Starting phenix.real_space_refine
on Thu Nov 14 02:13:34 2024 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9for_50628/11_2024/9for_50628.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9for_50628/11_2024/9for_50628.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9for_50628/11_2024/9for_50628.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9for_50628/11_2024/9for_50628.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9for_50628/11_2024/9for_50628.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9for_50628/11_2024/9for_50628.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    2060      2.51       5
     N     615      2.21       5
     O     680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 3405
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 416
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 1, 'TRANS': 60}
    Chain: "B"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 265
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 1, 'TRANS': 34}
  Restraints were copied for chains:
    C, E, G, o, D, F, H, p
  Time building chain proxies: 1.85, per 1000 atoms: 0.54
  Number of scatterers: 3405
  At special positions: 0
  Unit cell: (67.94, 84.28, 45.58, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O     680      8.00
     N     615      7.00
     C    2060      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 506.0 milliseconds
  

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  770

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 46.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 293
      removed outlier: 6.786A  pdb=" N   PHE A 289 " --> pdb=" O   GLY C 290 " (cutoff:3.500A)
      removed outlier: 8.490A  pdb=" N   SER C 292 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ASN A 291 " --> pdb=" O   SER C 292 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   PHE o 289 " --> pdb=" O   GLY E 290 " (cutoff:3.500A)
      removed outlier: 8.490A  pdb=" N   SER E 292 " --> pdb=" O   PHE o 289 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ASN o 291 " --> pdb=" O   SER E 292 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   PHE E 289 " --> pdb=" O   GLY G 290 " (cutoff:3.500A)
      removed outlier: 8.491A  pdb=" N   SER G 292 " --> pdb=" O   PHE E 289 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ASN E 291 " --> pdb=" O   SER G 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 297 through 298
      removed outlier: 6.725A  pdb=" N   ALA o 297 " --> pdb=" O   GLY C 298 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 312
      removed outlier: 6.395A  pdb=" N   MET o 311 " --> pdb=" O   ASN C 312 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 318
      removed outlier: 6.687A  pdb=" N   SER o 317 " --> pdb=" O   ILE C 318 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 338
      removed outlier: 6.709A  pdb=" N   MET A 322 " --> pdb=" O   MET C 323 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   ALA C 325 " --> pdb=" O   MET A 322 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ALA A 324 " --> pdb=" O   ALA C 325 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   GLN C 327 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
      removed outlier: 9.533A  pdb=" N   ALA A 326 " --> pdb=" O   GLN C 327 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   ALA C 329 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
      removed outlier: 9.307A  pdb=" N   ALA A 328 " --> pdb=" O   ALA C 329 " (cutoff:3.500A)
      removed outlier: 10.709A  pdb=" N   GLN C 331 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   LEU A 330 " --> pdb=" O   GLN C 331 " (cutoff:3.500A)
      removed outlier: 10.316A  pdb=" N   SER C 333 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      removed outlier: 9.097A  pdb=" N   SER A 332 " --> pdb=" O   SER C 333 " (cutoff:3.500A)
      removed outlier: 10.712A  pdb=" N   GLY C 335 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   TRP A 334 " --> pdb=" O   GLY C 335 " (cutoff:3.500A)
      removed outlier: 9.291A  pdb=" N   MET C 337 " --> pdb=" O   TRP A 334 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   MET A 336 " --> pdb=" O   MET C 337 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN o 327 " --> pdb=" O   ALA C 326 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   ALA C 328 " --> pdb=" O   GLN o 327 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ALA o 329 " --> pdb=" O   ALA C 328 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   LEU C 330 " --> pdb=" O   ALA o 329 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   GLN o 331 " --> pdb=" O   LEU C 330 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   SER C 332 " --> pdb=" O   GLN o 331 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   SER o 333 " --> pdb=" O   SER C 332 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   TRP C 334 " --> pdb=" O   SER o 333 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   GLY o 335 " --> pdb=" O   TRP C 334 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   MET o 322 " --> pdb=" O   MET E 323 " (cutoff:3.500A)
      removed outlier: 8.270A  pdb=" N   ALA E 325 " --> pdb=" O   MET o 322 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ALA o 324 " --> pdb=" O   ALA E 325 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   GLN E 327 " --> pdb=" O   ALA o 324 " (cutoff:3.500A)
      removed outlier: 9.533A  pdb=" N   ALA o 326 " --> pdb=" O   GLN E 327 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   ALA E 329 " --> pdb=" O   ALA o 326 " (cutoff:3.500A)
      removed outlier: 9.307A  pdb=" N   ALA o 328 " --> pdb=" O   ALA E 329 " (cutoff:3.500A)
      removed outlier: 10.709A  pdb=" N   GLN E 331 " --> pdb=" O   ALA o 328 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   LEU o 330 " --> pdb=" O   GLN E 331 " (cutoff:3.500A)
      removed outlier: 10.316A  pdb=" N   SER E 333 " --> pdb=" O   LEU o 330 " (cutoff:3.500A)
      removed outlier: 9.097A  pdb=" N   SER o 332 " --> pdb=" O   SER E 333 " (cutoff:3.500A)
      removed outlier: 10.712A  pdb=" N   GLY E 335 " --> pdb=" O   SER o 332 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   TRP o 334 " --> pdb=" O   GLY E 335 " (cutoff:3.500A)
      removed outlier: 9.291A  pdb=" N   MET E 337 " --> pdb=" O   TRP o 334 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   MET o 336 " --> pdb=" O   MET E 337 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   MET E 322 " --> pdb=" O   MET G 323 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   ALA G 325 " --> pdb=" O   MET E 322 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ALA E 324 " --> pdb=" O   ALA G 325 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   GLN G 327 " --> pdb=" O   ALA E 324 " (cutoff:3.500A)
      removed outlier: 9.534A  pdb=" N   ALA E 326 " --> pdb=" O   GLN G 327 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   ALA G 329 " --> pdb=" O   ALA E 326 " (cutoff:3.500A)
      removed outlier: 9.307A  pdb=" N   ALA E 328 " --> pdb=" O   ALA G 329 " (cutoff:3.500A)
      removed outlier: 10.709A  pdb=" N   GLN G 331 " --> pdb=" O   ALA E 328 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   LEU E 330 " --> pdb=" O   GLN G 331 " (cutoff:3.500A)
      removed outlier: 10.315A  pdb=" N   SER G 333 " --> pdb=" O   LEU E 330 " (cutoff:3.500A)
      removed outlier: 9.097A  pdb=" N   SER E 332 " --> pdb=" O   SER G 333 " (cutoff:3.500A)
      removed outlier: 10.711A  pdb=" N   GLY G 335 " --> pdb=" O   SER E 332 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   TRP E 334 " --> pdb=" O   GLY G 335 " (cutoff:3.500A)
      removed outlier: 9.291A  pdb=" N   MET G 337 " --> pdb=" O   TRP E 334 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   MET E 336 " --> pdb=" O   MET G 337 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 344
      removed outlier: 6.618A  pdb=" N   SER A 342 " --> pdb=" O   GLN C 343 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   SER o 342 " --> pdb=" O   GLN E 343 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   SER E 342 " --> pdb=" O   GLN G 343 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 40 through 50
      removed outlier: 9.431A  pdb=" N   ASN B  41 " --> pdb=" O   VAL D  42 " (cutoff:3.500A)
      removed outlier: 10.724A  pdb=" N   THR D  44 " --> pdb=" O   ASN B  41 " (cutoff:3.500A)
      removed outlier: 9.075A  pdb=" N   ALA B  43 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 10.323A  pdb=" N   ALA D  46 " --> pdb=" O   ALA B  43 " (cutoff:3.500A)
      removed outlier: 9.154A  pdb=" N   TYR B  45 " --> pdb=" O   ALA D  46 " (cutoff:3.500A)
      removed outlier: 10.784A  pdb=" N   GLN D  48 " --> pdb=" O   TYR B  45 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   GLY B  47 " --> pdb=" O   GLN D  48 " (cutoff:3.500A)
      removed outlier: 9.299A  pdb=" N   ASN D  50 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   PHE B  49 " --> pdb=" O   ASN D  50 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ASN D  41 " --> pdb=" O   ASP p  40 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   VAL p  42 " --> pdb=" O   ASN D  41 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   ALA D  43 " --> pdb=" O   VAL p  42 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   THR p  44 " --> pdb=" O   ALA D  43 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   TYR D  45 " --> pdb=" O   THR p  44 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   ALA p  46 " --> pdb=" O   TYR D  45 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   GLY D  47 " --> pdb=" O   ALA p  46 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   GLN p  48 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 9.431A  pdb=" N   ASN p  41 " --> pdb=" O   VAL F  42 " (cutoff:3.500A)
      removed outlier: 10.724A  pdb=" N   THR F  44 " --> pdb=" O   ASN p  41 " (cutoff:3.500A)
      removed outlier: 9.075A  pdb=" N   ALA p  43 " --> pdb=" O   THR F  44 " (cutoff:3.500A)
      removed outlier: 10.323A  pdb=" N   ALA F  46 " --> pdb=" O   ALA p  43 " (cutoff:3.500A)
      removed outlier: 9.154A  pdb=" N   TYR p  45 " --> pdb=" O   ALA F  46 " (cutoff:3.500A)
      removed outlier: 10.785A  pdb=" N   GLN F  48 " --> pdb=" O   TYR p  45 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   GLY p  47 " --> pdb=" O   GLN F  48 " (cutoff:3.500A)
      removed outlier: 9.299A  pdb=" N   ASN F  50 " --> pdb=" O   GLY p  47 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   PHE p  49 " --> pdb=" O   ASN F  50 " (cutoff:3.500A)
      removed outlier: 9.430A  pdb=" N   ASN F  41 " --> pdb=" O   VAL H  42 " (cutoff:3.500A)
      removed outlier: 10.724A  pdb=" N   THR H  44 " --> pdb=" O   ASN F  41 " (cutoff:3.500A)
      removed outlier: 9.075A  pdb=" N   ALA F  43 " --> pdb=" O   THR H  44 " (cutoff:3.500A)
      removed outlier: 10.324A  pdb=" N   ALA H  46 " --> pdb=" O   ALA F  43 " (cutoff:3.500A)
      removed outlier: 9.155A  pdb=" N   TYR F  45 " --> pdb=" O   ALA H  46 " (cutoff:3.500A)
      removed outlier: 10.784A  pdb=" N   GLN H  48 " --> pdb=" O   TYR F  45 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   GLY F  47 " --> pdb=" O   GLN H  48 " (cutoff:3.500A)
      removed outlier: 9.299A  pdb=" N   ASN H  50 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   PHE F  49 " --> pdb=" O   ASN H  50 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 57 through 65
      removed outlier: 6.813A  pdb=" N   MET p  57 " --> pdb=" O   ALA D  58 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   ASN D  60 " --> pdb=" O   MET p  57 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ALA p  59 " --> pdb=" O   ASN D  60 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   SER D  62 " --> pdb=" O   ALA p  59 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   MET p  61 " --> pdb=" O   SER D  62 " (cutoff:3.500A)
      removed outlier: 8.357A  pdb=" N   THR D  64 " --> pdb=" O   MET p  61 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   GLY p  63 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 73
      removed outlier: 6.851A  pdb=" N   ASN B  72 " --> pdb=" O   LEU D  73 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASN p  72 " --> pdb=" O   LEU F  73 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASN F  72 " --> pdb=" O   LEU H  73 " (cutoff:3.500A)

    51 hydrogen bonds defined for protein.
    153 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.79

  Time building geometry restraints manager: 0.79 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 824
        1.33 -     1.46: 899
        1.46 -     1.58: 1632
        1.58 -     1.70: 0
        1.70 -     1.82: 100
  Bond restraints: 3455
  Sorted by residual:
  bond pdb=" CA  SER F  55 "
       pdb=" CB  SER F  55 "
    ideal  model  delta    sigma   weight residual
    1.536  1.472  0.064 1.58e-02 4.01e+03 1.66e+01
  bond pdb=" CA  SER H  55 "
       pdb=" CB  SER H  55 "
    ideal  model  delta    sigma   weight residual
    1.536  1.472  0.064 1.58e-02 4.01e+03 1.64e+01
  bond pdb=" CA  SER p  55 "
       pdb=" CB  SER p  55 "
    ideal  model  delta    sigma   weight residual
    1.536  1.473  0.064 1.58e-02 4.01e+03 1.63e+01
  bond pdb=" CA  SER D  55 "
       pdb=" CB  SER D  55 "
    ideal  model  delta    sigma   weight residual
    1.536  1.473  0.063 1.58e-02 4.01e+03 1.61e+01
  bond pdb=" CA  SER B  55 "
       pdb=" CB  SER B  55 "
    ideal  model  delta    sigma   weight residual
    1.536  1.473  0.063 1.58e-02 4.01e+03 1.61e+01
  ... (remaining 3450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 3688
        2.42 -     4.84: 812
        4.84 -     7.26: 80
        7.26 -     9.68: 16
        9.68 -    12.10: 24
  Bond angle restraints: 4620
  Sorted by residual:
  angle pdb=" C   ASN C 319 "
        pdb=" CA  ASN C 319 "
        pdb=" CB  ASN C 319 "
      ideal   model   delta    sigma   weight residual
     110.87  100.79   10.08 1.39e+00 5.18e-01 5.26e+01
  angle pdb=" C   ASN E 319 "
        pdb=" CA  ASN E 319 "
        pdb=" CB  ASN E 319 "
      ideal   model   delta    sigma   weight residual
     110.87  100.80   10.07 1.39e+00 5.18e-01 5.25e+01
  angle pdb=" C   ASN o 319 "
        pdb=" CA  ASN o 319 "
        pdb=" CB  ASN o 319 "
      ideal   model   delta    sigma   weight residual
     110.87  100.80   10.07 1.39e+00 5.18e-01 5.24e+01
  angle pdb=" C   ASN G 319 "
        pdb=" CA  ASN G 319 "
        pdb=" CB  ASN G 319 "
      ideal   model   delta    sigma   weight residual
     110.87  100.81   10.06 1.39e+00 5.18e-01 5.24e+01
  angle pdb=" C   ASN A 319 "
        pdb=" CA  ASN A 319 "
        pdb=" CB  ASN A 319 "
      ideal   model   delta    sigma   weight residual
     110.87  100.82   10.05 1.39e+00 5.18e-01 5.23e+01
  ... (remaining 4615 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.16: 1563
       10.16 -    20.32: 257
       20.32 -    30.47: 105
       30.47 -    40.63: 5
       40.63 -    50.79: 25
  Dihedral angle restraints: 1955
    sinusoidal: 690
      harmonic: 1265
  Sorted by residual:
  dihedral pdb=" CA  GLY D  67 "
           pdb=" C   GLY D  67 "
           pdb=" N   ALA D  68 "
           pdb=" CA  ALA D  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.43   29.57     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  GLY F  67 "
           pdb=" C   GLY F  67 "
           pdb=" N   ALA F  68 "
           pdb=" CA  ALA F  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.45   29.55     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  GLY p  67 "
           pdb=" C   GLY p  67 "
           pdb=" N   ALA p  68 "
           pdb=" CA  ALA p  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.47   29.53     0      5.00e+00 4.00e-02 3.49e+01
  ... (remaining 1952 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.044: 159
       0.044 -    0.088: 116
       0.088 -    0.132: 75
       0.132 -    0.175: 45
       0.175 -    0.219: 40
  Chirality restraints: 435
  Sorted by residual:
  chirality pdb=" CA  PHE C 289 "
            pdb=" N   PHE C 289 "
            pdb=" C   PHE C 289 "
            pdb=" CB  PHE C 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  PHE A 289 "
            pdb=" N   PHE A 289 "
            pdb=" C   PHE A 289 "
            pdb=" CB  PHE A 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  PHE G 289 "
            pdb=" N   PHE G 289 "
            pdb=" C   PHE G 289 "
            pdb=" CB  PHE G 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 432 not shown)

  Planarity restraints: 655
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C 322 "    0.016 2.00e-02 2.50e+03   3.20e-02 1.02e+01
        pdb=" C   MET C 322 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   MET C 322 "    0.021 2.00e-02 2.50e+03
        pdb=" N   MET C 323 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET o 322 "    0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   MET o 322 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   MET o 322 "    0.021 2.00e-02 2.50e+03
        pdb=" N   MET o 323 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET G 322 "    0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   MET G 322 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   MET G 322 "    0.021 2.00e-02 2.50e+03
        pdb=" N   MET G 323 "    0.018 2.00e-02 2.50e+03
  ... (remaining 652 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 1577
        2.98 -     3.46: 2640
        3.46 -     3.94: 5136
        3.94 -     4.42: 5859
        4.42 -     4.90: 9934
  Nonbonded interactions: 25146
  Sorted by model distance:
  nonbonded pdb=" O   ASN E 319 "
            pdb=" CB  ASN E 319 "
     model   vdw
     2.496 2.752
  nonbonded pdb=" O   ASN A 319 "
            pdb=" CB  ASN A 319 "
     model   vdw
     2.496 2.752
  nonbonded pdb=" O   ASN o 319 "
            pdb=" CB  ASN o 319 "
     model   vdw
     2.496 2.752
  nonbonded pdb=" O   ASN C 319 "
            pdb=" CB  ASN C 319 "
     model   vdw
     2.496 2.752
  nonbonded pdb=" O   ASN G 319 "
            pdb=" CB  ASN G 319 "
     model   vdw
     2.496 2.752
  ... (remaining 25141 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'o'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'p'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.620
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.064   3455  Z= 0.838
  Angle     :  2.105  12.104   4620  Z= 1.345
  Chirality :  0.097   0.219    435
  Planarity :  0.010   0.032    655
  Dihedral  : 12.860  50.790   1185
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  :  7.45 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  :  4.76 %
    Favored  : 92.06 %
  Cbeta Deviations :  1.30 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.01 (0.20), residues: 470
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.81 (0.15), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.013   TRP G 334 
 PHE   0.022   0.008   PHE D  49 
 TYR   0.024   0.005   TYR D  45 
 ARG   0.003   0.001   ARG A 293 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.354 
Fit side-chains
REVERT: o  345 ASN cc_start: 0.8365 (m-40) cc_final: 0.8115 (m110)
REVERT: A  323 MET cc_start: 0.9162 (ttm) cc_final: 0.8899 (ttp)
REVERT: D   48 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8342 (tt0)
REVERT: F   52 ASP cc_start: 0.8707 (m-30) cc_final: 0.8506 (m-30)
REVERT: G  293 ARG cc_start: 0.7726 (mtt-85) cc_final: 0.7208 (mtp180)
REVERT: H   60 ASN cc_start: 0.9044 (m-40) cc_final: 0.8835 (m110)
REVERT: H   61 MET cc_start: 0.8935 (mtp) cc_final: 0.8665 (mtp)
  outliers start: 10
  outliers final: 0
  residues processed: 131
  average time/residue: 0.8957
  time to fit residues: 121.3848
Evaluate side-chains
  112 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    8.9990
   overall best weight:    3.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
o 291 ASN
o 319 ASN
A 291 ASN
A 306 ASN
A 319 ASN
B  60 ASN
C 291 ASN
C 319 ASN
C 345 ASN
D  60 ASN
E 302 ASN
E 319 ASN
F  41 ASN
F  60 ASN
G 291 ASN
G 319 ASN
H  72 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3455  Z= 0.221
  Angle     :  0.871   7.886   4620  Z= 0.456
  Chirality :  0.048   0.195    435
  Planarity :  0.004   0.032    655
  Dihedral  :  7.141  40.963    503
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 0.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  :  9.84 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.04 (0.19), residues: 470
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.14), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP G 334 
 PHE   0.011   0.002   PHE E 289 
 TYR   0.007   0.001   TYR B  45 
 ARG   0.001   0.000   ARG G 293 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.346 
Fit side-chains
REVERT: C  292 SER cc_start: 0.8945 (p) cc_final: 0.8660 (t)
REVERT: G  339 MET cc_start: 0.8603 (ttt) cc_final: 0.8396 (ttt)
REVERT: H   60 ASN cc_start: 0.8991 (m-40) cc_final: 0.8566 (m110)
  outliers start: 9
  outliers final: 2
  residues processed: 108
  average time/residue: 1.0178
  time to fit residues: 113.3588
Evaluate side-chains
  103 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   48 GLN
Chi-restraints excluded: chain H residue   62 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 27 optimal weight:   30.0000
   chunk 11 optimal weight:    8.9990
   chunk 40 optimal weight:   10.0000
   chunk 44 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
o 319 ASN
A 306 ASN
H  41 ASN
H  72 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   3455  Z= 0.377
  Angle     :  1.016   8.251   4620  Z= 0.536
  Chirality :  0.050   0.201    435
  Planarity :  0.005   0.042    655
  Dihedral  :  6.811  22.297    500
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 0.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 11.75 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.21 (0.18), residues: 470
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.97 (0.13), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP G 334 
 PHE   0.012   0.002   PHE E 289 
 TYR   0.014   0.002   TYR D  45 
 ARG   0.001   0.000   ARG o 293 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.297 
Fit side-chains
REVERT: C  292 SER cc_start: 0.9014 (p) cc_final: 0.8745 (t)
REVERT: G  339 MET cc_start: 0.8665 (ttt) cc_final: 0.8419 (ttt)
  outliers start: 6
  outliers final: 2
  residues processed: 98
  average time/residue: 1.1178
  time to fit residues: 112.8723
Evaluate side-chains
  95 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 93
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   48 GLN
Chi-restraints excluded: chain H residue   62 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 4 optimal weight:   20.0000
   chunk 19 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0980
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    6.4188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
o 319 ASN
E 319 ASN
H  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   3455  Z= 0.375
  Angle     :  1.009   8.734   4620  Z= 0.530
  Chirality :  0.049   0.197    435
  Planarity :  0.006   0.045    655
  Dihedral  :  6.770  23.334    500
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 0.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 12.06 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.30 (0.17), residues: 470
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.03 (0.13), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP G 334 
 PHE   0.012   0.002   PHE A 316 
 TYR   0.014   0.002   TYR B  45 
 ARG   0.001   0.000   ARG o 293 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.403 
Fit side-chains
REVERT: C  292 SER cc_start: 0.9023 (p) cc_final: 0.8765 (t)
REVERT: G  339 MET cc_start: 0.8684 (ttt) cc_final: 0.8427 (ttt)
  outliers start: 8
  outliers final: 4
  residues processed: 98
  average time/residue: 1.0806
  time to fit residues: 109.1256
Evaluate side-chains
  95 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain o residue  319 ASN
Chi-restraints excluded: chain E residue  327 GLN
Chi-restraints excluded: chain F residue   48 GLN
Chi-restraints excluded: chain H residue   62 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 17 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 22 optimal weight:    9.9990
   chunk 39 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
o 319 ASN
A 319 ASN
H  41 ASN
H  72 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   3455  Z= 0.414
  Angle     :  1.044   9.486   4620  Z= 0.549
  Chirality :  0.050   0.204    435
  Planarity :  0.006   0.049    655
  Dihedral  :  6.796  23.094    500
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 0.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 12.70 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.37 (0.17), residues: 470
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.09 (0.13), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP G 334 
 PHE   0.013   0.003   PHE o 316 
 TYR   0.015   0.002   TYR B  45 
 ARG   0.001   0.000   ARG o 293 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.443 
Fit side-chains
REVERT: C  292 SER cc_start: 0.9024 (p) cc_final: 0.8757 (t)
  outliers start: 10
  outliers final: 5
  residues processed: 100
  average time/residue: 1.0843
  time to fit residues: 111.7299
Evaluate side-chains
  96 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  340 LEU
Chi-restraints excluded: chain E residue  319 ASN
Chi-restraints excluded: chain E residue  327 GLN
Chi-restraints excluded: chain F residue   48 GLN
Chi-restraints excluded: chain H residue   62 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 36 optimal weight:   20.0000
   chunk 20 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
o 319 ASN
A 319 ASN
E 319 ASN
H  72 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8842
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3455  Z= 0.300
  Angle     :  0.923   8.566   4620  Z= 0.482
  Chirality :  0.047   0.183    435
  Planarity :  0.006   0.050    655
  Dihedral  :  6.554  22.790    500
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 0.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 12.70 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.38 (0.17), residues: 470
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.09 (0.13), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.004   TRP G 334 
 PHE   0.013   0.002   PHE A 316 
 TYR   0.012   0.002   TYR B  45 
 ARG   0.001   0.000   ARG o 293 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.321 
Fit side-chains
REVERT: o  342 SER cc_start: 0.9111 (t) cc_final: 0.8874 (p)
REVERT: C  292 SER cc_start: 0.9066 (p) cc_final: 0.8831 (t)
  outliers start: 9
  outliers final: 4
  residues processed: 98
  average time/residue: 1.0475
  time to fit residues: 105.8645
Evaluate side-chains
  95 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain o residue  319 ASN
Chi-restraints excluded: chain E residue  319 ASN
Chi-restraints excluded: chain F residue   48 GLN
Chi-restraints excluded: chain H residue   62 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 36 optimal weight:   20.0000
   chunk 43 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 29 optimal weight:   20.0000
   overall best weight:    4.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
H  41 ASN
H  72 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3455  Z= 0.269
  Angle     :  0.886   8.207   4620  Z= 0.462
  Chirality :  0.046   0.178    435
  Planarity :  0.005   0.048    655
  Dihedral  :  6.414  21.938    500
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 0.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.97 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.38 (0.17), residues: 470
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.09 (0.13), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP G 334 
 PHE   0.013   0.002   PHE o 316 
 TYR   0.012   0.002   TYR B  45 
 ARG   0.001   0.000   ARG o 293 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.362 
Fit side-chains
REVERT: o  342 SER cc_start: 0.9108 (t) cc_final: 0.8895 (p)
REVERT: C  292 SER cc_start: 0.9067 (p) cc_final: 0.8841 (t)
  outliers start: 6
  outliers final: 2
  residues processed: 96
  average time/residue: 1.0207
  time to fit residues: 101.0678
Evaluate side-chains
  93 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   48 GLN
Chi-restraints excluded: chain H residue   62 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    4.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
o 319 ASN
A 319 ASN
H  41 ASN
H  72 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3455  Z= 0.266
  Angle     :  0.875   8.037   4620  Z= 0.457
  Chirality :  0.046   0.174    435
  Planarity :  0.005   0.050    655
  Dihedral  :  6.368  22.054    500
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 0.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.29 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.35 (0.17), residues: 470
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.07 (0.13), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP G 334 
 PHE   0.012   0.002   PHE A 316 
 TYR   0.011   0.002   TYR B  45 
 ARG   0.001   0.000   ARG o 293 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.385 
Fit side-chains
REVERT: o  342 SER cc_start: 0.9131 (t) cc_final: 0.8915 (p)
REVERT: C  292 SER cc_start: 0.9060 (p) cc_final: 0.8832 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 96
  average time/residue: 1.0518
  time to fit residues: 104.1662
Evaluate side-chains
  94 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  340 LEU
Chi-restraints excluded: chain E residue  319 ASN
Chi-restraints excluded: chain F residue   48 GLN
Chi-restraints excluded: chain H residue   62 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 44 optimal weight:    0.0770
   chunk 41 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   chunk 3 optimal weight:    6.9990
   overall best weight:    3.5544

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
H  41 ASN
H  72 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3455  Z= 0.226
  Angle     :  0.826   7.629   4620  Z= 0.429
  Chirality :  0.044   0.161    435
  Planarity :  0.005   0.048    655
  Dihedral  :  6.214  21.425    500
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 0.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.92 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.33 (0.17), residues: 470
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.05 (0.13), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP E 334 
 PHE   0.013   0.002   PHE A 316 
 TYR   0.011   0.001   TYR B  45 
 ARG   0.001   0.000   ARG o 293 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.360 
Fit side-chains
REVERT: o  342 SER cc_start: 0.9091 (t) cc_final: 0.8855 (p)
REVERT: C  292 SER cc_start: 0.9111 (p) cc_final: 0.8890 (t)
  outliers start: 5
  outliers final: 4
  residues processed: 97
  average time/residue: 1.0303
  time to fit residues: 103.0646
Evaluate side-chains
  95 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain o residue  319 ASN
Chi-restraints excluded: chain E residue  319 ASN
Chi-restraints excluded: chain F residue   48 GLN
Chi-restraints excluded: chain H residue   62 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 21 optimal weight:    0.4980
   chunk 28 optimal weight:   10.0000
   chunk 38 optimal weight:   20.0000
   chunk 10 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 36 optimal weight:   20.0000
   overall best weight:    7.2990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
o 291 ASN
H  41 ASN
H  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   3455  Z= 0.419
  Angle     :  1.029   8.922   4620  Z= 0.543
  Chirality :  0.049   0.198    435
  Planarity :  0.006   0.052    655
  Dihedral  :  6.668  23.005    500
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 0.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 15.24 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.33 (0.17), residues: 470
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.06 (0.13), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP G 334 
 PHE   0.013   0.003   PHE A 316 
 TYR   0.014   0.002   TYR D  45 
 ARG   0.001   0.000   ARG o 293 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.389 
Fit side-chains
REVERT: C  292 SER cc_start: 0.9094 (p) cc_final: 0.8842 (t)
  outliers start: 5
  outliers final: 2
  residues processed: 94
  average time/residue: 1.1080
  time to fit residues: 107.3679
Evaluate side-chains
  91 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   48 GLN
Chi-restraints excluded: chain H residue   62 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 6 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 25 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 1 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   overall best weight:    2.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
o 319 ASN
A 319 ASN
H  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.100773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.091469 restraints weight = 3530.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.29
r_work: 0.3102 rms_B_bonded: 1.30 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 2.24 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3455  Z= 0.193
  Angle     :  0.789   7.331   4620  Z= 0.409
  Chirality :  0.044   0.157    435
  Planarity :  0.005   0.049    655
  Dihedral  :  6.122  21.512    500
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 1.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 15.87 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.31 (0.17), residues: 470
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.04 (0.13), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP E 334 
 PHE   0.012   0.002   PHE A 316 
 TYR   0.011   0.001   TYR p  74 
 ARG   0.001   0.000   ARG o 293 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2002.55 seconds
wall clock time: 36 minutes 28.14 seconds (2188.14 seconds total)