Starting phenix.real_space_refine
on Mon Feb 10 22:15:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cg3_16628/02_2025/8cg3_16628.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cg3_16628/02_2025/8cg3_16628.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cg3_16628/02_2025/8cg3_16628.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cg3_16628/02_2025/8cg3_16628.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cg3_16628/02_2025/8cg3_16628.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cg3_16628/02_2025/8cg3_16628.cif"
  }
  resolution = 2.39
  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=   0.004
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      40      5.16       5
     C    1785      2.51       5
     N     610      2.21       5
     O     605      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3040
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 608
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
  Restraints were copied for chains:
    C, B, U, D
  Time building chain proxies: 1.72, per 1000 atoms: 0.57
  Number of scatterers: 3040
  At special positions: 0
  Unit cell: (77.4, 67.94, 50.74, 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      40     16.00
     O     605      8.00
     N     610      7.00
     C    1785      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: 0.54
  Conformation dependent library (CDL) restraints added in 805.8 milliseconds
  

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  650

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 39.3% 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 273 through 275
      removed outlier: 8.696A  pdb=" N   SER U 273 " --> pdb=" O   GLY A 274 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ARG B 275 " --> pdb=" O   GLY U 274 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ARG C 275 " --> pdb=" O   GLY B 274 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ARG D 275 " --> pdb=" O   GLY C 274 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293
      removed outlier: 6.781A  pdb=" N   SER U 292 " --> pdb=" O   ARG B 293 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   SER B 292 " --> pdb=" O   ARG C 293 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   SER C 292 " --> pdb=" O   ARG D 293 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 300
      removed outlier: 6.769A  pdb=" N   GLY U 296 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 8.518A  pdb=" N   LEU A 299 " --> pdb=" O   GLY U 296 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   GLY U 298 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 308
      removed outlier: 6.560A  pdb=" N   ASN U 306 " --> pdb=" O   MET A 307 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315
      removed outlier: 6.611A  pdb=" N   MET U 311 " --> pdb=" O   ASN B 312 " (cutoff:3.500A)
      removed outlier: 8.325A  pdb=" N   GLY B 314 " --> pdb=" O   MET U 311 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   PHE U 313 " --> pdb=" O   GLY B 314 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   MET B 311 " --> pdb=" O   ASN C 312 " (cutoff:3.500A)
      removed outlier: 8.325A  pdb=" N   GLY C 314 " --> pdb=" O   MET B 311 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   PHE B 313 " --> pdb=" O   GLY C 314 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   MET C 311 " --> pdb=" O   ASN D 312 " (cutoff:3.500A)
      removed outlier: 8.325A  pdb=" N   GLY D 314 " --> pdb=" O   MET C 311 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   PHE C 313 " --> pdb=" O   GLY D 314 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 336
      removed outlier: 6.738A  pdb=" N   ALA U 321 " --> pdb=" O   MET B 322 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   ALA B 324 " --> pdb=" O   ALA U 321 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   MET U 323 " --> pdb=" O   ALA B 324 " (cutoff:3.500A)
      removed outlier: 8.430A  pdb=" N   ALA B 326 " --> pdb=" O   MET U 323 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ALA U 325 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   ALA B 328 " --> pdb=" O   ALA U 325 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   GLN U 327 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 8.521A  pdb=" N   LEU B 330 " --> pdb=" O   GLN U 327 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ALA U 329 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
      removed outlier: 8.556A  pdb=" N   SER B 332 " --> pdb=" O   ALA U 329 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLN U 331 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 8.815A  pdb=" N   TRP B 334 " --> pdb=" O   GLN U 331 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   SER U 333 " --> pdb=" O   TRP B 334 " (cutoff:3.500A)
      removed outlier: 8.656A  pdb=" N   MET B 336 " --> pdb=" O   SER U 333 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   GLY U 335 " --> pdb=" O   MET B 336 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ALA B 321 " --> pdb=" O   MET C 322 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   ALA C 324 " --> pdb=" O   ALA B 321 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   MET B 323 " --> pdb=" O   ALA C 324 " (cutoff:3.500A)
      removed outlier: 8.430A  pdb=" N   ALA C 326 " --> pdb=" O   MET B 323 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ALA B 325 " --> pdb=" O   ALA C 326 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   ALA C 328 " --> pdb=" O   ALA B 325 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   GLN B 327 " --> pdb=" O   ALA C 328 " (cutoff:3.500A)
      removed outlier: 8.520A  pdb=" N   LEU C 330 " --> pdb=" O   GLN B 327 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ALA B 329 " --> pdb=" O   LEU C 330 " (cutoff:3.500A)
      removed outlier: 8.555A  pdb=" N   SER C 332 " --> pdb=" O   ALA B 329 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLN B 331 " --> pdb=" O   SER C 332 " (cutoff:3.500A)
      removed outlier: 8.815A  pdb=" N   TRP C 334 " --> pdb=" O   GLN B 331 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   SER B 333 " --> pdb=" O   TRP C 334 " (cutoff:3.500A)
      removed outlier: 8.656A  pdb=" N   MET C 336 " --> pdb=" O   SER B 333 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   GLY B 335 " --> pdb=" O   MET C 336 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ALA C 321 " --> pdb=" O   MET D 322 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   ALA D 324 " --> pdb=" O   ALA C 321 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   MET C 323 " --> pdb=" O   ALA D 324 " (cutoff:3.500A)
      removed outlier: 8.431A  pdb=" N   ALA D 326 " --> pdb=" O   MET C 323 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ALA C 325 " --> pdb=" O   ALA D 326 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   ALA D 328 " --> pdb=" O   ALA C 325 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   GLN C 327 " --> pdb=" O   ALA D 328 " (cutoff:3.500A)
      removed outlier: 8.520A  pdb=" N   LEU D 330 " --> pdb=" O   GLN C 327 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ALA C 329 " --> pdb=" O   LEU D 330 " (cutoff:3.500A)
      removed outlier: 8.555A  pdb=" N   SER D 332 " --> pdb=" O   ALA C 329 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLN C 331 " --> pdb=" O   SER D 332 " (cutoff:3.500A)
      removed outlier: 8.815A  pdb=" N   TRP D 334 " --> pdb=" O   GLN C 331 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   SER C 333 " --> pdb=" O   TRP D 334 " (cutoff:3.500A)
      removed outlier: 8.656A  pdb=" N   MET D 336 " --> pdb=" O   SER C 333 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   GLY C 335 " --> pdb=" O   MET D 336 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 347
      removed outlier: 6.609A  pdb=" N   GLN U 344 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   SER B 347 " --> pdb=" O   GLN U 344 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLN U 346 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   GLN B 344 " --> pdb=" O   ASN C 345 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   SER C 347 " --> pdb=" O   GLN B 344 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLN B 346 " --> pdb=" O   SER C 347 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   GLN C 344 " --> pdb=" O   ASN D 345 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   SER D 347 " --> pdb=" O   GLN C 344 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   GLN C 346 " --> pdb=" O   SER D 347 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 353 through 356
      removed outlier: 6.878A  pdb=" N   ASN U 353 " --> pdb=" O   GLN A 354 " (cutoff:3.500A)
      removed outlier: 8.587A  pdb=" N   GLN A 356 " --> pdb=" O   ASN U 353 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ASN U 355 " --> pdb=" O   GLN A 356 " (cutoff:3.500A)

    54 hydrogen bonds defined for protein.
    162 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: 0.71

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1070
        1.35 -     1.48: 805
        1.48 -     1.61: 1130
        1.61 -     1.74: 0
        1.74 -     1.87: 80
  Bond restraints: 3085
  Sorted by residual:
  bond pdb=" CA  SER D 333 "
       pdb=" CB  SER D 333 "
    ideal  model  delta    sigma   weight residual
    1.534  1.484  0.050 1.64e-02 3.72e+03 9.27e+00
  bond pdb=" CA  SER A 333 "
       pdb=" CB  SER A 333 "
    ideal  model  delta    sigma   weight residual
    1.534  1.484  0.050 1.64e-02 3.72e+03 9.26e+00
  bond pdb=" CA  SER U 333 "
       pdb=" CB  SER U 333 "
    ideal  model  delta    sigma   weight residual
    1.534  1.484  0.050 1.64e-02 3.72e+03 9.15e+00
  bond pdb=" CA  SER B 333 "
       pdb=" CB  SER B 333 "
    ideal  model  delta    sigma   weight residual
    1.534  1.484  0.049 1.64e-02 3.72e+03 9.10e+00
  bond pdb=" CA  SER C 333 "
       pdb=" CB  SER C 333 "
    ideal  model  delta    sigma   weight residual
    1.534  1.485  0.049 1.64e-02 3.72e+03 8.90e+00
  ... (remaining 3080 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 2415
        1.25 -     2.50: 1167
        2.50 -     3.76: 394
        3.76 -     5.01: 84
        5.01 -     6.26: 40
  Bond angle restraints: 4100
  Sorted by residual:
  angle pdb=" C   ASN B 319 "
        pdb=" CA  ASN B 319 "
        pdb=" CB  ASN B 319 "
      ideal   model   delta    sigma   weight residual
     110.71  106.12    4.59 9.40e-01 1.13e+00 2.39e+01
  angle pdb=" CA  ASN D 319 "
        pdb=" C   ASN D 319 "
        pdb=" N   PRO D 320 "
      ideal   model   delta    sigma   weight residual
     118.16  121.58   -3.42 7.00e-01 2.04e+00 2.38e+01
  angle pdb=" CA  ASN C 319 "
        pdb=" C   ASN C 319 "
        pdb=" N   PRO C 320 "
      ideal   model   delta    sigma   weight residual
     118.16  121.57   -3.41 7.00e-01 2.04e+00 2.38e+01
  angle pdb=" C   ASN C 319 "
        pdb=" CA  ASN C 319 "
        pdb=" CB  ASN C 319 "
      ideal   model   delta    sigma   weight residual
     110.71  106.13    4.58 9.40e-01 1.13e+00 2.37e+01
  angle pdb=" CA  ASN U 319 "
        pdb=" C   ASN U 319 "
        pdb=" N   PRO U 320 "
      ideal   model   delta    sigma   weight residual
     118.16  121.57   -3.41 7.00e-01 2.04e+00 2.37e+01
  ... (remaining 4095 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.35: 1510
       13.35 -    26.70: 190
       26.70 -    40.04: 20
       40.04 -    53.39: 10
       53.39 -    66.74: 25
  Dihedral angle restraints: 1755
    sinusoidal: 665
      harmonic: 1090
  Sorted by residual:
  dihedral pdb=" CA  GLN B 327 "
           pdb=" C   GLN B 327 "
           pdb=" N   ALA B 328 "
           pdb=" CA  ALA B 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.67  -19.33     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  GLN A 327 "
           pdb=" C   GLN A 327 "
           pdb=" N   ALA A 328 "
           pdb=" CA  ALA A 328 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.67  -19.33     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  GLN U 327 "
           pdb=" C   GLN U 327 "
           pdb=" N   ALA U 328 "
           pdb=" CA  ALA U 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.68  -19.32     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 1752 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 108
       0.038 -    0.076: 114
       0.076 -    0.113: 88
       0.113 -    0.151: 20
       0.151 -    0.189: 15
  Chirality restraints: 345
  Sorted by residual:
  chirality pdb=" CA  GLN B 344 "
            pdb=" N   GLN B 344 "
            pdb=" C   GLN B 344 "
            pdb=" CB  GLN B 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.92e-01
  chirality pdb=" CA  GLN D 344 "
            pdb=" N   GLN D 344 "
            pdb=" C   GLN D 344 "
            pdb=" CB  GLN D 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.91e-01
  chirality pdb=" CA  GLN U 344 "
            pdb=" N   GLN U 344 "
            pdb=" C   GLN U 344 "
            pdb=" CB  GLN U 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.88e-01
  ... (remaining 342 not shown)

  Planarity restraints: 615
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 334 "   -0.029 2.00e-02 2.50e+03   1.82e-02 8.27e+00
        pdb=" CG  TRP A 334 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 334 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 334 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 334 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 334 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 334 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 334 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 334 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP U 334 "   -0.029 2.00e-02 2.50e+03   1.82e-02 8.25e+00
        pdb=" CG  TRP U 334 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TRP U 334 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP U 334 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP U 334 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP U 334 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP U 334 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP U 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP U 334 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP U 334 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 334 "   -0.029 2.00e-02 2.50e+03   1.82e-02 8.24e+00
        pdb=" CG  TRP C 334 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 334 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 334 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 334 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 334 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 334 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 334 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 334 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 612 not shown)

  Histogram of nonbonded interaction distances:
        2.62 -     3.07: 1732
        3.07 -     3.53: 2504
        3.53 -     3.99: 4573
        3.99 -     4.44: 5320
        4.44 -     4.90: 8739
  Nonbonded interactions: 22868
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 319 "
            pdb=" CB  ASN A 319 "
     model   vdw
     2.619 2.752
  nonbonded pdb=" O   ASN U 319 "
            pdb=" CB  ASN U 319 "
     model   vdw
     2.619 2.752
  nonbonded pdb=" O   ASN B 319 "
            pdb=" CB  ASN B 319 "
     model   vdw
     2.619 2.752
  nonbonded pdb=" O   ASN C 319 "
            pdb=" CB  ASN C 319 "
     model   vdw
     2.619 2.752
  nonbonded pdb=" O   ASN D 319 "
            pdb=" CB  ASN D 319 "
     model   vdw
     2.619 2.752
  ... (remaining 22863 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'U'
  selection = chain 'D'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.270
  Find NCS groups from input model:        0.060
  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:12.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9349
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   0.065   3085  Z= 0.863
  Angle     :  1.687   6.258   4100  Z= 1.162
  Chirality :  0.076   0.189    345
  Planarity :  0.008   0.063    615
  Dihedral  : 14.766  66.738   1105
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  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: -4.90 (0.19), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.73 (0.15), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.012   TRP A 334 
 PHE   0.010   0.003   PHE C 276 
 ARG   0.003   0.001   ARG B 293 

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.320 
Fit side-chains
REVERT: B  336 MET cc_start: 0.9327 (ttp) cc_final: 0.9106 (ttm)
REVERT: C  339 MET cc_start: 0.8693 (tpt) cc_final: 0.8251 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 1.2619
  time to fit residues: 82.7674
Evaluate side-chains
  58 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:   20.0000
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:   20.0000
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
U 354 GLN
A 354 GLN
B 354 GLN
C 354 GLN
D 354 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.105773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.075443 restraints weight = 2790.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.94
r_work: 0.2877 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9175
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3085  Z= 0.254
  Angle     :  0.811   4.803   4100  Z= 0.458
  Chirality :  0.042   0.141    345
  Planarity :  0.003   0.018    615
  Dihedral  :  6.039  18.223    455
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 0.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  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: -4.67 (0.19), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.55 (0.14), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP C 334 
 PHE   0.012   0.002   PHE B 316 
 ARG   0.002   0.000   ARG U 272 

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.281 
Fit side-chains
REVERT: U  311 MET cc_start: 0.9262 (ttt) cc_final: 0.9034 (ttp)
REVERT: D  355 ASN cc_start: 0.8641 (m-40) cc_final: 0.8412 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 1.3392
  time to fit residues: 85.0379
Evaluate side-chains
  60 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 26 optimal weight:   30.0000
   chunk 35 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 30 optimal weight:   20.0000
   chunk 25 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0970
   chunk 11 optimal weight:    9.9990
   overall best weight:    7.4186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.103571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.073793 restraints weight = 2760.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 1.87
r_work: 0.2852 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9222
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   3085  Z= 0.422
  Angle     :  1.000   6.230   4100  Z= 0.570
  Chirality :  0.047   0.171    345
  Planarity :  0.005   0.033    615
  Dihedral  :  6.126  20.308    455
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 0.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  4.64 %
    Favored  : 94.64 %
  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: -4.86 (0.17), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.70 (0.13), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.005   TRP C 334 
 PHE   0.014   0.003   PHE C 316 
 ARG   0.003   0.001   ARG A 275 

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.352 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 59
  average time/residue: 1.3783
  time to fit residues: 83.3031
Evaluate side-chains
  57 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 11 optimal weight:    0.2980
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 39 optimal weight:    8.9990
   chunk 23 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 26 optimal weight:   30.0000
   chunk 17 optimal weight:    4.9990
   chunk 4 optimal weight:   30.0000
   overall best weight:    4.2588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.105389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.075728 restraints weight = 2785.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.89
r_work: 0.2888 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9187
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3085  Z= 0.280
  Angle     :  0.825   5.086   4100  Z= 0.467
  Chirality :  0.043   0.145    345
  Planarity :  0.004   0.027    615
  Dihedral  :  5.881  19.171    455
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 0.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  5.00 %
    Favored  : 93.57 %
  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: -4.81 (0.17), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.66 (0.13), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.004   TRP U 334 
 PHE   0.012   0.002   PHE C 316 
 ARG   0.002   0.000   ARG A 275 

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.299 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 61
  average time/residue: 1.3663
  time to fit residues: 85.3606
Evaluate side-chains
  56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 17 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   chunk 15 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 24 optimal weight:   20.0000
   overall best weight:    3.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.106014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.076280 restraints weight = 2806.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 1.90
r_work: 0.2906 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2802 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9187
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3085  Z= 0.267
  Angle     :  0.798   5.063   4100  Z= 0.451
  Chirality :  0.042   0.145    345
  Planarity :  0.004   0.027    615
  Dihedral  :  5.764  18.793    455
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 0.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  5.71 %
    Favored  : 92.86 %
  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: -4.76 (0.16), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.62 (0.13), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.004   TRP U 334 
 PHE   0.011   0.002   PHE C 316 
 ARG   0.002   0.000   ARG A 275 

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.336 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 59
  average time/residue: 1.3585
  time to fit residues: 82.0616
Evaluate side-chains
  55 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 5 optimal weight:    5.9990
   chunk 34 optimal weight:   20.0000
   chunk 37 optimal weight:    0.6980
   chunk 27 optimal weight:   20.0000
   chunk 12 optimal weight:    0.0010
   chunk 23 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   overall best weight:    4.1392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.106170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.076152 restraints weight = 2837.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 1.90
r_work: 0.2907 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9190
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3085  Z= 0.272
  Angle     :  0.804   5.086   4100  Z= 0.455
  Chirality :  0.043   0.146    345
  Planarity :  0.004   0.026    615
  Dihedral  :  5.755  18.975    455
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 0.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  7.14 %
    Favored  : 92.50 %
  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: -4.76 (0.16), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.62 (0.12), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP U 334 
 PHE   0.011   0.002   PHE C 316 
 ARG   0.002   0.000   ARG A 275 

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.273 
Fit side-chains
REVERT: C  311 MET cc_start: 0.9191 (ttt) cc_final: 0.8986 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 55
  average time/residue: 1.4783
  time to fit residues: 83.1893
Evaluate side-chains
  54 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 18 optimal weight:   30.0000
   chunk 7 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:   20.0000
   chunk 1 optimal weight:    8.9990
   chunk 4 optimal weight:    0.2980
   chunk 10 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    2.8588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.107699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.077764 restraints weight = 2779.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.91
r_work: 0.2934 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9165
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3085  Z= 0.210
  Angle     :  0.718   4.683   4100  Z= 0.404
  Chirality :  0.041   0.136    345
  Planarity :  0.003   0.025    615
  Dihedral  :  5.568  18.215    455
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 0.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  7.50 %
    Favored  : 91.79 %
  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: -4.70 (0.17), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.13), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP U 334 
 PHE   0.009   0.002   PHE C 316 
 ARG   0.001   0.000   ARG A 275 

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.336 
Fit side-chains
REVERT: C  311 MET cc_start: 0.9186 (ttt) cc_final: 0.8975 (ttp)
REVERT: D  355 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8451 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 55
  average time/residue: 1.4727
  time to fit residues: 82.8366
Evaluate side-chains
  54 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  355 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 32 optimal weight:    0.0670
   chunk 25 optimal weight:   20.0000
   chunk 24 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:   30.0000
   chunk 17 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    3.4126

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.107026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.077193 restraints weight = 2767.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 1.90
r_work: 0.2924 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9177
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3085  Z= 0.236
  Angle     :  0.752   4.931   4100  Z= 0.425
  Chirality :  0.041   0.136    345
  Planarity :  0.004   0.027    615
  Dihedral  :  5.600  18.498    455
  Min Nonbonded Distance : 2.656

Molprobity Statistics.
  All-atom Clashscore : 0.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.57 %
    Favored  : 90.71 %
  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: -4.71 (0.17), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.58 (0.13), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP U 334 
 PHE   0.011   0.002   PHE C 316 
 ARG   0.001   0.000   ARG A 275 

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.299 
Fit side-chains
REVERT: C  311 MET cc_start: 0.9191 (ttt) cc_final: 0.8981 (ttp)
  outliers start: 2
  outliers final: 0
  residues processed: 56
  average time/residue: 1.4647
  time to fit residues: 83.8732
Evaluate side-chains
  54 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:   20.0000
   chunk 30 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 4 optimal weight:   20.0000
   chunk 32 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   overall best weight:    6.5990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.104679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.074698 restraints weight = 2823.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.91
r_work: 0.2879 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9219
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3085  Z= 0.380
  Angle     :  0.927   5.678   4100  Z= 0.528
  Chirality :  0.046   0.156    345
  Planarity :  0.005   0.029    615
  Dihedral  :  5.897  20.004    455
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 0.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  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: -4.81 (0.16), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.66 (0.12), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.004   TRP C 334 
 PHE   0.013   0.003   PHE C 316 
 ARG   0.003   0.001   ARG A 275 

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.302 
Fit side-chains
REVERT: C  311 MET cc_start: 0.9205 (ttt) cc_final: 0.9002 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 1.4469
  time to fit residues: 82.8970
Evaluate side-chains
  56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 18 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0470
   overall best weight:    7.2086

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.104291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.074529 restraints weight = 2755.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 1.88
r_work: 0.2877 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9223
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   3085  Z= 0.409
  Angle     :  0.977   7.120   4100  Z= 0.553
  Chirality :  0.046   0.168    345
  Planarity :  0.005   0.031    615
  Dihedral  :  5.993  20.267    455
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 0.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  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: -4.87 (0.16), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.71 (0.12), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.004   TRP C 334 
 PHE   0.013   0.003   PHE A 313 
 ARG   0.003   0.001   ARG A 275 

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.294 
Fit side-chains
REVERT: C  311 MET cc_start: 0.9204 (ttt) cc_final: 0.8992 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 1.4164
  time to fit residues: 82.6516
Evaluate side-chains
  57 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 30 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    4.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.105910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.076136 restraints weight = 2790.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 1.89
r_work: 0.2909 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2802 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9194
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3085  Z= 0.284
  Angle     :  0.828   6.151   4100  Z= 0.465
  Chirality :  0.043   0.149    345
  Planarity :  0.004   0.025    615
  Dihedral  :  5.823  19.308    455
  Min Nonbonded Distance : 2.656

Molprobity Statistics.
  All-atom Clashscore : 0.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.00 %
    Favored  : 89.64 %
  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: -4.80 (0.16), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.65 (0.12), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.004   TRP C 334 
 PHE   0.011   0.002   PHE C 316 
 ARG   0.002   0.000   ARG A 275 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2838.94 seconds
wall clock time: 50 minutes 44.49 seconds (3044.49 seconds total)