Arcimboldo

Rotation clustering

#Cluster	#Rotations	#Distinct Pdb	Top LLG	LLG Mean	Top Zscore	Zscore Mean
0	87	87	11.60	7.38	5.83	3.93
1	33	33	7.70	6.17	4.38	3.56
2	79	79	10.00	7.17	4.83	3.80
3	71	71	9.50	7.28	4.86	3.83
4	58	58	8.20	6.56	4.61	3.60
5	25	25	8.60	6.33	4.50	3.44
6	16	16	8.10	6.73	4.00	3.45
7	38	38	9.30	6.67	4.43	3.67
8	42	42	8.70	6.74	4.35	3.72
9	33	33	8.00	6.12	4.47	3.48
10	4	4	7.60	6.88	4.11	3.56
11	5	5	7.90	5.98	4.06	3.52
12	19	19	7.30	6.09	4.14	3.50

Search and expansion

#Cluster	Rotation and Model Refinement					Translation Function					Packing					Rigid Body Refinement					Initial CC		Best Trace CC/aa
	#Rots.	Top LLG	Mean LLG	Top Zscore	Mean Zscore	#Trans.	Top LLG	Mean LLG	Top Zscore	Mean Zscore	#Sol.	Top LLG	Mean LLG	Top Zscore	Mean Zscore	#Sol.	Top LLG	Mean LLG	Top TFZ==	Mean TFZ==	Before Refinement CC	After Refinement CC	MODE	Cycle	CC	#Res. traced
0	174	20.00	10.53	5.83	1.97	174	44.97	29.17	6.80	5.28	120	44.97	28.92	6.80	5.24	120	68.60	33.51	11.10	6.41	7.66	8.45	FAST	7	10.03	59
3	142	23.00	10.20	4.86	1.91	142	41.64	27.66	6.47	5.16	103	41.64	27.62	6.47	5.10	103	50.50	31.64	8.70	6.24	7.06	7.48	FAST	1	8.48	45
2	158	20.00	10.12	4.83	1.90	158	44.85	28.09	6.46	5.25	107	44.85	28.67	5.91	5.19	107	51.10	32.45	8.80	6.24	7.65	7.47
7	76	17.00	9.68	4.43	1.84	76	40.21	27.36	6.23	5.24	50	36.61	27.43	6.07	5.22	50	45.40	32.21	8.20	6.38	8.06	7.54

Backtracking

The current best solution is: frag255_0_0.pdb with FINALCC: 10.03 and n. residues traced 59
file is: /localdata2/MICROED/TEST_MICROED/SPHERES_5JXG/./ARCIMBOLDO_BORGES/./11_EXP/0/7/0/frag255_0_0_rnp.pdb

FRF: Pos. in Rank: 1 LLG: 11.60 ZSCORE: 5.83 Top LLG in Cluster 0: 11.60 Top ZSCORE in Cluster 0: 5.83
REFINEMENT ROTATION AND MODEL

FTF: Pos. in Rank: 5 LLG: 41.87 ZSCORE: 6.36 Top LLG in Cluster 0: 44.97 Top ZSCORE in Cluster 0: 6.80

PACK: Pos. in Rank: 3 LLG: 41.87 ZSCORE: 6.36 Top LLG in Cluster 0: 44.97 Top ZSCORE in Cluster 0: 6.80

RNP: Pos. in Rank: 1 LLG: 56.80 ZSCORE: 6.36 TFZ==: 6.10 Top LLG in Cluster 0: 56.80 Top ZSCORE in Cluster 0: 6.80

INITIAL CC

Before Refinement: Pos. in Rank: 1 INITCC: 7.66 Top INITCC in Cluster 0: 7.66
After Refinement: Pos. in Rank: 1 INITCC: 8.45 Top INITCC in Cluster 0: 8.45

EXPANSION

Cycle 7:: Final CC: 10.03% N. Residues Traced: 59.00

Instruction file

[ARCIMBOLDO-BORGES]
formfactors = FORMFACTORS ELECTRON
aniso = True
datacorrect = 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 = False
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
nautotraccyc = -1
nbunchautotraccyc = 1
model_shredder = /localdata2/MICROED/TEST_MICROED/SPHERES_5JXG/5JXGA_10_330.pdb
shelxe_line = -m15 -a8 -s0.5 -v0 -t10 -q -o -y1.60 -B3
shelxe_line_last = -m15 -a1 -s0.45 -v0 -t10 -q -o -y1.60 -e1.10 -B3
molecular_weight = 28900.0
library_path = /localdata2/MICROED/TEST_MICROED/SPHERES_5JXG/./models/
i_label = IMEAN
sigi_label = SIGIMEAN
name_job = 5jxg_sph_08rmsd_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 = /localdata2/MICROED/TEST_MICROED/SPHERES_5JXG/5k7s.ent
pdb_path = 
working_directory = /localdata2/MICROED/TEST_MICROED/SPHERES_5JXG/./ARCIMBOLDO_BORGES/
mtz_path = /localdata2/MICROED/TEST_MICROED/SPHERES_5JXG/input.mtz
hkl_path = /localdata2/MICROED/TEST_MICROED/SPHERES_5JXG/input.hkl

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

[ANOMALOUS]
hkl_fa_path = none
ins_fa_path = none
expphasing = none
nsites_expected = 0
ha_present_in_native = False
recycle_ha = True
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
minusz_zero = True
minuso = False
evaluateanom = True
patterson = True
referencehafixed = none
referencehashredder = none
hardfilter = False
n_ha_refine_cycles = 0
anomalous_filtering = True
anomalous_expansion = True
filterlitefromfragnumber = 1
ha_substructure = none
hres_cutoff = 0
geometrycheck = none

Log file

Log file has not been found.Timestamp information

Time MODE: ARCIMBOLDO-BORGES STEP: FRF 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FRF 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: TABLE 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FTF 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: PACK 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: RNP 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: INITCC 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: TABLE 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FTF 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: PACK 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: RNP 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: INITCC 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: TABLE 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FTF 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: PACK 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: RNP 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: INITCC 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: TABLE 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FTF 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: PACK 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: RNP 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: INITCC 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: TABLE 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FTF 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: PACK 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: RNP 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: INITCC 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FAST_1_0 2019-07-15 11:48
Time MODE: ARCIMBOLDO-SHREDDER STEP: FAST_2_0 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FAST_3_0 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FAST_4_0 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FAST_5_0 2019-07-15 11:48
Time MODE: ARCIMBOLDO-SHREDDER STEP: FAST_6_0 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FAST_7_0 2019-07-15 11:48
Time MODE: ARCIMBOLDO-SHREDDER STEP: FAST_8_0 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: TABLE 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: FTF 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: PACK 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: RNP 2019-07-15 11:48
Time MODE: ARCIMBOLDO-BORGES STEP: INITCC 2019-07-15 11:48
Time MODE: ARCIMBOLDO-SHREDDER STEP: FAST_1_3 2019-07-15 12:59
Time MODE: ARCIMBOLDO-SHREDDER STEP: FAST_2_3 2019-07-15 14:00

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