[phenixbb] error message on dev-1145 during den session

[fulvio saccoccia]

Dear Phenix users,
	
	here you have an error occurred during a DEN refinement cycle on a
twinned structure. Please, help me in order to overcome the problem.

This is the command line I used to run phenix: 
phenix.den_refine data.mtz model.pdb twin_law=h,-k,-l
output.prefix=DEN10 --overwrite main.ncs=true set_b_iso=50
convert_to_isotropic=true xray_data.high_resolution=3.6 nproc=4
secondary_structure_restraints=true optimize_xyz_weight=true
optimize_adp_weight=true reference_model.file=3ZVJ-coot1.pdb
use_geometry_restraints=true den.params fix_rotamers=true 

den.params is attached

I was running phenix dev-1145 on a 64bit Debian machine.

This is the error message:

Running DEN torsion optimization on 4 processors...
Running torsion simulated annealing
  ...trying gamma 0.0, weight 100.0
  ...trying gamma 0.2, weight 100.0
  ...trying gamma 0.0, weight 300.0
  ...trying gamma 0.2, weight 300.0
Traceback (most recent call last):
  File
"/usr/local/phenix-dev-1145/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/den_refine.py", line 21, in <module>
    den_refine.run(command_name="phenix.den_refine", args=sys.argv[1:])
  File
"/usr/local/phenix-dev-1145/phenix/phenix/refinement/den_refine.py",
line 113, in run
    customized_master_params=master_phil)
  File
"/usr/local/phenix-dev-1145/phenix/phenix/refinement/command_line.py",
line 146, in run
    call_back_handler=call_back_handler)
  File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/driver.py",
line 1532, in run
    ncs_manager             = self.ncs_manager)
  File
"/usr/local/phenix-dev-1145/phenix/phenix/refinement/strategies.py",
line 830, in refinement_machine
    log=log)
  File
"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line
88, in __init__
    "serious error; please contact bugs at phenix-online.org.") % so)
RuntimeError: DEN weight optimization failed:
DEN cycle 1
rfree at start of SA cycle: 0.4642
k_rep = 1.00
tardy_tree summary:
  number of vertices: 16570
  number of edges: 16855
  find cluster loops: 0 repeats
  number of fixed vertex lists: 0
  number of fixed vertices: 0
  number of clusters: 7857
  merge clusters with multiple connections: 1 pass
  number of hinge edges: 7857
  number of loop edges: 0
  number of loop edge bendings: 0
  number of fixed hinges: 0

CAUGHT EXCEPTION: (argument #0)
ARGUMENT LEADING TO EXCEPTION: (0.0, 100.0)
Traceback (most recent call last):
  File "/usr/local/phenix-dev-1145/cctbx_project/libtbx/easy_mp.py",
line 155, in __call__
    result = O.func(arg)
  File
"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line
227, in try_den_weight_torsion
    call_back_after_step=False)
  File
"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py",
line 228, in run
    reduced_geo_manager=reduced_geo_manager)
  File
"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py",
line 86, in __init__
    O.weights = target_weights.xyz_weights_result
AttributeError: 'NoneType' object has no attribute 'xyz_weights_result'

This is a serious error; please contact bugs at phenix-online.org.

Thanks in advance

Fulvio Saccoccia
PhD student
Dept. of Biochemical Sciences
Sapienza University of Rome
+390649910556

-------------- next part --------------
refinement {
  main {
    nproc = 4
  }
  refine {
    strategy = individual_sites rigid_body individual_adp \
    group_adp tls occupancies group_anomalous *den
  }
  den {
    reference_file = none
    gamma = 0.0
    kappa = 0.1
    weight = 300
    sigma = 0.44
    optimize = true
    opt_gamma_values = 0 0.2
    opt_weight_values = 100 300
    num_cycles = 2
    kappa_burn_in_cycles = 2
    bulk_solvent_and_scale = True
    refine_adp = False
    final_refinement_cycle = False
    verbose = True
    annealing_type = *torsion cartesian
    output_kinemage = False
    restraint_network {
      lower_distance_cutoff = 5
      upper_distance_cutoff = 20
      sequence_separation_low = 0
      sequence_separation_limit = 10
      exclude_hydrogens = True
      ndistance_ratio = 1
      export_den_pairs = False
      den_network_file = None
    }
  }
  tardy {
    mode = every_macro_cycle second_and_before_last *once first first_half
    start_temperature_kelvin = 3300
    final_temperature_kelvin = 300
    number_of_cooling_steps = 1440
    number_of_time_steps = 1
    time_step_pico_seconds = 0.001
    prolsq_repulsion_function_changes {
      c_rep = 100
      k_rep = 1
    }
  }
  simulated_annealing {
    start_temperature = 3300
    final_temperature = 300
    cool_rate = 50
    number_of_steps = 24
    time_step = 0.001
  }
}