Starting phenix.real_space_refine
on Fri Aug 22 13:09:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8owk_17239/08_2025/8owk_17239.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8owk_17239/08_2025/8owk_17239.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8owk_17239/08_2025/8owk_17239.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8owk_17239/08_2025/8owk_17239.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8owk_17239/08_2025/8owk_17239.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8owk_17239/08_2025/8owk_17239.map"
  }
  resolution = 3.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.006
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      10      5.16       5
     C    1940      2.51       5
     N     530      2.21       5
     O     570      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3050
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 305
          Classifications: {'peptide': 40}
          Link IDs: {'TRANS': 39}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.66, per 1000 atoms: 0.22
  Number of scatterers: 3050
  At special positions: 0
  Unit cell: (89.25, 120.75, 42, 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      10     16.00
     O     570      8.00
     N     530      7.00
     C    1940      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: 0.27
  Conformation dependent library (CDL) restraints added in 75.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  680

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 4 sheets defined
      0.0% alpha, 67.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 23
      removed outlier: 6.766A  pdb=" N   TYR C  10 " --> pdb=" O   GLY B   9 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   GLU B  11 " --> pdb=" O   TYR C  10 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL C  12 " --> pdb=" O   GLU B  11 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   HIS B  13 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   TYR A  10 " --> pdb=" O   GLY C   9 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   GLU C  11 " --> pdb=" O   TYR A  10 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL A  12 " --> pdb=" O   GLU C  11 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   HIS C  13 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   TYR D  10 " --> pdb=" O   GLY A   9 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLU A  11 " --> pdb=" O   TYR D  10 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL D  12 " --> pdb=" O   GLU A  11 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   HIS A  13 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   GLU D   3 " --> pdb=" O   PHE E   4 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   HIS E   6 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ARG D   5 " --> pdb=" O   HIS E   6 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   SER E   8 " --> pdb=" O   ARG D   5 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ASP D   7 " --> pdb=" O   SER E   8 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   TYR E  10 " --> pdb=" O   ASP D   7 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   GLY D   9 " --> pdb=" O   TYR E  10 " (cutoff:3.500A)
      removed outlier: 10.199A  pdb=" N   VAL E  12 " --> pdb=" O   GLY D   9 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   GLU D  11 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 8.817A  pdb=" N   HIS E  14 " --> pdb=" O   GLU D  11 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   HIS D  13 " --> pdb=" O   HIS E  14 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   LYS E  16 " --> pdb=" O   HIS D  13 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   GLN D  15 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   VAL E  18 " --> pdb=" O   GLN D  15 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LEU D  17 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   PHE E  20 " --> pdb=" O   LEU D  17 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   PHE D  19 " --> pdb=" O   PHE E  20 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   GLU E  22 " --> pdb=" O   PHE D  19 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ALA D  21 " --> pdb=" O   GLU E  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 36
      removed outlier: 6.876A  pdb=" N   ALA C  30 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ILE B  31 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ILE C  32 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLY B  33 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
      removed outlier: 8.660A  pdb=" N   ALA A  30 " --> pdb=" O   ILE C  31 " (cutoff:3.500A)
      removed outlier: 9.741A  pdb=" N   GLY C  33 " --> pdb=" O   ALA A  30 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE A  32 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   MET C  35 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   LEU A  34 " --> pdb=" O   MET C  35 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ALA D  30 " --> pdb=" O   GLY A  29 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ILE A  31 " --> pdb=" O   ALA D  30 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ILE D  32 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   GLY A  33 " --> pdb=" O   ILE D  32 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ALA E  30 " --> pdb=" O   GLY D  29 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ILE D  31 " --> pdb=" O   ALA E  30 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ILE E  32 " --> pdb=" O   ILE D  31 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   GLY D  33 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 3 through 23
      removed outlier: 6.766A  pdb=" N   TYR H  10 " --> pdb=" O   GLY G   9 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   GLU G  11 " --> pdb=" O   TYR H  10 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL H  12 " --> pdb=" O   GLU G  11 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   HIS G  13 " --> pdb=" O   VAL H  12 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   TYR F  10 " --> pdb=" O   GLY H   9 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   GLU H  11 " --> pdb=" O   TYR F  10 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   VAL F  12 " --> pdb=" O   GLU H  11 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   HIS H  13 " --> pdb=" O   VAL F  12 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   GLU F   3 " --> pdb=" O   PHE I   4 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   HIS I   6 " --> pdb=" O   GLU F   3 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ARG F   5 " --> pdb=" O   HIS I   6 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   SER I   8 " --> pdb=" O   ARG F   5 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ASP F   7 " --> pdb=" O   SER I   8 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   TYR I  10 " --> pdb=" O   ASP F   7 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLY F   9 " --> pdb=" O   TYR I  10 " (cutoff:3.500A)
      removed outlier: 10.191A  pdb=" N   VAL I  12 " --> pdb=" O   GLY F   9 " (cutoff:3.500A)
      removed outlier: 8.689A  pdb=" N   GLU F  11 " --> pdb=" O   VAL I  12 " (cutoff:3.500A)
      removed outlier: 8.824A  pdb=" N   HIS I  14 " --> pdb=" O   GLU F  11 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   HIS F  13 " --> pdb=" O   HIS I  14 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   LYS I  16 " --> pdb=" O   HIS F  13 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   GLN F  15 " --> pdb=" O   LYS I  16 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   VAL I  18 " --> pdb=" O   GLN F  15 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   LEU F  17 " --> pdb=" O   VAL I  18 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   PHE I  20 " --> pdb=" O   LEU F  17 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   PHE F  19 " --> pdb=" O   PHE I  20 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   GLU I  22 " --> pdb=" O   PHE F  19 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ALA F  21 " --> pdb=" O   GLU I  22 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   GLU I   3 " --> pdb=" O   PHE J   4 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   HIS J   6 " --> pdb=" O   GLU I   3 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ARG I   5 " --> pdb=" O   HIS J   6 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   SER J   8 " --> pdb=" O   ARG I   5 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ASP I   7 " --> pdb=" O   SER J   8 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   TYR J  10 " --> pdb=" O   ASP I   7 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   GLY I   9 " --> pdb=" O   TYR J  10 " (cutoff:3.500A)
      removed outlier: 10.199A  pdb=" N   VAL J  12 " --> pdb=" O   GLY I   9 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   GLU I  11 " --> pdb=" O   VAL J  12 " (cutoff:3.500A)
      removed outlier: 8.817A  pdb=" N   HIS J  14 " --> pdb=" O   GLU I  11 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   HIS I  13 " --> pdb=" O   HIS J  14 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   LYS J  16 " --> pdb=" O   HIS I  13 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   GLN I  15 " --> pdb=" O   LYS J  16 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   VAL J  18 " --> pdb=" O   GLN I  15 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LEU I  17 " --> pdb=" O   VAL J  18 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   PHE J  20 " --> pdb=" O   LEU I  17 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   PHE I  19 " --> pdb=" O   PHE J  20 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   GLU J  22 " --> pdb=" O   PHE I  19 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ALA I  21 " --> pdb=" O   GLU J  22 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 29 through 36
      removed outlier: 6.876A  pdb=" N   ALA H  30 " --> pdb=" O   GLY G  29 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ILE G  31 " --> pdb=" O   ALA H  30 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ILE H  32 " --> pdb=" O   ILE G  31 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLY G  33 " --> pdb=" O   ILE H  32 " (cutoff:3.500A)
      removed outlier: 8.691A  pdb=" N   ALA F  30 " --> pdb=" O   ILE H  31 " (cutoff:3.500A)
      removed outlier: 9.777A  pdb=" N   GLY H  33 " --> pdb=" O   ALA F  30 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ILE F  32 " --> pdb=" O   GLY H  33 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   MET H  35 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   LEU F  34 " --> pdb=" O   MET H  35 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ALA I  30 " --> pdb=" O   GLY F  29 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ILE F  31 " --> pdb=" O   ALA I  30 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   ILE I  32 " --> pdb=" O   ILE F  31 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   GLY F  33 " --> pdb=" O   ILE I  32 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ALA J  30 " --> pdb=" O   GLY I  29 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ILE I  31 " --> pdb=" O   ALA J  30 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ILE J  32 " --> pdb=" O   ILE I  31 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   GLY I  33 " --> pdb=" O   ILE J  32 " (cutoff:3.500A)

    98 hydrogen bonds defined for protein.
    294 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: 0.44

  Time building geometry restraints manager: 0.37 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: 950
        1.33 -     1.44: 492
        1.44 -     1.56: 1648
        1.56 -     1.67: 0
        1.67 -     1.79: 20
  Bond restraints: 3110
  Sorted by residual:
  bond pdb=" CA  HIS B   6 "
       pdb=" C   HIS B   6 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 1.19e-02 7.06e+03 1.44e+01
  bond pdb=" CA  HIS G   6 "
       pdb=" C   HIS G   6 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 1.19e-02 7.06e+03 1.44e+01
  bond pdb=" CA  HIS C   6 "
       pdb=" C   HIS C   6 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 1.19e-02 7.06e+03 1.44e+01
  bond pdb=" CA  HIS H   6 "
       pdb=" C   HIS H   6 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 1.19e-02 7.06e+03 1.44e+01
  bond pdb=" CA  HIS F   6 "
       pdb=" C   HIS F   6 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 1.19e-02 7.06e+03 1.43e+01
  ... (remaining 3105 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.45: 4050
        6.45 -    12.90: 92
       12.90 -    19.35: 18
       19.35 -    25.80: 0
       25.80 -    32.25: 10
  Bond angle restraints: 4170
  Sorted by residual:
  angle pdb=" N   GLY I  25 "
        pdb=" CA  GLY I  25 "
        pdb=" C   GLY I  25 "
      ideal   model   delta    sigma   weight residual
     111.36  143.61  -32.25 1.17e+00 7.31e-01 7.60e+02
  angle pdb=" N   GLY D  25 "
        pdb=" CA  GLY D  25 "
        pdb=" C   GLY D  25 "
      ideal   model   delta    sigma   weight residual
     111.36  143.61  -32.25 1.17e+00 7.31e-01 7.60e+02
  angle pdb=" N   GLY A  25 "
        pdb=" CA  GLY A  25 "
        pdb=" C   GLY A  25 "
      ideal   model   delta    sigma   weight residual
     111.36  143.61  -32.25 1.17e+00 7.31e-01 7.60e+02
  angle pdb=" N   GLY C  25 "
        pdb=" CA  GLY C  25 "
        pdb=" C   GLY C  25 "
      ideal   model   delta    sigma   weight residual
     111.36  143.60  -32.24 1.17e+00 7.31e-01 7.59e+02
  angle pdb=" N   GLY H  25 "
        pdb=" CA  GLY H  25 "
        pdb=" C   GLY H  25 "
      ideal   model   delta    sigma   weight residual
     111.36  143.60  -32.24 1.17e+00 7.31e-01 7.59e+02
  ... (remaining 4165 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.42: 1425
        7.42 -    14.85: 285
       14.85 -    22.27: 10
       22.27 -    29.70: 10
       29.70 -    37.12: 10
  Dihedral angle restraints: 1740
    sinusoidal: 660
      harmonic: 1080
  Sorted by residual:
  dihedral pdb=" N   ILE E  32 "
           pdb=" C   ILE E  32 "
           pdb=" CA  ILE E  32 "
           pdb=" CB  ILE E  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  115.41    7.99     0      2.50e+00 1.60e-01 1.02e+01
  dihedral pdb=" N   ILE J  32 "
           pdb=" C   ILE J  32 "
           pdb=" CA  ILE J  32 "
           pdb=" CB  ILE J  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  115.41    7.99     0      2.50e+00 1.60e-01 1.02e+01
  dihedral pdb=" N   ILE A  32 "
           pdb=" C   ILE A  32 "
           pdb=" CA  ILE A  32 "
           pdb=" CB  ILE A  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  115.46    7.94     0      2.50e+00 1.60e-01 1.01e+01
  ... (remaining 1737 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.056: 150
       0.056 -    0.110: 125
       0.110 -    0.165: 95
       0.165 -    0.220: 30
       0.220 -    0.275: 40
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CG  LEU C  17 "
            pdb=" CB  LEU C  17 "
            pdb=" CD1 LEU C  17 "
            pdb=" CD2 LEU C  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.86    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CG  LEU H  17 "
            pdb=" CB  LEU H  17 "
            pdb=" CD1 LEU H  17 "
            pdb=" CD2 LEU H  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.86    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CG  LEU J  17 "
            pdb=" CB  LEU J  17 "
            pdb=" CD1 LEU J  17 "
            pdb=" CD2 LEU J  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.86    0.27 2.00e-01 2.50e+01 1.88e+00
  ... (remaining 437 not shown)

  Planarity restraints: 550
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  19 "    0.023 2.00e-02 2.50e+03   1.91e-02 6.41e+00
        pdb=" CG  PHE C  19 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  19 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  19 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  19 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  19 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  19 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  19 "   -0.023 2.00e-02 2.50e+03   1.91e-02 6.41e+00
        pdb=" CG  PHE H  19 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  19 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  19 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  19 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  19 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  19 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  19 "    0.023 2.00e-02 2.50e+03   1.90e-02 6.31e+00
        pdb=" CG  PHE A  19 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  19 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  19 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  19 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  19 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  19 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 547 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 1772
        2.99 -     3.47: 2833
        3.47 -     3.94: 5149
        3.94 -     4.42: 5764
        4.42 -     4.90: 11141
  Nonbonded interactions: 26659
  Sorted by model distance:
  nonbonded pdb=" O   ASP A   1 "
            pdb=" OE1 GLU A   3 "
     model   vdw
     2.508 3.040
  nonbonded pdb=" O   ASP F   1 "
            pdb=" OE1 GLU F   3 "
     model   vdw
     2.509 3.040
  nonbonded pdb=" O   ASP C   1 "
            pdb=" OE1 GLU C   3 "
     model   vdw
     2.509 3.040
  nonbonded pdb=" O   ASP H   1 "
            pdb=" OE1 GLU H   3 "
     model   vdw
     2.509 3.040
  nonbonded pdb=" O   ASP J   1 "
            pdb=" OE1 GLU J   3 "
     model   vdw
     2.510 3.040
  ... (remaining 26654 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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 group one per residue
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:             1.030
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.780
  Find NCS groups from input model:        0.020
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
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      :  0.013   0.045   3110  Z= 0.962
  Angle     :  3.090  32.249   4170  Z= 2.193
  Chirality :  0.121   0.275    440
  Planarity :  0.008   0.022    550
  Dihedral  :  7.402  37.119   1060
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  :  6.45 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.43), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.58 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C   5 
 TYR   0.042   0.010   TYR G  10 
 PHE   0.039   0.012   PHE C  19 
 HIS   0.010   0.005   HIS G   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.01257 ( 3110)
  covalent geometry    : angle       3.09036 ( 4170)
  hydrogen bonds       : bond        0.12604 (   98)
  hydrogen bonds       : angle       8.86014 (  294)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 GLU cc_start: 0.5564 (mp0) cc_final: 0.4830 (tm-30)
REVERT: B   16 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.7043 (ttpt)
REVERT: E   19 PHE cc_start: 0.7706 (m-80) cc_final: 0.7343 (m-80)
REVERT: G    3 GLU cc_start: 0.5571 (mp0) cc_final: 0.4837 (tm-30)
REVERT: G   16 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.7048 (ttpt)
REVERT: J   23 ASP cc_start: 0.6333 (t0) cc_final: 0.6127 (t0)
  outliers start: 10
  outliers final: 0
  residues processed: 150
  average time/residue: 0.0679
  time to fit residues: 12.1649
Evaluate side-chains
  99 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LYS
Chi-restraints excluded: chain G residue   16 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A   6 HIS
C   6 HIS
D   6 HIS
E   6 HIS
F   6 HIS
H   6 HIS
I   6 HIS
J   6 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.110007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.089950 restraints weight = 5468.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.092426 restraints weight = 2213.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.093991 restraints weight = 1414.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.094758 restraints weight = 1118.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.094931 restraints weight = 998.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3110  Z= 0.158
  Angle     :  0.815   8.347   4170  Z= 0.411
  Chirality :  0.054   0.138    440
  Planarity :  0.003   0.014    550
  Dihedral  :  6.615  20.002    418
  Min Nonbonded Distance : 2.659

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.52 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (0.36), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG J   5 
 TYR   0.017   0.004   TYR F  10 
 PHE   0.013   0.003   PHE J  20 
 HIS   0.006   0.002   HIS D   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3110)
  covalent geometry    : angle       0.81475 ( 4170)
  hydrogen bonds       : bond        0.02275 (   98)
  hydrogen bonds       : angle       5.76661 (  294)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 GLU cc_start: 0.6747 (mp0) cc_final: 0.5865 (tm-30)
  outliers start: 10
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0542
  time to fit residues: 7.0722
Evaluate side-chains
  71 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   chunk 16 optimal weight:   20.0000
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 32 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
A   6 HIS
E   6 HIS
F   6 HIS
J   6 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.100304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.080851 restraints weight = 5735.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.083053 restraints weight = 2336.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.084403 restraints weight = 1496.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.085066 restraints weight = 1194.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.085494 restraints weight = 1076.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.4520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   3110  Z= 0.238
  Angle     :  0.715   8.213   4170  Z= 0.371
  Chirality :  0.053   0.142    440
  Planarity :  0.003   0.016    550
  Dihedral  :  5.620  14.332    410
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 17.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 10.97 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.21 (0.33), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.002   ARG I   5 
 TYR   0.014   0.003   TYR C  10 
 PHE   0.012   0.002   PHE I   4 
 HIS   0.007   0.002   HIS J  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 3110)
  covalent geometry    : angle       0.71470 ( 4170)
  hydrogen bonds       : bond        0.02417 (   98)
  hydrogen bonds       : angle       5.08628 (  294)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 5
  residues processed: 85
  average time/residue: 0.0431
  time to fit residues: 4.7825
Evaluate side-chains
  76 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain E residue    6 HIS
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain J residue    6 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 12 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 25 optimal weight:    9.9990
   chunk 9 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   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   6 HIS
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   6 HIS
H   6 HIS
** J  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.094827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.076103 restraints weight = 6069.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.078099 restraints weight = 2461.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.079216 restraints weight = 1599.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.079770 restraints weight = 1304.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.080090 restraints weight = 1184.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.5272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038   3110  Z= 0.373
  Angle     :  0.755   7.323   4170  Z= 0.412
  Chirality :  0.057   0.172    440
  Planarity :  0.004   0.028    550
  Dihedral  :  5.798  13.759    410
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 19.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 10.97 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.59 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG I   5 
 TYR   0.016   0.003   TYR C  10 
 PHE   0.013   0.003   PHE H   4 
 HIS   0.011   0.005   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00733 ( 3110)
  covalent geometry    : angle       0.75527 ( 4170)
  hydrogen bonds       : bond        0.02385 (   98)
  hydrogen bonds       : angle       5.17973 (  294)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0534
  time to fit residues: 5.1746
Evaluate side-chains
  74 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 HIS
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain F residue    6 HIS
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   12 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:   20.0000
   chunk 35 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 3 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 39 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 HIS
F   6 HIS
J   6 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.097775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.077529 restraints weight = 5824.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.079588 restraints weight = 2314.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.080705 restraints weight = 1525.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.081251 restraints weight = 1259.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.081298 restraints weight = 1159.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.5541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   3110  Z= 0.204
  Angle     :  0.644   6.992   4170  Z= 0.333
  Chirality :  0.052   0.131    440
  Planarity :  0.003   0.027    550
  Dihedral  :  5.097  12.892    410
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.58 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.71 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D   5 
 TYR   0.010   0.002   TYR I  10 
 PHE   0.010   0.002   PHE F  19 
 HIS   0.006   0.002   HIS F   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 3110)
  covalent geometry    : angle       0.64439 ( 4170)
  hydrogen bonds       : bond        0.01902 (   98)
  hydrogen bonds       : angle       5.09770 (  294)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 GLU cc_start: 0.6616 (mp0) cc_final: 0.5671 (tm-30)
REVERT: G    3 GLU cc_start: 0.6638 (mp0) cc_final: 0.5668 (tm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 83
  average time/residue: 0.0507
  time to fit residues: 5.2881
Evaluate side-chains
  75 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   16 LYS
Chi-restraints excluded: chain E residue    6 HIS
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain J residue    6 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 39 optimal weight:    0.4980
   chunk 20 optimal weight:   20.0000
   chunk 12 optimal weight:   10.0000
   chunk 23 optimal weight:    0.1980
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 HIS
F   6 HIS
J   6 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.096894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.076941 restraints weight = 5783.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.078944 restraints weight = 2329.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.079961 restraints weight = 1541.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.080630 restraints weight = 1283.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.080801 restraints weight = 1166.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.5759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   3110  Z= 0.193
  Angle     :  0.614   6.357   4170  Z= 0.320
  Chirality :  0.051   0.131    440
  Planarity :  0.003   0.029    550
  Dihedral  :  5.004  14.698    410
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.55 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.87 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D   5 
 TYR   0.008   0.002   TYR I  10 
 PHE   0.015   0.002   PHE E   4 
 HIS   0.010   0.002   HIS J   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3110)
  covalent geometry    : angle       0.61411 ( 4170)
  hydrogen bonds       : bond        0.01743 (   98)
  hydrogen bonds       : angle       4.94041 (  294)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 GLU cc_start: 0.6749 (mp0) cc_final: 0.5925 (tm-30)
REVERT: C    3 GLU cc_start: 0.6398 (mp0) cc_final: 0.5601 (tm-30)
REVERT: G    3 GLU cc_start: 0.6636 (mp0) cc_final: 0.5688 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 80
  average time/residue: 0.0432
  time to fit residues: 4.6318
Evaluate side-chains
  76 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain D residue   16 LYS
Chi-restraints excluded: chain F residue    6 HIS
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 20 optimal weight:   20.0000
   chunk 29 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 34 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    6.9992

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

Flipped N/Q/H residues before XYZ refinement:
E   6 HIS
F   6 HIS
J   6 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.091733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.073210 restraints weight = 6452.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.074941 restraints weight = 2717.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.075947 restraints weight = 1804.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.076404 restraints weight = 1475.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.076716 restraints weight = 1356.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.6165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.034   3110  Z= 0.386
  Angle     :  0.742   6.126   4170  Z= 0.411
  Chirality :  0.055   0.159    440
  Planarity :  0.004   0.032    550
  Dihedral  :  5.785  13.979    410
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 19.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 12.90 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.38 (0.27), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.21), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D   5 
 TYR   0.011   0.002   TYR E  10 
 PHE   0.014   0.003   PHE G  19 
 HIS   0.013   0.005   HIS E  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00757 ( 3110)
  covalent geometry    : angle       0.74185 ( 4170)
  hydrogen bonds       : bond        0.02212 (   98)
  hydrogen bonds       : angle       5.33830 (  294)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.131 
Fit side-chains
REVERT: B    3 GLU cc_start: 0.6651 (mp0) cc_final: 0.5679 (tm-30)
REVERT: G    3 GLU cc_start: 0.6681 (mp0) cc_final: 0.5683 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 79
  average time/residue: 0.0406
  time to fit residues: 4.3336
Evaluate side-chains
  74 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   16 LYS
Chi-restraints excluded: chain E residue    6 HIS
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain J residue    6 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 35 optimal weight:   20.0000
   chunk 22 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   overall best weight:    4.9388

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

Flipped N/Q/H residues before XYZ refinement:
E   6 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.093140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.074194 restraints weight = 6271.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.075898 restraints weight = 2601.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.076845 restraints weight = 1732.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.077312 restraints weight = 1439.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.077372 restraints weight = 1327.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.6333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3110  Z= 0.284
  Angle     :  0.680   5.981   4170  Z= 0.370
  Chirality :  0.054   0.149    440
  Planarity :  0.003   0.023    550
  Dihedral  :  5.501  13.469    410
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 18.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.16 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.43 (0.27), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.61 (0.21), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D   5 
 TYR   0.010   0.002   TYR E  10 
 PHE   0.011   0.002   PHE E   4 
 HIS   0.009   0.003   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 3110)
  covalent geometry    : angle       0.68039 ( 4170)
  hydrogen bonds       : bond        0.01673 (   98)
  hydrogen bonds       : angle       5.38344 (  294)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.133 
Fit side-chains
REVERT: B    3 GLU cc_start: 0.6490 (mp0) cc_final: 0.5640 (tm-30)
REVERT: C    3 GLU cc_start: 0.6429 (mp0) cc_final: 0.5722 (tm-30)
REVERT: G    3 GLU cc_start: 0.6539 (mp0) cc_final: 0.5656 (tm-30)
REVERT: H    3 GLU cc_start: 0.6492 (mp0) cc_final: 0.5665 (tm-30)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.0396
  time to fit residues: 4.3049
Evaluate side-chains
  76 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   12 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.092928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.073783 restraints weight = 6312.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.075453 restraints weight = 2699.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.076452 restraints weight = 1808.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.076892 restraints weight = 1497.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.077179 restraints weight = 1381.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.6503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   3110  Z= 0.274
  Angle     :  0.684   6.393   4170  Z= 0.370
  Chirality :  0.054   0.151    440
  Planarity :  0.003   0.020    550
  Dihedral  :  5.385  13.567    410
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 18.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.48 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.55 (0.27), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.21), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D   5 
 TYR   0.008   0.002   TYR E  10 
 PHE   0.013   0.002   PHE F  19 
 HIS   0.009   0.003   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 ( 3110)
  covalent geometry    : angle       0.68434 ( 4170)
  hydrogen bonds       : bond        0.01682 (   98)
  hydrogen bonds       : angle       5.22181 (  294)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.127 
Fit side-chains
REVERT: B    3 GLU cc_start: 0.6677 (mp0) cc_final: 0.5844 (tm-30)
REVERT: C    3 GLU cc_start: 0.6442 (mp0) cc_final: 0.5662 (tm-30)
REVERT: F   15 GLN cc_start: 0.8356 (tt0) cc_final: 0.8065 (mt0)
REVERT: G    3 GLU cc_start: 0.6585 (mp0) cc_final: 0.5684 (tm-30)
REVERT: H    3 GLU cc_start: 0.6445 (mp0) cc_final: 0.5772 (tm-30)
  outliers start: 5
  outliers final: 4
  residues processed: 78
  average time/residue: 0.0380
  time to fit residues: 4.0436
Evaluate side-chains
  77 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   12 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 3 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.091069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.072221 restraints weight = 6349.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.073809 restraints weight = 2791.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.074761 restraints weight = 1890.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.075203 restraints weight = 1569.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.075325 restraints weight = 1443.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.6660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.034   3110  Z= 0.333
  Angle     :  0.720   5.962   4170  Z= 0.396
  Chirality :  0.055   0.153    440
  Planarity :  0.004   0.026    550
  Dihedral  :  5.649  13.833    410
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.13 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.62 (0.28), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.21), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D   5 
 TYR   0.011   0.002   TYR E  10 
 PHE   0.013   0.003   PHE F  19 
 HIS   0.011   0.004   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00668 ( 3110)
  covalent geometry    : angle       0.72039 ( 4170)
  hydrogen bonds       : bond        0.01833 (   98)
  hydrogen bonds       : angle       5.32502 (  294)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.222 
Fit side-chains
REVERT: B    3 GLU cc_start: 0.6552 (mp0) cc_final: 0.5591 (tm-30)
REVERT: G    3 GLU cc_start: 0.6644 (mp0) cc_final: 0.5614 (tm-30)
  outliers start: 5
  outliers final: 4
  residues processed: 74
  average time/residue: 0.0379
  time to fit residues: 3.9195
Evaluate side-chains
  71 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   12 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 26 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   overall best weight:    4.9388

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.091975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.072836 restraints weight = 6357.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.074484 restraints weight = 2716.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.075458 restraints weight = 1824.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.075915 restraints weight = 1513.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.076021 restraints weight = 1392.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.6729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   3110  Z= 0.275
  Angle     :  0.689   6.124   4170  Z= 0.374
  Chirality :  0.054   0.155    440
  Planarity :  0.003   0.019    550
  Dihedral  :  5.434  14.280    410
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 17.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 16.45 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.65 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D   5 
 TYR   0.010   0.002   TYR E  10 
 PHE   0.013   0.002   PHE F  19 
 HIS   0.009   0.003   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 ( 3110)
  covalent geometry    : angle       0.68858 ( 4170)
  hydrogen bonds       : bond        0.01695 (   98)
  hydrogen bonds       : angle       5.34762 (  294)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 636.00 seconds
wall clock time: 11 minutes 38.79 seconds (698.79 seconds total)