Command line arguments: I432.sca 200 C

------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  Version: 1.24.1b
  Platform: intel-linux-2.6 linux
  User: phzwart
------------------------------------------------------------------------------

                       HySS: Hybrid Substructure Search

------------------------------------------------------------------------------
Phenix developers include:
  P.D. Adams, P. Afonine, K. Gopal, R.W. Grosse-Kunstleve, L.-W. Hung,
  T.R. Ioerger, A.J. McCoy, E.W. McKee, N.W. Moriarty, R.K. Pai, R.J. Read,
  T.D. Romo, J.C. Sacchettini, N.K. Sauter, J.N. Smith, L.C. Storoni,
  T.C. Terwilliger, P.H. Zwart
Phenix home page:
  http://www.phenix-online.org/
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxPython, Boost, SCons, Clipper, CCP4 Monomer Library,
    CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
------------------------------------------------------------------------------

Reading reflection file: I432.sca

Space group found in file: I 4 3 2
Is this the correct space group? [Y/N]: Please enter the correct
space group symbol: Input Miller array:
Miller array info: I432.sca:i_obs,sigma
Observation type: xray.intensity
Type of data: double, size=5236
Type of sigmas: double, size=5236
Number of Miller indices: 5236
Anomalous flag: False
Unit cell: (76.855, 76.855, 76.855, 90, 90, 90)
Space group: I 41 3 2 (No. 214)
Systematic absences: 12
Systematic absences not included in following:
Centric reflections: 1055
Resolution range: 31.3759 1.61737
Completeness in resolution range: 0.998471
Completeness with d_max=infinity: 0.99828

Removing systematic absences:
Number of reflections: 5224

Removing zero or negative observations:
Number of reflections: 5088

Applying resolution limits: 15 3
Number of reflections: 884

Applying sigma cutoff: 1
Number of reflections: 883

Using pre-processed anomalous differences or FA structure factors.

Writing anomalous differences as SHELX HKLF file: I432_anom_diffs.hkl

Writing SHELXD ins file: I432_anom_diffs.ins

Starting the search procedure (fast mode):

Miller array info: None
Observation type: xray.intensity
Type of data: double, size=883
Type of sigmas: double, size=883
Number of Miller indices: 883
Anomalous flag: False
Unit cell: (76.855, 76.855, 76.855, 90, 90, 90)
Space group: I 41 3 2 (No. 214)

Transformation to Niggli cell: y+z,x+z,x+y
Miller array info: Primitive Niggli setting
Observation type: xray.intensity
Type of data: double, size=883
Type of sigmas: double, size=883
Number of Miller indices: 883
Anomalous flag: False
Unit cell: (66.5584, 66.5584, 66.5584, 109.471, 109.471, 109.471)
Space group: Hall:  I 4bd 2c 3 (y+z,x+z,x+y) (No. 214)

Substructure parameter: n_sites: 200
Substructure parameter: min_cross_distance: 3.5
Substructure parameter: min_distance_sym_equiv: 3.5
Substructure parameter: general_positions_only: False
Substructure parameter: min_distance: 3.5
hyss: using shelxd.q_value_estimation
Search parameter: n_high_extrapolation_scan_correlation_group: 0
Search parameter: min_low_correlation: 0.1
Search parameter: n_chunk: 1
Search parameter: real_space_squaring: None
Search parameter: high_low_correlation_factor: 2
Search parameter: peak_search_effective_resolution: None
Search parameter: site_recycling_min_use: 0
Search parameter: n_candidate_sites: 180
Search parameter: n_use_sites: 134
Search parameter: enable_early_termination: True
Search parameter: n_recycling_cycles: 10
Search parameter: occupancy_minimization: False
Search parameter: site_recycling_candidate_factor: 0.9
Search parameter: truncate_consensus_model: True
Search parameter: n_patterson_vectors: 100
Search parameter: max_relative_spread_top_correlations: 0.1
Search parameter: n_sites_final_factor: 1
Search parameter: min_top_n_matches: 134
Search parameter: e_min: 1.5
Search parameter: p1_n_recycling_cycles: 10
Search parameter: cos_sin_table: True
Search parameter: n_fragments: 10
Search parameter: i_chunk: 0
Search parameter: site_recycling_use_heights_as_occupancies: False
Search parameter: factor_top_n_matches: 0.666666666667
Search parameter: n_sites_final: 200
Search parameter: site_recycling_use_factor: 0.666666666667
Search parameter: n_top_models_to_compare: 2
Search parameter: minimize_consensus_model: False
Search parameter: compare_sites_if_correlation_is_over: 0.2
Patterson: harker_plane_min_distance: 1.75
Patterson: keep_map: False
Patterson: origin_peak_removal: False
Patterson: grid_resolution_factor: 0.333333333333
Patterson: number of reflections: 883
Patterson: suppressing peaks near Harker planes.
Patterson: map gridding: (72, 72, 72)
Patterson: map min: -11.12 sigma
Patterson: map max: 74.20 sigma
Two-site translation: grid_resolution_factor: 0.333333333333
Two-site translation: number of reflections: 883
Squaring: minimal_grid: True
Squaring: use_q_000: False
Squaring: fraction_fixed_phases: 0.4
Squaring: zero_out_negative: False
Squaring: use_fixed_only: True
Squaring: number of reflections: 99
Squaring: n_fixed: 40
Squaring: n_variable: 59
Squaring: q_000: None
Squaring: gridding: (45, 45, 45)
Squaring: minimal_grid: True
Squaring: use_q_000: False
Squaring: fraction_fixed_phases: 0.4
Squaring: zero_out_negative: False
Squaring: use_fixed_only: True
Squaring: number of reflections: 1874
Squaring: n_fixed: 750
Squaring: n_variable: 1124
Squaring: q_000: None
Squaring: gridding: (45, 45, 45)

Entering search loop:

p = peaklist index in Patterson map
f = peaklist index in two-site translation function
cc = correlation coefficient after extrapolation scan
r = number of dual-space recycling cycles
cc = final correlation coefficient

p=000 f=000 cc=0.389 r=010 cc=0.619 [ best cc: 0.619 ]
p=000 f=001 cc=0.389 r=010 cc=0.613 [ best cc: 0.619 0.613 ]
Number of matching sites of top 2 structures: 112
p=000 f=002 cc=0.357 r=010 cc=0.591 [ best cc: 0.619 0.613 ]
p=000 f=003 cc=0.342 r=010 cc=0.588 [ best cc: 0.619 0.613 ]
p=000 f=004 cc=0.350 r=010 cc=0.611 [ best cc: 0.619 0.613 ]
p=000 f=005 cc=0.362 r=010 cc=0.607 [ best cc: 0.619 0.613 ]
p=000 f=006 cc=0.393 r=010 cc=0.615 [ best cc: 0.619 0.615 ]
Number of matching sites of top 2 structures: 114
p=000 f=007 cc=0.386 r=010 cc=0.579 [ best cc: 0.619 0.615 ]
p=000 f=008 cc=0.381 r=010 cc=0.607 [ best cc: 0.619 0.615 ]
p=000 f=009 cc=0.372 r=010 cc=0.599 [ best cc: 0.619 0.615 ]
p=001 f=000 cc=0.362 r=010 cc=0.593 [ best cc: 0.619 0.615 ]
p=001 f=001 cc=0.359 r=010 cc=0.600 [ best cc: 0.619 0.615 ]
p=001 f=002 cc=0.352 r=010 cc=0.604 [ best cc: 0.619 0.615 ]
p=001 f=003 cc=0.334 r=010 cc=0.586 [ best cc: 0.619 0.615 ]
p=001 f=004 cc=0.333 r=010 cc=0.612 [ best cc: 0.619 0.615 ]
p=001 f=005 cc=0.372 r=010 cc=0.579 [ best cc: 0.619 0.615 ]
p=001 f=006 cc=0.321 r=010 cc=0.578 [ best cc: 0.619 0.615 ]
p=001 f=007 cc=0.395 r=010 cc=0.605 [ best cc: 0.619 0.615 ]
p=001 f=008 cc=0.336 r=010 cc=0.568 [ best cc: 0.619 0.615 ]
p=001 f=009 cc=0.294 r=010 cc=0.565 [ best cc: 0.619 0.615 ]
p=002 f=000 cc=0.395 r=010 cc=0.592 [ best cc: 0.619 0.615 ]
p=002 f=001 cc=0.366 r=010 cc=0.579 [ best cc: 0.619 0.615 ]
p=002 f=002 cc=0.367 r=010 cc=0.606 [ best cc: 0.619 0.615 ]
p=002 f=003 cc=0.395 r=010 cc=0.591 [ best cc: 0.619 0.615 ]
p=002 f=004 cc=0.390 r=010 cc=0.608 [ best cc: 0.619 0.615 ]
p=002 f=005 cc=0.375 r=010 cc=0.603 [ best cc: 0.619 0.615 ]
p=002 f=006 cc=0.352 r=010 cc=0.575 [ best cc: 0.619 0.615 ]
p=002 f=007 cc=0.342 r=010 cc=0.611 [ best cc: 0.619 0.615 ]
p=002 f=008 cc=0.371 r=010 cc=0.594 [ best cc: 0.619 0.615 ]
p=002 f=009 cc=0.372 r=010 cc=0.566 [ best cc: 0.619 0.615 ]
p=003 f=000 cc=0.386 r=010 cc=0.611 [ best cc: 0.619 0.615 ]
p=003 f=001 cc=0.373 r=010 cc=0.591 [ best cc: 0.619 0.615 ]
p=003 f=002 cc=0.376 r=010 cc=0.609 [ best cc: 0.619 0.615 ]
p=003 f=003 cc=0.384 r=010 cc=0.618 [ best cc: 0.619 0.618 ]
Number of matching sites of top 2 structures: 109
p=003 f=004 cc=0.367 r=010 cc=0.605 [ best cc: 0.619 0.618 ]
p=003 f=005 cc=0.351 r=010 cc=0.578 [ best cc: 0.619 0.618 ]
p=003 f=006 cc=0.431 r=010 cc=0.621 [ best cc: 0.621 0.619 ]
Number of matching sites of top 2 structures: 111
p=003 f=007 cc=0.426 r=010 cc=0.593 [ best cc: 0.621 0.619 ]
p=003 f=008 cc=0.356 r=010 cc=0.606 [ best cc: 0.621 0.619 ]
p=003 f=009 cc=0.426 r=010 cc=0.624 [ best cc: 0.624 0.621 ]
Number of matching sites of top 2 structures: 115
p=004 f=000 cc=0.379 r=010 cc=0.579 [ best cc: 0.624 0.621 ]
p=004 f=001 cc=0.373 r=010 cc=0.589 [ best cc: 0.624 0.621 ]
p=004 f=002 cc=0.310 r=010 cc=0.600 [ best cc: 0.624 0.621 ]
p=004 f=003 cc=0.324 r=010 cc=0.607 [ best cc: 0.624 0.621 ]
p=004 f=004 cc=0.390 r=010 cc=0.611 [ best cc: 0.624 0.621 ]
p=004 f=005 cc=0.334 r=010 cc=0.584 [ best cc: 0.624 0.621 ]
p=004 f=006 cc=0.357 r=010 cc=0.632 [ best cc: 0.632 0.624 ]
Number of matching sites of top 2 structures: 115
p=004 f=007 cc=0.346 r=010 cc=0.604 [ best cc: 0.632 0.624 ]
p=004 f=008 cc=0.339 r=010 cc=0.626 [ best cc: 0.632 0.626 ]
Number of matching sites of top 2 structures: 107
p=004 f=009 cc=0.362 r=010 cc=0.595 [ best cc: 0.632 0.626 ]
p=005 f=000 cc=0.458 r=010 cc=0.572 [ best cc: 0.632 0.626 ]
p=005 f=001 cc=0.450 r=010 cc=0.564 [ best cc: 0.632 0.626 ]
p=005 f=002 cc=0.405 r=010 cc=0.609 [ best cc: 0.632 0.626 ]
p=005 f=003 cc=0.471 r=010 cc=0.589 [ best cc: 0.632 0.626 ]
p=005 f=004 cc=0.480 r=010 cc=0.567 [ best cc: 0.632 0.626 ]
p=005 f=005 cc=0.434 r=010 cc=0.582 [ best cc: 0.632 0.626 ]
p=005 f=006 cc=0.431 r=010 cc=0.567 [ best cc: 0.632 0.626 ]
p=005 f=007 cc=0.452 r=010 cc=0.611 [ best cc: 0.632 0.626 ]
p=005 f=008 cc=0.377 r=010 cc=0.592 [ best cc: 0.632 0.626 ]
p=005 f=009 cc=0.478 r=010 cc=0.589 [ best cc: 0.632 0.626 ]
p=006 f=000 cc=0.373 r=010 cc=0.595 [ best cc: 0.632 0.626 ]
p=006 f=001 cc=0.356 r=010 cc=0.613 [ best cc: 0.632 0.626 ]
p=006 f=002 cc=0.372 r=010 cc=0.613 [ best cc: 0.632 0.626 ]
p=006 f=003 cc=0.357 r=010 cc=0.579 [ best cc: 0.632 0.626 ]
p=006 f=004 cc=0.406 r=010 cc=0.536 [ best cc: 0.632 0.626 ]
p=006 f=005 cc=0.426 r=010 cc=0.612 [ best cc: 0.632 0.626 ]
p=006 f=006 cc=0.386 r=010 cc=0.586 [ best cc: 0.632 0.626 ]
p=006 f=007 cc=0.363 r=010 cc=0.623 [ best cc: 0.632 0.626 ]
p=006 f=008 cc=0.359 r=010 cc=0.575 [ best cc: 0.632 0.626 ]
p=006 f=009 cc=0.436 r=010 cc=0.574 [ best cc: 0.632 0.626 ]
p=007 f=000 cc=0.352 r=010 cc=0.626 [ best cc: 0.632 0.626 ]
Number of matching sites of top 2 structures: 112
p=007 f=001 cc=0.340 r=010 cc=0.584 [ best cc: 0.632 0.626 ]
p=007 f=002 cc=0.396 r=010 cc=0.634 [ best cc: 0.634 0.632 ]
Number of matching sites of top 2 structures: 112
p=007 f=003 cc=0.343 r=010 cc=0.612 [ best cc: 0.634 0.632 ]
p=007 f=004 cc=0.306 r=010 cc=0.577 [ best cc: 0.634 0.632 ]
p=007 f=005 cc=0.347 r=010 cc=0.577 [ best cc: 0.634 0.632 ]
p=007 f=006 cc=0.353 r=010 cc=0.607 [ best cc: 0.634 0.632 ]
p=007 f=007 cc=0.334 r=010 cc=0.602 [ best cc: 0.634 0.632 ]
p=007 f=008 cc=0.388 r=010 cc=0.590 [ best cc: 0.634 0.632 ]
p=007 f=009 cc=0.362 r=010 cc=0.576 [ best cc: 0.634 0.632 ]
p=008 f=000 cc=0.345 r=010 cc=0.597 [ best cc: 0.634 0.632 ]
p=008 f=001 cc=0.357 r=010 cc=0.597 [ best cc: 0.634 0.632 ]
p=008 f=002 cc=0.324 r=010 cc=0.611 [ best cc: 0.634 0.632 ]
p=008 f=003 cc=0.335 r=010 cc=0.581 [ best cc: 0.634 0.632 ]
p=008 f=004 cc=0.311 r=010 cc=0.580 [ best cc: 0.634 0.632 ]
p=008 f=005 cc=0.329 r=010 cc=0.596 [ best cc: 0.634 0.632 ]
p=008 f=006 cc=0.379 r=010 cc=0.573 [ best cc: 0.634 0.632 ]
p=008 f=007 cc=0.336 r=010 cc=0.609 [ best cc: 0.634 0.632 ]
p=008 f=008 cc=0.339 r=010 cc=0.585 [ best cc: 0.634 0.632 ]
p=008 f=009 cc=0.318 r=010 cc=0.594 [ best cc: 0.634 0.632 ]
p=009 f=000 cc=0.368 r=010 cc=0.616 [ best cc: 0.634 0.632 ]
p=009 f=001 cc=0.354 r=010 cc=0.584 [ best cc: 0.634 0.632 ]
p=009 f=002 cc=0.350 r=010 cc=0.605 [ best cc: 0.634 0.632 ]
p=009 f=003 cc=0.352 r=010 cc=0.609 [ best cc: 0.634 0.632 ]
p=009 f=004 cc=0.331 r=010 cc=0.613 [ best cc: 0.634 0.632 ]
p=009 f=005 cc=0.339 r=010 cc=0.590 [ best cc: 0.634 0.632 ]
p=009 f=006 cc=0.360 r=010 cc=0.602 [ best cc: 0.634 0.632 ]
p=009 f=007 cc=0.333 r=010 cc=0.607 [ best cc: 0.634 0.632 ]
p=009 f=008 cc=0.347 r=010 cc=0.575 [ best cc: 0.634 0.632 ]
p=009 f=009 cc=0.355 r=010 cc=0.563 [ best cc: 0.634 0.632 ]
p=010 f=000 cc=0.374 r=010 cc=0.594 [ best cc: 0.634 0.632 ]
p=010 f=001 cc=0.366 r=010 cc=0.582 [ best cc: 0.634 0.632 ]
p=010 f=002 cc=0.385 r=010 cc=0.578 [ best cc: 0.634 0.632 ]
p=010 f=003 cc=0.378 r=010 cc=0.599 [ best cc: 0.634 0.632 ]
p=010 f=004 cc=0.352 r=010 cc=0.585 [ best cc: 0.634 0.632 ]
p=010 f=005 cc=0.324 r=010 cc=0.599 [ best cc: 0.634 0.632 ]
p=010 f=006 cc=0.337 r=010 cc=0.575 [ best cc: 0.634 0.632 ]
p=010 f=007 cc=0.352 r=010 cc=0.611 [ best cc: 0.634 0.632 ]
p=010 f=008 cc=0.346 r=010 cc=0.617 [ best cc: 0.634 0.632 ]
p=010 f=009 cc=0.372 r=010 cc=0.607 [ best cc: 0.634 0.632 ]
p=011 f=000 cc=0.388 r=010 cc=0.589 [ best cc: 0.634 0.632 ]
p=011 f=001 cc=0.388 r=010 cc=0.602 [ best cc: 0.634 0.632 ]
p=011 f=002 cc=0.409 r=010 cc=0.612 [ best cc: 0.634 0.632 ]
p=011 f=003 cc=0.383 r=010 cc=0.583 [ best cc: 0.634 0.632 ]
p=011 f=004 cc=0.403 r=010 cc=0.599 [ best cc: 0.634 0.632 ]
p=011 f=005 cc=0.406 r=010 cc=0.596 [ best cc: 0.634 0.632 ]
p=011 f=006 cc=0.448 r=010 cc=0.585 [ best cc: 0.634 0.632 ]
p=011 f=007 cc=0.455 r=010 cc=0.596 [ best cc: 0.634 0.632 ]
p=011 f=008 cc=0.399 r=010 cc=0.591 [ best cc: 0.634 0.632 ]
p=011 f=009 cc=0.448 r=010 cc=0.602 [ best cc: 0.634 0.632 ]
p=012 f=000 cc=0.396 r=010 cc=0.618 [ best cc: 0.634 0.632 ]
p=012 f=001 cc=0.332 r=010 cc=0.605 [ best cc: 0.634 0.632 ]
p=012 f=002 cc=0.362 r=010 cc=0.574 [ best cc: 0.634 0.632 ]
p=012 f=003 cc=0.376 r=010 cc=0.634 [ best cc: 0.634 0.634 ]
Number of matching sites of top 2 structures: 109
p=012 f=004 cc=0.383 r=010 cc=0.577 [ best cc: 0.634 0.634 ]
p=012 f=005 cc=0.373 r=010 cc=0.605 [ best cc: 0.634 0.634 ]
p=012 f=006 cc=0.363 r=010 cc=0.605 [ best cc: 0.634 0.634 ]
p=012 f=007 cc=0.381 r=010 cc=0.614 [ best cc: 0.634 0.634 ]
p=012 f=008 cc=0.364 r=010 cc=0.611 [ best cc: 0.634 0.634 ]
p=012 f=009 cc=0.368 r=010 cc=0.599 [ best cc: 0.634 0.634 ]
p=013 f=000 cc=0.375 r=010 cc=0.594 [ best cc: 0.634 0.634 ]
p=013 f=001 cc=0.360 r=010 cc=0.596 [ best cc: 0.634 0.634 ]
p=013 f=002 cc=0.355 r=010 cc=0.605 [ best cc: 0.634 0.634 ]
p=013 f=003 cc=0.370 r=010 cc=0.634 [ best cc: 0.634 0.634 ]
Number of matching sites of top 2 structures: 110
p=013 f=004 cc=0.347 r=010 cc=0.548 [ best cc: 0.634 0.634 ]
p=013 f=005 cc=0.349 r=010 cc=0.629 [ best cc: 0.634 0.634 ]
p=013 f=006 cc=0.340 r=010 cc=0.588 [ best cc: 0.634 0.634 ]
p=013 f=007 cc=0.338 r=010 cc=0.573 [ best cc: 0.634 0.634 ]
p=013 f=008 cc=0.365 r=010 cc=0.604 [ best cc: 0.634 0.634 ]
p=013 f=009 cc=0.399 r=010 cc=0.599 [ best cc: 0.634 0.634 ]
p=014 f=000 cc=0.369 r=010 cc=0.608 [ best cc: 0.634 0.634 ]
p=014 f=001 cc=0.368 r=010 cc=0.579 [ best cc: 0.634 0.634 ]
p=014 f=002 cc=0.372 r=010 cc=0.603 [ best cc: 0.634 0.634 ]
p=014 f=003 cc=0.373 r=010 cc=0.609 [ best cc: 0.634 0.634 ]
p=014 f=004 cc=0.353 r=010 cc=0.605 [ best cc: 0.634 0.634 ]
p=014 f=005 cc=0.373 r=010 cc=0.574 [ best cc: 0.634 0.634 ]
p=014 f=006 cc=0.311 r=010 cc=0.591 [ best cc: 0.634 0.634 ]
p=014 f=007 cc=0.354 r=010 cc=0.599 [ best cc: 0.634 0.634 ]
p=014 f=008 cc=0.365 r=010 cc=0.601 [ best cc: 0.634 0.634 ]
p=014 f=009 cc=0.326 r=010 cc=0.598 [ best cc: 0.634 0.634 ]
p=015 f=000 cc=0.391 r=010 cc=0.595 [ best cc: 0.634 0.634 ]
p=015 f=001 cc=0.386 r=010 cc=0.554 [ best cc: 0.634 0.634 ]
p=015 f=002 cc=0.392 r=010 cc=0.584 [ best cc: 0.634 0.634 ]
p=015 f=003 cc=0.364 r=010 cc=0.589 [ best cc: 0.634 0.634 ]
p=015 f=004 cc=0.394 r=010 cc=0.591 [ best cc: 0.634 0.634 ]
p=015 f=005 cc=0.351 r=010 cc=0.593 [ best cc: 0.634 0.634 ]
p=015 f=006 cc=0.331 r=010 cc=0.594 [ best cc: 0.634 0.634 ]
p=015 f=007 cc=0.340 r=010 cc=0.609 [ best cc: 0.634 0.634 ]
p=015 f=008 cc=0.360 r=010 cc=0.606 [ best cc: 0.634 0.634 ]
p=015 f=009 cc=0.340 r=010 cc=0.584 [ best cc: 0.634 0.634 ]
p=016 f=000 cc=0.370 r=010 cc=0.607 [ best cc: 0.634 0.634 ]
p=016 f=001 cc=0.363 r=010 cc=0.588 [ best cc: 0.634 0.634 ]
p=016 f=002 cc=0.359 r=010 cc=0.572 [ best cc: 0.634 0.634 ]
p=016 f=003 cc=0.334 r=010 cc=0.590 [ best cc: 0.634 0.634 ]
p=016 f=004 cc=0.358 r=010 cc=0.581 [ best cc: 0.634 0.634 ]
p=016 f=005 cc=0.330 r=010 cc=0.578 [ best cc: 0.634 0.634 ]
p=016 f=006 cc=0.345 r=010 cc=0.627 [ best cc: 0.634 0.634 ]
p=016 f=007 cc=0.324 r=010 cc=0.578 [ best cc: 0.634 0.634 ]
p=016 f=008 cc=0.356 r=010 cc=0.561 [ best cc: 0.634 0.634 ]
p=016 f=009 cc=0.283 r=010 cc=0.593 [ best cc: 0.634 0.634 ]
p=017 f=000 cc=0.318 r=010 cc=0.610 [ best cc: 0.634 0.634 ]
p=017 f=001 cc=0.396 r=010 cc=0.623 [ best cc: 0.634 0.634 ]
p=017 f=002 cc=0.346 r=010 cc=0.604 [ best cc: 0.634 0.634 ]
p=017 f=003 cc=0.363 r=010 cc=0.581 [ best cc: 0.634 0.634 ]
p=017 f=004 cc=0.308 r=010 cc=0.607 [ best cc: 0.634 0.634 ]
p=017 f=005 cc=0.351 r=010 cc=0.583 [ best cc: 0.634 0.634 ]
p=017 f=006 cc=0.379 r=010 cc=0.586 [ best cc: 0.634 0.634 ]
p=017 f=007 cc=0.333 r=010 cc=0.587 [ best cc: 0.634 0.634 ]
p=017 f=008 cc=0.457 r=010 cc=0.606 [ best cc: 0.634 0.634 ]
p=017 f=009 cc=0.361 r=010 cc=0.559 [ best cc: 0.634 0.634 ]
p=018 f=000 cc=0.363 r=010 cc=0.613 [ best cc: 0.634 0.634 ]
p=018 f=001 cc=0.367 r=010 cc=0.590 [ best cc: 0.634 0.634 ]
p=018 f=002 cc=0.393 r=010 cc=0.603 [ best cc: 0.634 0.634 ]
p=018 f=003 cc=0.418 r=010 cc=0.585 [ best cc: 0.634 0.634 ]
p=018 f=004 cc=0.321 r=010 cc=0.607 [ best cc: 0.634 0.634 ]
p=018 f=005 cc=0.318 r=010 cc=0.605 [ best cc: 0.634 0.634 ]
p=018 f=006 cc=0.367 r=010 cc=0.582 [ best cc: 0.634 0.634 ]
p=018 f=007 cc=0.366 r=010 cc=0.589 [ best cc: 0.634 0.634 ]
p=018 f=008 cc=0.407 r=010 cc=0.600 [ best cc: 0.634 0.634 ]
p=018 f=009 cc=0.375 r=010 cc=0.596 [ best cc: 0.634 0.634 ]
p=019 f=000 cc=0.338 r=010 cc=0.605 [ best cc: 0.634 0.634 ]
p=019 f=001 cc=0.343 r=010 cc=0.570 [ best cc: 0.634 0.634 ]
p=019 f=002 cc=0.333 r=010 cc=0.611 [ best cc: 0.634 0.634 ]
p=019 f=003 cc=0.340 r=010 cc=0.581 [ best cc: 0.634 0.634 ]
p=019 f=004 cc=0.360 r=010 cc=0.587 [ best cc: 0.634 0.634 ]
p=019 f=005 cc=0.357 r=010 cc=0.601 [ best cc: 0.634 0.634 ]
p=019 f=006 cc=0.330 r=010 cc=0.582 [ best cc: 0.634 0.634 ]
p=019 f=007 cc=0.337 r=010 cc=0.612 [ best cc: 0.634 0.634 ]
p=019 f=008 cc=0.337 r=010 cc=0.595 [ best cc: 0.634 0.634 ]
p=019 f=009 cc=0.369 r=010 cc=0.592 [ best cc: 0.634 0.634 ]
p=020 f=000 cc=0.350 r=010 cc=0.574 [ best cc: 0.634 0.634 ]
p=020 f=001 cc=0.375 r=010 cc=0.614 [ best cc: 0.634 0.634 ]
p=020 f=002 cc=0.363 r=010 cc=0.578 [ best cc: 0.634 0.634 ]
p=020 f=003 cc=0.372 r=010 cc=0.593 [ best cc: 0.634 0.634 ]
p=020 f=004 cc=0.343 r=010 cc=0.576 [ best cc: 0.634 0.634 ]
p=020 f=005 cc=0.350 r=010 cc=0.562 [ best cc: 0.634 0.634 ]
p=020 f=006 cc=0.351 r=010 cc=0.573 [ best cc: 0.634 0.634 ]
p=020 f=007 cc=0.364 r=010 cc=0.535 [ best cc: 0.634 0.634 ]
p=020 f=008 cc=0.378 r=010 cc=0.624 [ best cc: 0.634 0.634 ]
p=020 f=009 cc=0.306 r=010 cc=0.620 [ best cc: 0.634 0.634 ]
p=021 f=000 cc=0.332 r=010 cc=0.593 [ best cc: 0.634 0.634 ]
p=021 f=001 cc=0.369 r=010 cc=0.595 [ best cc: 0.634 0.634 ]
p=021 f=002 cc=0.320 r=010 cc=0.605 [ best cc: 0.634 0.634 ]
p=021 f=003 cc=0.331 r=010 cc=0.561 [ best cc: 0.634 0.634 ]
p=021 f=004 cc=0.347 r=010 cc=0.571 [ best cc: 0.634 0.634 ]
p=021 f=005 cc=0.347 r=010 cc=0.596 [ best cc: 0.634 0.634 ]
p=021 f=006 cc=0.366 r=010 cc=0.579 [ best cc: 0.634 0.634 ]
p=021 f=007 cc=0.360 r=010 cc=0.581 [ best cc: 0.634 0.634 ]
p=021 f=008 cc=0.374 r=010 cc=0.595 [ best cc: 0.634 0.634 ]
p=021 f=009 cc=0.327 r=010 cc=0.587 [ best cc: 0.634 0.634 ]
p=022 f=000 cc=0.350 r=010 cc=0.579 [ best cc: 0.634 0.634 ]
p=022 f=001 cc=0.381 r=010 cc=0.592 [ best cc: 0.634 0.634 ]
p=022 f=002 cc=0.352 r=010 cc=0.584 [ best cc: 0.634 0.634 ]
p=022 f=003 cc=0.356 r=010 cc=0.615 [ best cc: 0.634 0.634 ]
p=022 f=004 cc=0.324 r=010 cc=0.578 [ best cc: 0.634 0.634 ]
p=022 f=005 cc=0.376 r=010 cc=0.599 [ best cc: 0.634 0.634 ]
p=022 f=006 cc=0.420 r=010 cc=0.595 [ best cc: 0.634 0.634 ]
p=022 f=007 cc=0.378 r=010 cc=0.613 [ best cc: 0.634 0.634 ]
p=022 f=008 cc=0.361 r=010 cc=0.585 [ best cc: 0.634 0.634 ]
p=022 f=009 cc=0.334 r=010 cc=0.594 [ best cc: 0.634 0.634 ]
p=023 f=000 cc=0.416 r=010 cc=0.631 [ best cc: 0.634 0.634 ]
p=023 f=001 cc=0.402 r=010 cc=0.595 [ best cc: 0.634 0.634 ]
p=023 f=002 cc=0.392 r=010 cc=0.599 [ best cc: 0.634 0.634 ]
p=023 f=003 cc=0.390 r=010 cc=0.600 [ best cc: 0.634 0.634 ]
p=023 f=004 cc=0.405 r=010 cc=0.577 [ best cc: 0.634 0.634 ]
p=023 f=005 cc=0.333 r=010 cc=0.581 [ best cc: 0.634 0.634 ]
p=023 f=006 cc=0.334 r=010 cc=0.599 [ best cc: 0.634 0.634 ]
p=023 f=007 cc=0.401 r=010 cc=0.604 [ best cc: 0.634 0.634 ]
p=023 f=008 cc=0.392 r=010 cc=0.615 [ best cc: 0.634 0.634 ]
p=023 f=009 cc=0.350 r=010 cc=0.590 [ best cc: 0.634 0.634 ]
p=024 f=000 cc=0.343 r=010 cc=0.593 [ best cc: 0.634 0.634 ]
p=024 f=001 cc=0.350 r=010 cc=0.595 [ best cc: 0.634 0.634 ]
p=024 f=002 cc=0.330 r=010 cc=0.584 [ best cc: 0.634 0.634 ]
p=024 f=003 cc=0.361 r=010 cc=0.615 [ best cc: 0.634 0.634 ]
p=024 f=004 cc=0.362 r=010 cc=0.557 [ best cc: 0.634 0.634 ]
p=024 f=005 cc=0.352 r=010 cc=0.581 [ best cc: 0.634 0.634 ]
p=024 f=006 cc=0.326 r=010 cc=0.629 [ best cc: 0.634 0.634 ]
p=024 f=007 cc=0.350 r=010 cc=0.545 [ best cc: 0.634 0.634 ]
p=024 f=008 cc=0.435 r=010 cc=0.581 [ best cc: 0.634 0.634 ]
p=024 f=009 cc=0.369 r=010 cc=0.616 [ best cc: 0.634 0.634 ]
p=025 f=000 cc=0.367 r=010 cc=0.607 [ best cc: 0.634 0.634 ]
p=025 f=001 cc=0.369 r=010 cc=0.599 [ best cc: 0.634 0.634 ]
p=025 f=002 cc=0.372 r=010 cc=0.573 [ best cc: 0.634 0.634 ]
p=025 f=003 cc=0.348 r=010 cc=0.607 [ best cc: 0.634 0.634 ]
p=025 f=004 cc=0.348 r=010 cc=0.596 [ best cc: 0.634 0.634 ]
p=025 f=005 cc=0.358 r=010 cc=0.599 [ best cc: 0.634 0.634 ]
p=025 f=006 cc=0.376 r=010 cc=0.609 [ best cc: 0.634 0.634 ]
p=025 f=007 cc=0.357 r=010 cc=0.602 [ best cc: 0.634 0.634 ]
p=025 f=008 cc=0.346 r=010 cc=0.594 [ best cc: 0.634 0.634 ]
p=025 f=009 cc=0.356 r=010 cc=0.611 [ best cc: 0.634 0.634 ]
p=026 f=000 cc=0.358 r=010 cc=0.602 [ best cc: 0.634 0.634 ]
p=026 f=001 cc=0.348 r=010 cc=0.588 [ best cc: 0.634 0.634 ]
p=026 f=002 cc=0.362 r=010 cc=0.629 [ best cc: 0.634 0.634 ]
p=026 f=003 cc=0.369 r=010 cc=0.610 [ best cc: 0.634 0.634 ]
p=026 f=004 cc=0.348 r=010 cc=0.604 [ best cc: 0.634 0.634 ]
p=026 f=005 cc=0.361 r=010 cc=0.602 [ best cc: 0.634 0.634 ]
p=026 f=006 cc=0.363 r=010 cc=0.576 [ best cc: 0.634 0.634 ]
p=026 f=007 cc=0.335 r=010 cc=0.580 [ best cc: 0.634 0.634 ]
p=026 f=008 cc=0.344 r=010 cc=0.580 [ best cc: 0.634 0.634 ]
p=026 f=009 cc=0.329 r=010 cc=0.632 [ best cc: 0.634 0.634 ]
p=027 f=000 cc=0.359 r=010 cc=0.583 [ best cc: 0.634 0.634 ]
p=027 f=001 cc=0.352 r=010 cc=0.574 [ best cc: 0.634 0.634 ]
p=027 f=002 cc=0.373 r=010 cc=0.590 [ best cc: 0.634 0.634 ]
p=027 f=003 cc=0.366 r=010 cc=0.569 [ best cc: 0.634 0.634 ]
p=027 f=004 cc=0.304 r=010 cc=0.595 [ best cc: 0.634 0.634 ]
p=027 f=005 cc=0.314 r=010 cc=0.587 [ best cc: 0.634 0.634 ]
p=027 f=006 cc=0.315 r=010 cc=0.600 [ best cc: 0.634 0.634 ]
p=027 f=007 cc=0.332 r=010 cc=0.620 [ best cc: 0.634 0.634 ]
p=027 f=008 cc=0.314 r=010 cc=0.580 [ best cc: 0.634 0.634 ]
p=027 f=009 cc=0.333 r=010 cc=0.565 [ best cc: 0.634 0.634 ]
p=028 f=000 cc=0.353 r=010 cc=0.588 [ best cc: 0.634 0.634 ]
p=028 f=001 cc=0.327 r=010 cc=0.613 [ best cc: 0.634 0.634 ]
p=028 f=002 cc=0.327 r=010 cc=0.590 [ best cc: 0.634 0.634 ]
p=028 f=003 cc=0.321 r=010 cc=0.591 [ best cc: 0.634 0.634 ]
p=028 f=004 cc=0.316 r=010 cc=0.576 [ best cc: 0.634 0.634 ]
p=028 f=005 cc=0.352 r=010 cc=0.608 [ best cc: 0.634 0.634 ]
p=028 f=006 cc=0.344 r=010 cc=0.587 [ best cc: 0.634 0.634 ]
p=028 f=007 cc=0.332 r=010 cc=0.618 [ best cc: 0.634 0.634 ]
p=028 f=008 cc=0.285 r=010 cc=0.612 [ best cc: 0.634 0.634 ]
p=028 f=009 cc=0.319 r=010 cc=0.621 [ best cc: 0.634 0.634 ]
p=029 f=000 cc=0.358 r=010 cc=0.612 [ best cc: 0.634 0.634 ]
p=029 f=001 cc=0.345 r=010 cc=0.626 [ best cc: 0.634 0.634 ]
p=029 f=002 cc=0.439 r=010 cc=0.592 [ best cc: 0.634 0.634 ]
p=029 f=003 cc=0.451 r=010 cc=0.574 [ best cc: 0.634 0.634 ]
p=029 f=004 cc=0.343 r=010 cc=0.571 [ best cc: 0.634 0.634 ]
p=029 f=005 cc=0.360 r=010 cc=0.607 [ best cc: 0.634 0.634 ]
p=029 f=006 cc=0.375 r=010 cc=0.588 [ best cc: 0.634 0.634 ]
p=029 f=007 cc=0.373 r=010 cc=0.587 [ best cc: 0.634 0.634 ]
p=029 f=008 cc=0.396 r=010 cc=0.611 [ best cc: 0.634 0.634 ]
p=029 f=009 cc=0.452 r=010 cc=0.584 [ best cc: 0.634 0.634 ]
p=030 f=000 cc=0.312 r=010 cc=0.578 [ best cc: 0.634 0.634 ]
p=030 f=001 cc=0.323 r=010 cc=0.576 [ best cc: 0.634 0.634 ]
p=030 f=002 cc=0.318 r=010 cc=0.606 [ best cc: 0.634 0.634 ]
p=030 f=003 cc=0.343 r=010 cc=0.599 [ best cc: 0.634 0.634 ]
p=030 f=004 cc=0.324 r=010 cc=0.614 [ best cc: 0.634 0.634 ]
p=030 f=005 cc=0.297 r=010 cc=0.606 [ best cc: 0.634 0.634 ]
p=030 f=006 cc=0.303 r=010 cc=0.601 [ best cc: 0.634 0.634 ]
p=030 f=007 cc=0.313 r=010 cc=0.561 [ best cc: 0.634 0.634 ]
p=030 f=008 cc=0.376 r=010 cc=0.592 [ best cc: 0.634 0.634 ]
p=030 f=009 cc=0.380 r=010 cc=0.589 [ best cc: 0.634 0.634 ]

Top 2 correlations:
p=012 f=003 cc=0.376 r=010 cc=0.634
p=013 f=003 cc=0.370 r=010 cc=0.634
Match summary:
  Operator:
       rotation: {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}}
    translation: {0, 0, 0}
  rms coordinate differences: 1.87
  Pairs: 110
    site002 site066 2.673
    site003 site060 0.323
    site004 site004 0.067
    site005 site093 1.484
    site006 site061 2.182
    site008 site020 1.709
    site009 site021 1.736
    site010 site101 0.750
    site011 site108 2.365
    site016 site122 1.331
    site017 site063 0.901
    site018 site125 1.110
    site019 site076 2.212
    site020 site043 2.180
    site021 site030 1.452
    site022 site116 2.750
    site023 site098 2.410
    site024 site008 0.652
    site025 site019 2.977
    site026 site117 1.269
    site027 site003 1.658
    site028 site088 1.185
    site029 site039 1.847
    site030 site092 2.679
    site032 site081 2.121
    site033 site079 2.106
    site034 site023 2.085
    site035 site069 2.090
    site036 site015 2.011
    site037 site001 1.925
    site038 site022 3.136
    site039 site017 2.181
    site040 site012 1.525
    site041 site029 2.504
    site042 site049 1.521
    site043 site016 1.232
    site044 site027 1.777
    site045 site126 1.736
    site047 site037 1.618
    site048 site065 1.433
    site050 site041 1.317
    site051 site128 1.182
    site052 site058 1.295
    site053 site099 1.873
    site054 site103 2.223
    site055 site120 0.394
    site056 site055 1.017
    site057 site113 2.164
    site058 site104 3.257
    site059 site033 1.439
    site061 site057 2.177
    site062 site062 2.278
    site063 site078 2.338
    site064 site077 1.392
    site065 site068 1.431
    site067 site024 0.684
    site068 site070 0.323
    site069 site025 1.352
    site070 site090 1.780
    site071 site054 1.927
    site072 site013 0.805
    site073 site073 0.415
    site076 site042 0.629
    site077 site009 1.859
    site078 site028 1.897
    site080 site036 1.282
    site081 site050 2.683
    site082 site091 2.645
    site083 site119 0.379
    site085 site052 0.940
    site086 site112 0.575
    site087 site095 1.492
    site088 site018 2.528
    site089 site123 0.474
    site090 site121 2.214
    site091 site080 1.988
    site092 site127 2.919
    site093 site071 0.994
    site095 site014 2.053
    site096 site083 1.405
    site097 site111 0.917
    site098 site100 1.919
    site099 site109 1.491
    site100 site082 2.192
    site101 site075 1.282
    site102 site059 1.670
    site103 site074 2.275
    site104 site085 1.473
    site105 site115 1.972
    site107 site032 2.231
    site108 site106 0.933
    site109 site044 2.676
    site110 site105 2.381
    site111 site002 1.577
    site112 site006 2.606
    site113 site096 3.087
    site114 site053 2.706
    site118 site047 2.180
    site119 site086 0.960
    site120 site048 2.020
    site121 site031 3.126
    site122 site072 2.215
    site123 site011 2.395
    site124 site084 1.675
    site125 site038 2.281
    site126 site046 1.733
    site128 site124 0.000
    site129 site056 1.020
    site130 site035 2.307
    site132 site007 1.387
  Singles model 1: 22
    site001   site007   site012   site013   site014
  Singles model 2: 19
    site005   site010   site026   site034   site040

Correlation coefficient for consensus model (110 sites): 0.618

time_log: label: n accumulation delta average
time_log: patterson_peaks: 1 31.74 31.7 31.7
time_log: two_site_search: 31 759.04 25.7 24.5
time_log: extrapolation_scan: 310 8185.11 26.3 26.4
time_log: p1_recycling: 310 12688.31 40.7 40.9
time_log: p1_recycling q_large_calc: 3100 292.04 0.1 0.0942
time_log: p1_recycling tangent_refinement: 0 0.00 0 0
time_log: p1_recycling squaring: 3100 75.69 0.03 0.0244
time_log: p1_recycling fft_map: 3100 213.59 0.07 0.0689
time_log: p1_recycling peak_search: 3100 3850.54 1.18 1.24
time_log: p1_recycling random_omit: 3100 592.40 0.19 0.191
time_log: p1_recycling recover_origin: 310 7627.48 24.5 24.6
time_log: p1_recycling combine_duplicates: 310 18.19 0.06 0.0587
time_log: p1_recycling total: 310 12687.68 40.7 40.9
p1_recycling time unaccounted for: 17.75
time_log: compute_correlation: 621 33.51 0.06 0.054
time_log: q_large_calc: 2790 137.07 0.04 0.0491
time_log: tangent_refinement: 0 0.00 0 0
time_log: squaring: 2790 66.01 0.02 0.0237
time_log: fft_map: 3100 214.75 0.08 0.0693
time_log: peak_search: 3100 1518.30 0.47 0.49
time_log: random_omit: 2790 134.96 0.05 0.0484
time_log: minimization: 0 0.00 0 0
time_log: euclidean_model_matching: 11 5847.04 504 532
time_log: hyss total: 1 29815.76 2.98e+04 2.98e+04
time unaccounted for: 199.92

Storing all substructures found: I432_hyss_models.pickle

Storing consensus model: I432_hyss_consensus_model.pickle

Writing consensus model as PDB file: I432_hyss_consensus_model.pdb

Writing consensus model as CNS SDB file: I432_hyss_consensus_model.sdb

Writing consensus model as SOLVE xyz records: I432_hyss_consensus_model.xyz
The fractional coordinates may also be useful in other programs.

If HySS was helpful please cite:
  Acta Cryst. 2003, D59, 1966-1973
  http://cci.lbl.gov/publications/download/ba5048_reprint.pdf
See also:
  http://www.phenix-online.org/download/documentation/cci_apps/hyss/
For help enter:
  phenix.hyss --help

Send bug reports to: bugs@phenix-online.org
For help write to: help@phenix-online.org

Time per interpreted Python bytecode instruction: 5.656 micro seconds
Total CPU time: 8.29 hours