ARCIMBOLDO-BORGES: Library search with PHASER and density modification and map interpretation with SHELXE

Summary

NAME: tere_shredsphere_phaser28_BORGESARCI
SPACEGROUP: P 63
CELL DIMENSIONS: 163.98, 163.98, 56.71, 90.00, 90.00, 120.00
RESOLUTION: 2.10
NUMBER OF UNIQUE REFLECTIONS: 51132.00

It seems you have a good solution!
Here you can find the best solution and map for further refinement.

Rotation clustering

#Cluster #Rotations #Distinct Pdb Top LLG LLG Mean Top Zscore Zscore Mean
0 231 231 18.50 11.24 5.66 3.80
1 114 114 14.90 10.32 5.14 3.59
2 173 173 15.30 10.58 5.00 3.60
3 193 193 16.10 10.56 5.24 3.64
4 159 159 14.40 10.16 4.66 3.61
5 148 148 15.10 10.54 5.10 3.62
6 102 102 14.10 10.20 4.62 3.63
7 197 197 19.30 11.30 6.06 3.82
8 119 119 16.70 11.04 5.08 3.69
10 155 155 15.80 10.68 5.36 3.56
13 117 117 12.70 10.06 4.50 3.43

Backtracking

The current best solution is: frag589_0_0.pdb with FINALCC: 36.76 and n. residues traced 475
file is: /localdata1/TEST_TERESA/TEST_PHASER29/./ARCIMBOLDO_BORGES/./11_EXP_alixe/7/3/0/frag589_0_0_rbr_7_ref.pdb

It seems you have a good solution!
Here you can find the best solution and map for further refinement.

Instruction file

[ARCIMBOLDO-BORGES]
formfactors = FORMFACTORS XRAY
aniso = True
clusters = all
n_clusters = 4
prioritize_phasers = True
f_p1_label = 
sigf_p1_label = 
number_of_component = 1
number_of_component_p1 = 
rmsd = 0.8
rotation_clustering_algorithm = rot_matrices
threshold_algorithm = 15
resolution_rotation = 1.0
sampling_rotation = -1.0
resolution_translation = 1.0
sampling_translation = -1
resolution_refinement = 1.0
sampling_refinement = -1
resolution_gyre = 1.0
exclude_llg = 0
exclude_zscore = 0
spacegroup = 
use_packing = True
number_cycles_model_refinement = 2
tncs = True
pack_clashes = 10
nice = 0
randomize_trans_per_rot = 0
nma = False
make_positive_llg = False
rotation_model_refinement = BOTH
step_rmsd_decrease_gyre = 0.2
sigr = 0.0
sigt = 0.0
pack_tra = False
base_sum_from_wd = True
gyre_preserve_chains = True
nma_p1 = False
occ = False
vrms = True
vrms_gyre = False
bfac = False
bulk_fsol = -1
bulk_bsol = -1
gimble = True
alixe_mode = one_step
prioritize_occ = True
solution_sorting_scheme = LLG
sampling_gyre = -1
applytopnamefilter = True
nodminitcc = True
phs_fom_statistics = False
savephs = True
archivingasbigfile = False
alixe = True
filter_clusters_after_rot = False
extend_with_random_atoms = False
extend_with_secondary_structure = False
parameters_elongation = 4.8 60 150
topfrf = 200
topftf = 70
toppack = -1
toprnp = 200
topexp = 40
force_core = -1
force_nsol = -1
force_exp = False
ellg_target = 30.0
fixed_model = 
coiled_coil = False
stop_if_solved = True
unitcellcontentanalysis = False
solventcontent = 0
shelxe_line = -m10 -a8 -s0.6 -v0 -t10 -q -o -y2.10
shelxe_line_last = -m10 -a1 -s0.55 -v0 -t10 -q -o -y2.10 -e1.60
molecular_weight = 70153.0
library_path = /localdata1/TEST_TERESA/TEST_PHASER29/./models/
f_label = F
sigf_label = SIGF
name_job = tere_shredsphere_phaser28_BORGESARCI

[CONNECTION]
distribute_computing = local_grid
remote_frontend_passkey = ~/.ssh/id_rsa
setup_bor_path = /xtal/cri4-software/borges/PY/current_setup.bor

[GENERAL]
mtz_p1_path = 
ent_path = /localdata1/TEST_TERESA/data_teresa/partial.ent
pdb_path = 
working_directory = /localdata1/TEST_TERESA/TEST_PHASER29/./ARCIMBOLDO_BORGES/
mtz_path = /localdata1/TEST_TERESA/data_teresa/tere2.mtz
hkl_path = /localdata1/TEST_TERESA/data_teresa/tere2.hkl

[LOCAL]
path_local_phaser = phenix.phaser
path_local_shelxe = shelxe
path_local_arcimboldo = ARCIMBOLDO_BORGES

[ANOMALOUS]
hkl_fa_path = none
ins_fa_path = none
expphasing = none
nsites_expected = 0
ha_present_in_native = False
recycle_ha = False
sfac = none
dsul = 0
specialpos = False
rootanom = none
dano_label = none
sigdano_label = none
nat_path = none
peak_path = none
infl_path = none
hrem_path = none
lrem_path = none
sir_path = none
sira_path = none
before_path = none
after_path = none
minusz = False

Log file

Log file has not been found.Timestamp information

Time MODE: ARCIMBOLDO-BORGES STEP: FRF 2018-07-09 17:04
Time MODE: ARCIMBOLDO-BORGES STEP: FRF 2018-07-09 17:04
Time MODE: ARCIMBOLDO-BORGES STEP: TABLE 2018-07-09 17:18
Time MODE: ARCIMBOLDO-BORGES STEP: FTF 2018-07-09 17:21
Time MODE: ARCIMBOLDO-BORGES STEP: PACK 2018-07-09 17:22
Time MODE: ARCIMBOLDO-BORGES STEP: RNP 2018-07-09 18:15
Time MODE: ARCIMBOLDO-BORGES STEP: INITCC 2018-07-09 18:21
Time MODE: ARCIMBOLDO-BORGES STEP: TABLE 2018-07-09 18:41
Time MODE: ARCIMBOLDO-BORGES STEP: FTF 2018-07-09 18:44
Time MODE: ARCIMBOLDO-BORGES STEP: PACK 2018-07-09 18:45
Time MODE: ARCIMBOLDO-BORGES STEP: RNP 2018-07-09 19:48
Time MODE: ARCIMBOLDO-BORGES STEP: INITCC 2018-07-09 19:59
Time MODE: ARCIMBOLDO-BORGES STEP: TABLE 2018-07-09 20:16
Time MODE: ARCIMBOLDO-BORGES STEP: FTF 2018-07-09 20:18
Time MODE: ARCIMBOLDO-BORGES STEP: PACK 2018-07-09 20:18
Time MODE: ARCIMBOLDO-BORGES STEP: RNP 2018-07-09 20:46
Time MODE: ARCIMBOLDO-BORGES STEP: INITCC 2018-07-09 20:49
Time MODE: ARCIMBOLDO-BORGES STEP: TABLE 2018-07-09 21:06
Time MODE: ARCIMBOLDO-BORGES STEP: FTF 2018-07-09 21:08
Time MODE: ARCIMBOLDO-BORGES STEP: PACK 2018-07-09 21:08
Time MODE: ARCIMBOLDO-BORGES STEP: RNP 2018-07-09 21:47
Time MODE: ARCIMBOLDO-BORGES STEP: INITCC 2018-07-09 21:51
Time MODE: ARCIMBOLDO-BORGES STEP: TABLE 2018-07-09 21:51
Time MODE: ARCIMBOLDO-BORGES STEP: FTF 2018-07-09 21:51
Time MODE: ARCIMBOLDO-BORGES STEP: PACK 2018-07-09 21:51
Time MODE: ARCIMBOLDO-BORGES STEP: RNP 2018-07-09 21:51
Time MODE: ARCIMBOLDO-BORGES STEP: INITCC 2018-07-09 21:51
Time MODE: ARCIMBOLDO-BORGES STEP: FAST_1_7 2018-07-11 00:03
Time MODE: ARCIMBOLDO-BORGES STEP: FAST_2_7 2018-07-11 02:05
Time MODE: ARCIMBOLDO-BORGES STEP: FAST_3_7 2018-07-11 05:16

Citations

Phaser crystallographic software.
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J.
(2007) J Appl Cryst. 40, 658-674.

An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features.
Uson, I. & Sheldrick, G. M.
(2018) Acta Cryst. D74, 106-116.

Exploiting tertiary structure through local folds for ab initio phasing.
Sammito, M., Millan, C., Rodriguez, D. D., M. de Ilarduya, I., Meindl, K., De Marino, I., Petrillo, G., Buey, R. M., de Pereda, J. M., Zeth, K., Sheldrick, G. M. & Uson, I.
(2013) Nat Methods. 10, 1099-1101.

Support

For online documentation and tutorials visit www.chango.ibmb.csic.es
For developer support send an email to bugs-borges@ibmb.csic.es
Crystallographic Methods Group
Structural Biology Unit
Molecular Biology Institute of Barcelona