 2.4040 2488 115 0.80 26.92 1.99 1.83 318772.98|
| 11: 2.4040 - 2.3288 2176 109 0.80 27.04 2.01 1.79 305463.63|
| 12: 2.3288 - 2.2623 2018 110 0.81 26.41 2.04 1.78 298736.36|
| 13: 2.2623 - 2.2027 1742 104 0.76 30.75 2.14 1.86 366985.74|
| 14: 2.2027 - 2.1490 1395 76 0.63 41.90 2.25 1.80 624233.56|
|alpha: min = 1.78 max = 2.12 mean = 1.95|
|beta: min = 298736.36 max = 1706271.76 mean = 657914.19|
|figures of merit: min = 0.00 max = 1.00 mean = 0.84|
|phase err.(work): min = 0.00 max = 90.00 mean = 23.00|
|phase err.(test): min = 0.00 max = 89.39 mean = 23.30|
|-----------------------------------------------------------------------------|
====================== bulk solvent modeling and scaling ======================
|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
| |
| r_work= 0.1826 r_free= 0.2324 ksol= 0.34 Bsol= 65.65 scale= 2.111 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,-0.00); trace/3= 0.00 |
| |
| maximum likelihood estimate for coordinate error: 0.32 A |
| x-ray target function (ml) for work reflections: 7.421608 |
|-----------------------------------------------------------------------------|
----------X-ray data----------
|--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------|
| |
| r_work= 0.1826 r_free= 0.2324 ksol= 0.34 Bsol= 65.65 scale= 2.111 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,-0.00); trace/3= 0.00 |
| |
| maximum likelihood estimate for coordinate error: 0.32 A |
| x-ray target function (ml) for work reflections: 7.421608 |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
| Bin Resolution Compl. No. Refl. R-factors Targets |
|number range work test work test work test|
| 1: 75.6707 - 5.1788 0.97 3272 159 0.2125 0.2562 8.1276 8.23|
| 2: 5.1788 - 4.1106 0.98 3112 155 0.1356 0.1646 7.8765 8.0679|
| 3: 4.1106 - 3.5910 0.97 3000 188 0.1471 0.1753 7.7395 7.8223|
| 4: 3.5910 - 3.2627 0.97 2977 168 0.1557 0.1975 7.5862 7.8097|
| 5: 3.2627 - 3.0288 0.95 2930 152 0.1700 0.2270 7.4544 7.5859|
| 6: 3.0288 - 2.8502 0.93 2844 159 0.1744 0.2359 7.2964 7.4451|
| 7: 2.8502 - 2.7075 0.93 2860 139 0.1754 0.2619 7.227 7.4839|
| 8: 2.7075 - 2.5896 0.89 2705 156 0.1902 0.2712 7.1561 7.3014|
| 9: 2.5896 - 2.4899 0.89 2715 135 0.2054 0.2548 7.0962 7.3838|
| 10: 2.4899 - 2.4040 0.81 2488 115 0.2109 0.3026 7.0744 7.2786|
| 11: 2.4040 - 2.3288 0.72 2176 109 0.2295 0.3132 7.088 7.1878|
| 12: 2.3288 - 2.2623 0.67 2018 110 0.2309 0.2813 7.112 7.2824|
| 13: 2.2623 - 2.2027 0.58 1742 104 0.2704 0.3724 7.1801 7.5313|
| 14: 2.2027 - 2.1490 0.46 1395 76 0.3163 0.3749 7.3386 7.432|
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
| |
| Bin Resolution No. Refl. FOM Phase Scale Alpha Beta |
| # range work test error factor |
| 1: 75.6707 - 5.1788 3272 159 0.83 21.68 2.02 1.90 1729678.56|
| 2: 5.1788 - 4.1106 3112 155 0.92 13.76 2.19 2.11 1122862.76|
| 3: 4.1106 - 3.5910 3000 188 0.90 16.38 2.16 2.10 950321.91|
| 4: 3.5910 - 3.2627 2977 168 0.88 18.29 2.16 2.07 725331.21|
| 5: 3.2627 - 3.0288 2930 152 0.86 20.71 2.13 2.04 606450.12|
| 6: 3.0288 - 2.8502 2844 159 0.85 22.01 2.10 2.04 469766.50|
| 7: 2.8502 - 2.7075 2860 139 0.84 22.78 2.08 2.02 424394.38|
| 8: 2.7075 - 2.5896 2705 156 0.83 23.83 2.03 1.89 361907.39|
| 9: 2.5896 - 2.4899 2715 135 0.80 26.81 1.97 1.81 330530.78|
| 10: 2.4899 - 2.4040 2488 115 0.80 26.80 1.99 1.84 316100.00|
| 11: 2.4040 - 2.3288 2176 109 0.80 26.93 2.01 1.80 303267.90|
| 12: 2.3288 - 2.2623 2018 110 0.81 26.36 2.05 1.79 297871.94|
| 13: 2.2623 - 2.2027 1742 104 0.76 30.68 2.15 1.87 365788.30|
| 14: 2.2027 - 2.1490 1395 76 0.63 41.83 2.25 1.81 622797.66|
|alpha: min = 1.79 max = 2.11 mean = 1.95|
|beta: min = 297871.94 max = 1729678.56 mean = 660171.29|
|figures of merit: min = 0.00 max = 1.00 mean = 0.84|
|phase err.(work): min = 0.00 max = 89.91 mean = 23.00|
|phase err.(test): min = 0.00 max = 89.92 mean = 23.31|
|-----------------------------------------------------------------------------|
|-ADP statistics (Wilson B = 25.121)------------------------------------------|
| Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max |
| type |iso aniso | min max mean | min max mean |
| - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - |
| all : 6643 0 5.23 122.12 28.89 None None None |
| all(noH): 6643 0 5.23 122.12 28.89 None None None |
| Sol. : 388 0 6.73 53.19 34.57 None None None |
| Mac. : 6255 0 5.23 122.12 28.54 None None None |
| Hyd. : 0 0 None None None None None None |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Distribution of isotropic (or equivalent) ADP for non-H atoms: |
| Bin# value range #atoms | Bin# value range #atoms |
| 0: 5.229 - 16.918: 693 | 5: 63.676 - 75.366: 120 |
| 1: 16.918 - 28.608: 3694 | 6: 75.366 - 87.055: 73 |
| 2: 28.608 - 40.297: 1313 | 7: 87.055 - 98.744: 43 |
| 3: 40.297 - 51.987: 450 | 8: 98.744 - 110.434: 19 |
| 4: 51.987 - 63.676: 221 | 9: 110.434 - 122.123: 17 |
| =>continue=> |
|-----------------------------------------------------------------------------|
================= overall refinement statistics: step by step =================
****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle
0 : statistics at the very beginning when nothing is done yet
1_bss: bulk solvent correction and/or (anisotropic) scaling
1_xyz: refinement of coordinates
1_adp: refinement of ADPs (Atomic Displacement Parameters)
1_wat: ordered solvent update (add / remove)
------------------------------------------------------------------------
R-factors, x-ray target values and norm of gradient of x-ray target
stage r-work r-free xray_target_w xray_target_t
0 : 0.3243 0.3131 7.754289e+00 7.797944e+00
1_bss: 0.2582 0.2742 7.690252e+00 7.754360e+00
1_xyz: 0.2348 0.2713 7.623999e+00 7.734510e+00
1_adp: 0.2216 0.2676 7.578854e+00 7.714267e+00
2_bss: 0.2037 0.2379 7.486761e+00 7.615026e+00
2_xyz: 0.1944 0.2423 7.473436e+00 7.629683e+00
2_adp: 0.1882 0.2396 7.449879e+00 7.620893e+00
3_bss: 0.1875 0.2312 7.433926e+00 7.596287e+00
3_xyz: 0.1857 0.2341 7.435421e+00 7.607941e+00
3_adp: 0.1818 0.2331 7.418785e+00 7.599553e+00
3_bss: 0.1826 0.2324 7.421608e+00 7.597030e+00
------------------------------------------------------------------------
stage k_sol b_sol b11 b22 b33 b12 b13 b23
0 : 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
1_bss: 0.347 50.000 2.318 2.318 2.318 0.000 0.000 -0.000
1_xyz: 0.347 50.000 2.318 2.318 2.318 0.000 0.000 -0.000
1_adp: 0.347 50.000 2.318 2.318 2.318 0.000 0.000 -0.000
2_bss: 0.337 50.000 2.425 2.425 2.425 0.000 0.000 -0.000
2_xyz: 0.337 50.000 2.425 2.425 2.425 0.000 0.000 -0.000
2_adp: 0.337 50.000 2.425 2.425 2.425 0.000 0.000 -0.000
3_bss: 0.335 50.000 3.181 3.181 3.181 0.000 0.000 -0.000
3_xyz: 0.335 50.000 3.181 3.181 3.181 0.000 0.000 -0.000
3_adp: 0.335 50.000 3.181 3.181 3.181 0.000 0.000 -0.000
3_bss: 0.337 65.653 0.000 0.000 0.000 0.000 0.000 -0.000
------------------------------------------------------------------------
stage <pher> fom alpha beta
0 : 31.982 0.7396 1.7443 1387840.945
1_bss: 29.194 0.7699 1.9599 974799.679
1_xyz: 28.118 0.7819 1.9866 928279.367
1_adp: 27.348 0.7902 1.9633 892955.282
2_bss: 24.199 0.8225 1.9720 689127.593
2_xyz: 24.569 0.8186 1.9572 710017.017
2_adp: 23.913 0.8260 1.9393 697946.465
3_bss: 23.043 0.8347 1.9776 647848.901
3_xyz: 23.264 0.8326 1.9689 664228.536
3_adp: 22.951 0.8359 1.9502 655975.202
3_bss: 23.013 0.8352 1.9517 659994.149
------------------------------------------------------------------------
stage angl bond chir dihe plan repu geom_target
0 : 1.693 0.012 0.089 17.723 0.007 4.142 1.5608e-01
1_bss: 1.693 0.012 0.089 17.723 0.007 4.142 1.5608e-01
1_xyz: 1.635 0.010 0.087 18.407 0.008 4.141 1.4451e-01
1_adp: 1.635 0.010 0.087 18.407 0.008 4.141 1.4451e-01
2_bss: 1.635 0.010 0.087 18.407 0.008 4.135 1.6105e-01
2_xyz: 1.421 0.009 0.083 18.369 0.007 4.141 1.2821e-01
2_adp: 1.421 0.009 0.083 18.369 0.007 4.141 1.2821e-01
3_bss: 1.421 0.009 0.083 18.369 0.007 4.136 1.3974e-01
3_xyz: 1.283 0.007 0.075 17.946 0.007 4.138 1.0907e-01
3_adp: 1.283 0.007 0.075 17.946 0.007 4.138 1.0907e-01
3_bss: 1.283 0.007 0.075 17.946 0.007 4.138 1.0822e-01
------------------------------------------------------------------------
Maximal deviations:
stage angl bond chir dihe plan repu |grad|
0 : 25.044 0.095 0.406113.659 0.154 1.486 1.5120e-01
1_bss: 25.044 0.095 0.406113.659 0.154 1.486 1.5120e-01
1_xyz: 25.658 0.089 0.312115.970 0.157 1.921 6.5351e-02
1_adp: 25.658 0.089 0.312115.970 0.157 1.921 6.5351e-02
2_bss: 25.658 0.089 0.312115.970 0.157 1.816 6.3368e-02
2_xyz: 23.516 0.082 0.391119.400 0.155 1.926 4.8056e-02
2_adp: 23.516 0.082 0.391119.400 0.155 1.926 4.8056e-02
3_bss: 23.516 0.082 0.391119.400 0.155 1.802 4.8972e-02
3_xyz: 23.841 0.048 0.338113.663 0.152 1.976 3.4188e-02
3_adp: 23.841 0.048 0.338113.663 0.152 1.976 3.4188e-02
3_bss: 23.841 0.048 0.338113.663 0.152 1.976 3.4255e-02
------------------------------------------------------------------------
|-----overall-----|---macromolecule----|------solvent-------|
stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave
0 : 118.66 7.67 27.52 117.10 0.00 26.33 26.33 26.33 26.33
1_bss: 118.66 7.67 27.52 117.10 0.00 26.33 26.33 26.33 26.33
1_xyz: 118.66 7.67 27.52 119.19 2.33 25.79 59.44 3.23 29.93
1_adp: 117.10 0.00 26.33 119.19 2.33 25.79 49.81 3.23 28.22
2_bss: 117.10 0.00 26.33 119.19 2.33 25.79 49.81 3.23 28.22
2_xyz: 117.10 0.00 26.33 118.91 2.01 25.32 55.54 0.00 31.76
2_adp: 119.19 2.33 25.98 122.12 5.23 28.54 53.19 6.73 34.57
------------------------------------------------------------------------
stage Deviation of refined
model from start model
max min mean
0 : 0.000 0.000 0.000
1_bss: 0.000 0.000 0.000
1_xyz: 2.308 0.002 0.111
1_adp: 2.308 0.002 0.111
2_bss: 2.308 0.002 0.111
2_xyz: 2.461 0.002 0.117
2_adp: 2.461 0.002 0.117
3_bss: 2.461 0.002 0.117
3_xyz: 2.748 0.003 0.122
3_adp: 2.748 0.003 0.122
3_bss: 2.748 0.003 0.122
------------------------------------------------------------------------
stage number of ordered solvent
0 : 0
1_bss: 0
1_xyz: 0
1_adp: 0
2_bss: 291
2_xyz: 291
2_adp: 291
3_bss: 398
3_xyz: 398
3_adp: 398
3_bss: 388
------------------------------------------------------------------------
===================== NCS restraints at end of refinement =====================
NCS restraint group 1:
NCS operator 1:
Reference selection: "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
Other selection: "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )"
Number of atom pairs: 2603
Rotation={{-0.999497, -0.0191321, 0.0252909},
{0.0247831, 0.0263321, 0.999346},
{-0.0197855, 0.99947, -0.0258447}}
Translation={{38.4881}, {-44.0747}, {42.34}}
Histogram of differences:
0.002570 - 0.054938: 2350
0.054938 - 0.107305: 233
0.107305 - 0.159673: 16
0.159673 - 0.212040: 2
0.212040 - 0.264408: 1
0.264408 - 0.316775: 1
RMS difference with respect to the reference: 0.037521
Writing refined structure to PDB file:
AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3.pdb
n_use = 6643
n_use_u_iso = 6643
n_use_u_aniso = 0
n_grad_site = 0
n_grad_u_iso = 6643
n_grad_u_aniso = 0
n_grad_occupancy = 0
n_grad_fp = 0
n_grad_fdp = 0
n_anisotropic_flag = 0
total number of scatterers = 6643
Writing map coefficients to MTZ file:
/usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3_001_map_coeffs.mtz
Writing refined fmodel to MTZ file:
/usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz
# Date 2007/12/14 11:38:03
Final R(work) = 0.1826, R(free) = 0.2324
