Starting phenix.real_space_refine
on Fri Aug 22 18:29:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6shs_10204/08_2025/6shs_10204.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6shs_10204/08_2025/6shs_10204.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6shs_10204/08_2025/6shs_10204.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6shs_10204/08_2025/6shs_10204.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6shs_10204/08_2025/6shs_10204.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6shs_10204/08_2025/6shs_10204.cif"
  }
  resolution = 4.4
  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=   0.000 sd=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    2328      2.51       5
     N     636      2.21       5
     O     684      1.98       5
     H    3408      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  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: 7068
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 589
          Classifications: {'peptide': 40}
          Modifications used: {'NH3': 1}
          Link IDs: {'TRANS': 39}
  Restraints were copied for chains:
    B, C, H, D, I, E, J, F, K, G, L
  Time building chain proxies: 0.84, per 1000 atoms: 0.12
  Number of scatterers: 7068
  At special positions: 0
  Unit cell: (70.2, 98.55, 48.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     O     684      8.00
     N     636      7.00
     C    2328      6.00
     H    3408      1.00
    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: 0.58
  Conformation dependent library (CDL) restraints added in 227.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  816

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 36.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 12
      removed outlier: 7.103A  pdb=" N   TYR D  10 " --> pdb=" O   GLY C   9 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   GLU C  11 " --> pdb=" O   TYR D  10 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   VAL D  12 " --> pdb=" O   GLU C  11 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   TYR C  10 " --> pdb=" O   GLY A   9 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   GLU A  11 " --> pdb=" O   TYR C  10 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   VAL C  12 " --> pdb=" O   GLU A  11 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ALA A   2 " --> pdb=" O   GLU E   3 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   ARG E   5 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   PHE A   4 " --> pdb=" O   ARG E   5 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   ASP E   7 " --> pdb=" O   PHE A   4 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   HIS A   6 " --> pdb=" O   ASP E   7 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   GLY E   9 " --> pdb=" O   HIS A   6 " (cutoff:3.500A)
      removed outlier: 8.325A  pdb=" N   SER A   8 " --> pdb=" O   GLY E   9 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   GLU E  11 " --> pdb=" O   SER A   8 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   TYR A  10 " --> pdb=" O   GLU E  11 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ALA E   2 " --> pdb=" O   GLU F   3 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   ARG F   5 " --> pdb=" O   ALA E   2 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   PHE E   4 " --> pdb=" O   ARG F   5 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   ASP F   7 " --> pdb=" O   PHE E   4 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   HIS E   6 " --> pdb=" O   ASP F   7 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   GLY F   9 " --> pdb=" O   HIS E   6 " (cutoff:3.500A)
      removed outlier: 8.325A  pdb=" N   SER E   8 " --> pdb=" O   GLY F   9 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   GLU F  11 " --> pdb=" O   SER E   8 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   TYR E  10 " --> pdb=" O   GLU F  11 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ALA F   2 " --> pdb=" O   GLU G   3 " (cutoff:3.500A)
      removed outlier: 8.721A  pdb=" N   ARG G   5 " --> pdb=" O   ALA F   2 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   PHE F   4 " --> pdb=" O   ARG G   5 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   ASP G   7 " --> pdb=" O   PHE F   4 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   HIS F   6 " --> pdb=" O   ASP G   7 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   GLY G   9 " --> pdb=" O   HIS F   6 " (cutoff:3.500A)
      removed outlier: 8.326A  pdb=" N   SER F   8 " --> pdb=" O   GLY G   9 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   GLU G  11 " --> pdb=" O   SER F   8 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   TYR F  10 " --> pdb=" O   GLU G  11 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 15 through 19
      removed outlier: 6.497A  pdb=" N   LYS A  16 " --> pdb=" O   LEU E  17 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   PHE E  19 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL A  18 " --> pdb=" O   PHE E  19 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LYS E  16 " --> pdb=" O   LEU F  17 " (cutoff:3.500A)
      removed outlier: 8.300A  pdb=" N   PHE F  19 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL E  18 " --> pdb=" O   PHE F  19 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LYS F  16 " --> pdb=" O   LEU G  17 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   PHE G  19 " --> pdb=" O   LYS F  16 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL F  18 " --> pdb=" O   PHE G  19 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 33 through 34
      removed outlier: 6.754A  pdb=" N   GLY C  33 " --> pdb=" O   LEU D  34 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   GLY A  33 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'I' and resid 3 through 12
      removed outlier: 6.098A  pdb=" N   GLU H   3 " --> pdb=" O   PHE I   4 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   HIS I   6 " --> pdb=" O   GLU H   3 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ARG H   5 " --> pdb=" O   HIS I   6 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   SER I   8 " --> pdb=" O   ARG H   5 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ASP H   7 " --> pdb=" O   SER I   8 " (cutoff:3.500A)
      removed outlier: 8.839A  pdb=" N   TYR I  10 " --> pdb=" O   ASP H   7 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   GLY H   9 " --> pdb=" O   TYR I  10 " (cutoff:3.500A)
      removed outlier: 9.732A  pdb=" N   VAL I  12 " --> pdb=" O   GLY H   9 " (cutoff:3.500A)
      removed outlier: 9.033A  pdb=" N   GLU H  11 " --> pdb=" O   VAL I  12 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   GLU B   3 " --> pdb=" O   PHE H   4 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   HIS H   6 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ARG B   5 " --> pdb=" O   HIS H   6 " (cutoff:3.500A)
      removed outlier: 8.198A  pdb=" N   SER H   8 " --> pdb=" O   ARG B   5 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ASP B   7 " --> pdb=" O   SER H   8 " (cutoff:3.500A)
      removed outlier: 8.839A  pdb=" N   TYR H  10 " --> pdb=" O   ASP B   7 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   GLY B   9 " --> pdb=" O   TYR H  10 " (cutoff:3.500A)
      removed outlier: 9.732A  pdb=" N   VAL H  12 " --> pdb=" O   GLY B   9 " (cutoff:3.500A)
      removed outlier: 9.032A  pdb=" N   GLU B  11 " --> pdb=" O   VAL H  12 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   TYR B  10 " --> pdb=" O   GLY J   9 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   GLU J  11 " --> pdb=" O   TYR B  10 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   VAL B  12 " --> pdb=" O   GLU J  11 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   TYR J  10 " --> pdb=" O   GLY K   9 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   GLU K  11 " --> pdb=" O   TYR J  10 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   VAL J  12 " --> pdb=" O   GLU K  11 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   TYR K  10 " --> pdb=" O   GLY L   9 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   GLU L  11 " --> pdb=" O   TYR K  10 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   VAL K  12 " --> pdb=" O   GLU L  11 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'I' and resid 15 through 19
      removed outlier: 6.441A  pdb=" N   LYS B  16 " --> pdb=" O   LEU J  17 " (cutoff:3.500A)
      removed outlier: 8.243A  pdb=" N   PHE J  19 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   VAL B  18 " --> pdb=" O   PHE J  19 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   LYS J  16 " --> pdb=" O   LEU K  17 " (cutoff:3.500A)
      removed outlier: 8.243A  pdb=" N   PHE K  19 " --> pdb=" O   LYS J  16 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   VAL J  18 " --> pdb=" O   PHE K  19 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   LYS K  16 " --> pdb=" O   LEU L  17 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   PHE L  19 " --> pdb=" O   LYS K  16 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   VAL K  18 " --> pdb=" O   PHE L  19 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'I' and resid 33 through 34
      removed outlier: 6.806A  pdb=" N   GLY H  33 " --> pdb=" O   LEU I  34 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   GLY B  33 " --> pdb=" O   LEU H  34 " (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: 1.35

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3408
        1.03 -     1.22: 0
        1.22 -     1.41: 1668
        1.41 -     1.61: 2040
        1.61 -     1.80: 24
  Bond restraints: 7140
  Sorted by residual:
  bond pdb=" CG1 ILE H  31 "
       pdb=" CD1 ILE H  31 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.20e+00
  bond pdb=" CG1 ILE C  31 "
       pdb=" CD1 ILE C  31 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.18e+00
  bond pdb=" CG1 ILE E  31 "
       pdb=" CD1 ILE E  31 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.18e+00
  bond pdb=" CG1 ILE G  31 "
       pdb=" CD1 ILE G  31 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.18e+00
  bond pdb=" CG1 ILE A  31 "
       pdb=" CD1 ILE A  31 "
    ideal  model  delta    sigma   weight residual
    1.513  1.456  0.057 3.90e-02 6.57e+02 2.17e+00
  ... (remaining 7135 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 10163
        0.99 -     1.98: 2172
        1.98 -     2.96: 336
        2.96 -     3.95: 73
        3.95 -     4.94: 48
  Bond angle restraints: 12792
  Sorted by residual:
  angle pdb=" C   HIS J  13 "
        pdb=" CA  HIS J  13 "
        pdb=" CB  HIS J  13 "
      ideal   model   delta    sigma   weight residual
     111.95  107.01    4.94 2.38e+00 1.77e-01 4.31e+00
  angle pdb=" C   HIS C  13 "
        pdb=" CA  HIS C  13 "
        pdb=" CB  HIS C  13 "
      ideal   model   delta    sigma   weight residual
     111.95  107.02    4.93 2.38e+00 1.77e-01 4.29e+00
  angle pdb=" C   HIS E  13 "
        pdb=" CA  HIS E  13 "
        pdb=" CB  HIS E  13 "
      ideal   model   delta    sigma   weight residual
     111.95  107.03    4.92 2.38e+00 1.77e-01 4.27e+00
  angle pdb=" C   HIS L  13 "
        pdb=" CA  HIS L  13 "
        pdb=" CB  HIS L  13 "
      ideal   model   delta    sigma   weight residual
     111.95  107.03    4.92 2.38e+00 1.77e-01 4.27e+00
  angle pdb=" C   HIS F  13 "
        pdb=" CA  HIS F  13 "
        pdb=" CB  HIS F  13 "
      ideal   model   delta    sigma   weight residual
     111.95  107.04    4.91 2.38e+00 1.77e-01 4.26e+00
  ... (remaining 12787 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.81: 2640
       11.81 -    23.62: 420
       23.62 -    35.43: 108
       35.43 -    47.24: 60
       47.24 -    59.05: 24
  Dihedral angle restraints: 3252
    sinusoidal: 1608
      harmonic: 1644
  Sorted by residual:
  dihedral pdb=" CA  HIS J  13 "
           pdb=" C   HIS J  13 "
           pdb=" N   HIS J  14 "
           pdb=" CA  HIS J  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.26   25.74     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  HIS I  13 "
           pdb=" C   HIS I  13 "
           pdb=" N   HIS I  14 "
           pdb=" CA  HIS I  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.26   25.74     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  HIS G  13 "
           pdb=" C   HIS G  13 "
           pdb=" N   HIS G  14 "
           pdb=" CA  HIS G  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.28   25.72     0      5.00e+00 4.00e-02 2.65e+01
  ... (remaining 3249 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 194
       0.029 -    0.059: 89
       0.059 -    0.088: 116
       0.088 -    0.117: 105
       0.117 -    0.146: 24
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CB  ILE F  32 "
            pdb=" CA  ILE F  32 "
            pdb=" CG1 ILE F  32 "
            pdb=" CG2 ILE F  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CB  ILE C  32 "
            pdb=" CA  ILE C  32 "
            pdb=" CG1 ILE C  32 "
            pdb=" CG2 ILE C  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.32e-01
  chirality pdb=" CB  ILE H  32 "
            pdb=" CA  ILE H  32 "
            pdb=" CG1 ILE H  32 "
            pdb=" CG2 ILE H  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.31e-01
  ... (remaining 525 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU H  17 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.56e+00
        pdb=" C   LEU H  17 "    0.022 2.00e-02 2.50e+03
        pdb=" O   LEU H  17 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   VAL H  18 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E  17 "    0.006 2.00e-02 2.50e+03   1.25e-02 1.55e+00
        pdb=" C   LEU E  17 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   LEU E  17 "    0.008 2.00e-02 2.50e+03
        pdb=" N   VAL E  18 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F  17 "    0.006 2.00e-02 2.50e+03   1.24e-02 1.53e+00
        pdb=" C   LEU F  17 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   LEU F  17 "    0.008 2.00e-02 2.50e+03
        pdb=" N   VAL F  18 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.27: 1167
        2.27 -     2.85: 14919
        2.85 -     3.43: 16491
        3.43 -     4.02: 23667
        4.02 -     4.60: 34418
  Nonbonded interactions: 90662
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU E  11 "
            pdb=" HZ1 LYS E  16 "
     model   vdw
     1.684 2.450
  nonbonded pdb=" OE1 GLU C  11 "
            pdb=" HZ1 LYS C  16 "
     model   vdw
     1.684 2.450
  nonbonded pdb=" OE1 GLU F  11 "
            pdb=" HZ1 LYS F  16 "
     model   vdw
     1.684 2.450
  nonbonded pdb=" OE1 GLU K  11 "
            pdb=" HZ1 LYS K  16 "
     model   vdw
     1.684 2.450
  nonbonded pdb=" OE1 GLU G  11 "
            pdb=" HZ1 LYS G  16 "
     model   vdw
     1.684 2.450
  ... (remaining 90657 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'H'
  selection = chain 'D'
  selection = chain 'I'
  selection = chain 'E'
  selection = chain 'J'
  selection = chain 'F'
  selection = chain 'K'
  selection = chain 'G'
  selection = chain 'L'
}

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:             0.230
  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:             0.040
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.870
  Find NCS groups from input model:        0.050
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
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      :  0.009   0.058   3732  Z= 0.400
  Angle     :  1.019   4.938   5004  Z= 0.568
  Chirality :  0.065   0.146    528
  Planarity :  0.004   0.012    660
  Dihedral  : 12.042  39.868   1272
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 25.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.05 %
    Favored  : 78.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  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: -5.87 (0.22), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.47 (0.17), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG G   5 
 TYR   0.007   0.002   TYR F  10 
 PHE   0.010   0.003   PHE F   4 
 HIS   0.005   0.003   HIS K  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00871 ( 3732)
  covalent geometry    : angle       1.01919 ( 5004)
  hydrogen bonds       : bond        0.22793 (   54)
  hydrogen bonds       : angle       8.65436 (  162)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.7800 (m-10) cc_final: 0.7544 (m-10)
REVERT: B   19 PHE cc_start: 0.8540 (t80) cc_final: 0.8319 (t80)
REVERT: C   19 PHE cc_start: 0.8573 (t80) cc_final: 0.8114 (t80)
REVERT: C   32 ILE cc_start: 0.8080 (mt) cc_final: 0.7871 (mp)
REVERT: H   19 PHE cc_start: 0.8907 (t80) cc_final: 0.8679 (t80)
REVERT: J   19 PHE cc_start: 0.8864 (t80) cc_final: 0.8654 (t80)
REVERT: J   32 ILE cc_start: 0.7848 (mt) cc_final: 0.7533 (mp)
REVERT: L    5 ARG cc_start: 0.7687 (mtp180) cc_final: 0.7430 (ttm-80)
REVERT: L   20 PHE cc_start: 0.7825 (m-10) cc_final: 0.7077 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2279
  time to fit residues: 32.9188
Evaluate side-chains
  72 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.159002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.139939 restraints weight = 22961.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.144139 restraints weight = 14311.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.147379 restraints weight = 9777.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.149686 restraints weight = 7003.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.151537 restraints weight = 5253.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.4689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6450
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3732  Z= 0.132
  Angle     :  0.671   4.447   5004  Z= 0.360
  Chirality :  0.054   0.160    528
  Planarity :  0.003   0.046    660
  Dihedral  :  7.103  26.454    492
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.45 %
    Favored  : 83.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  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: -5.29 (0.23), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.03 (0.17), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG I   5 
 TYR   0.008   0.001   TYR B  10 
 PHE   0.013   0.002   PHE K  19 
 HIS   0.006   0.001   HIS J   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3732)
  covalent geometry    : angle       0.67061 ( 5004)
  hydrogen bonds       : bond        0.04650 (   54)
  hydrogen bonds       : angle       6.10641 (  162)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.8762 (t80) cc_final: 0.8510 (t80)
REVERT: B   20 PHE cc_start: 0.7975 (m-10) cc_final: 0.7557 (m-10)
REVERT: C    4 PHE cc_start: 0.5387 (m-10) cc_final: 0.4910 (m-10)
REVERT: C   19 PHE cc_start: 0.8679 (t80) cc_final: 0.8394 (t80)
REVERT: D   19 PHE cc_start: 0.8296 (t80) cc_final: 0.7818 (t80)
REVERT: E   35 MET cc_start: 0.4216 (ttt) cc_final: 0.3821 (ttt)
REVERT: F   23 ASP cc_start: 0.6213 (m-30) cc_final: 0.5929 (m-30)
REVERT: K   22 GLU cc_start: 0.7302 (tt0) cc_final: 0.5619 (mm-30)
REVERT: K   32 ILE cc_start: 0.8350 (mt) cc_final: 0.7985 (mp)
REVERT: G   35 MET cc_start: 0.4138 (ttt) cc_final: 0.3170 (mpp)
REVERT: L   20 PHE cc_start: 0.7769 (m-10) cc_final: 0.6951 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1527
  time to fit residues: 15.8455
Evaluate side-chains
  58 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 12 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    2.2166

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

Flipped N/Q/H residues before XYZ refinement:
** A  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.128770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.111835 restraints weight = 27061.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.115203 restraints weight = 16858.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.117787 restraints weight = 11560.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.119646 restraints weight = 8423.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.121174 restraints weight = 6470.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.4426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.5111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   3732  Z= 0.209
  Angle     :  0.695   4.732   5004  Z= 0.379
  Chirality :  0.053   0.138    528
  Planarity :  0.004   0.029    660
  Dihedral  :  7.258  29.018    492
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.39 %
    Favored  : 79.61 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  8.60 %
    Favored  : 91.13 %
  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: -5.65 (0.20), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.30 (0.15), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L   5 
 TYR   0.006   0.001   TYR J  10 
 PHE   0.028   0.003   PHE J   4 
 HIS   0.007   0.002   HIS K  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 3732)
  covalent geometry    : angle       0.69503 ( 5004)
  hydrogen bonds       : bond        0.05061 (   54)
  hydrogen bonds       : angle       5.84457 (  162)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8379 (m-10) cc_final: 0.7963 (m-10)
REVERT: H   35 MET cc_start: 0.3491 (ttt) cc_final: 0.3261 (ttt)
REVERT: I    4 PHE cc_start: 0.7345 (m-10) cc_final: 0.7066 (m-10)
REVERT: E   35 MET cc_start: 0.4371 (ttt) cc_final: 0.3966 (ttt)
REVERT: F   35 MET cc_start: 0.4747 (ttm) cc_final: 0.4453 (ttm)
REVERT: K   22 GLU cc_start: 0.7633 (tt0) cc_final: 0.6579 (mt-10)
REVERT: G    3 GLU cc_start: 0.7120 (tt0) cc_final: 0.6585 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1429
  time to fit residues: 13.1941
Evaluate side-chains
  53 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0970
   chunk 12 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    2.8184

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

Flipped N/Q/H residues before XYZ refinement:
** B  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  15 GLN
K  15 GLN
** G  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.122130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.105261 restraints weight = 29324.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.108176 restraints weight = 19168.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.110452 restraints weight = 13694.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.112164 restraints weight = 10359.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.113624 restraints weight = 8182.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.4314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.6382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3732  Z= 0.231
  Angle     :  0.695   5.066   5004  Z= 0.379
  Chirality :  0.054   0.144    528
  Planarity :  0.004   0.026    660
  Dihedral  :  7.034  26.342    492
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.27 %
    Favored  : 78.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  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: -5.92 (0.19), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.50 (0.15), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A   5 
 TYR   0.007   0.001   TYR J  10 
 PHE   0.018   0.004   PHE C  19 
 HIS   0.009   0.002   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 3732)
  covalent geometry    : angle       0.69466 ( 5004)
  hydrogen bonds       : bond        0.04303 (   54)
  hydrogen bonds       : angle       5.70440 (  162)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 VAL cc_start: 0.6179 (t) cc_final: 0.5949 (t)
REVERT: H   35 MET cc_start: 0.3694 (ttt) cc_final: 0.3396 (ttt)
REVERT: F   23 ASP cc_start: 0.6938 (m-30) cc_final: 0.6576 (m-30)
REVERT: K   22 GLU cc_start: 0.7416 (tt0) cc_final: 0.7214 (tt0)
REVERT: G    3 GLU cc_start: 0.7502 (tt0) cc_final: 0.6633 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1006
  time to fit residues: 8.2428
Evaluate side-chains
  47 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    0.2980
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** I  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.130535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.113722 restraints weight = 28237.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.116928 restraints weight = 17895.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.119412 restraints weight = 12475.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.121198 restraints weight = 9233.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.122680 restraints weight = 7185.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.4412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.6664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3732  Z= 0.121
  Angle     :  0.575   4.117   5004  Z= 0.316
  Chirality :  0.053   0.152    528
  Planarity :  0.002   0.014    660
  Dihedral  :  6.552  23.425    492
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.89 %
    Favored  : 83.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  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: -5.76 (0.20), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.39 (0.15), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG K   5 
 TYR   0.012   0.001   TYR J  10 
 PHE   0.019   0.003   PHE C  19 
 HIS   0.015   0.001   HIS I  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3732)
  covalent geometry    : angle       0.57543 ( 5004)
  hydrogen bonds       : bond        0.03288 (   54)
  hydrogen bonds       : angle       5.35657 (  162)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8477 (m-10) cc_final: 0.8089 (m-10)
REVERT: B   36 VAL cc_start: 0.6091 (t) cc_final: 0.5888 (t)
REVERT: C   10 TYR cc_start: 0.7056 (t80) cc_final: 0.6774 (t80)
REVERT: H   35 MET cc_start: 0.3615 (ttt) cc_final: 0.3387 (ttt)
REVERT: E   35 MET cc_start: 0.4260 (ttt) cc_final: 0.3950 (ttt)
REVERT: F   35 MET cc_start: 0.5425 (ttm) cc_final: 0.5148 (ttm)
REVERT: K   22 GLU cc_start: 0.7072 (tt0) cc_final: 0.6869 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0970
  time to fit residues: 8.4093
Evaluate side-chains
  48 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0000
   chunk 12 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
** G  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.123899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.106649 restraints weight = 28426.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.109658 restraints weight = 18271.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.112022 restraints weight = 12921.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.113827 restraints weight = 9722.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.115342 restraints weight = 7646.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.4356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.6998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3732  Z= 0.128
  Angle     :  0.564   4.209   5004  Z= 0.312
  Chirality :  0.053   0.145    528
  Planarity :  0.002   0.013    660
  Dihedral  :  6.408  22.939    492
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.20 %
    Favored  : 81.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  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: -5.71 (0.21), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.34 (0.16), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D   5 
 TYR   0.007   0.001   TYR J  10 
 PHE   0.014   0.002   PHE E  19 
 HIS   0.003   0.001   HIS K  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3732)
  covalent geometry    : angle       0.56445 ( 5004)
  hydrogen bonds       : bond        0.03226 (   54)
  hydrogen bonds       : angle       5.25501 (  162)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8300 (m-10) cc_final: 0.8055 (m-10)
REVERT: C   10 TYR cc_start: 0.7190 (t80) cc_final: 0.6981 (t80)
REVERT: E   35 MET cc_start: 0.4319 (ttt) cc_final: 0.4001 (ttt)
REVERT: F   35 MET cc_start: 0.5438 (ttm) cc_final: 0.5094 (ttm)
REVERT: L   20 PHE cc_start: 0.7655 (m-80) cc_final: 0.7355 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0911
  time to fit residues: 7.3286
Evaluate side-chains
  46 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0980
   chunk 24 optimal weight:    8.9990
   chunk 39 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** G  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.124858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.108709 restraints weight = 29001.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.111834 restraints weight = 18162.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.114172 restraints weight = 12549.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.116012 restraints weight = 9247.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.117378 restraints weight = 7093.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.7234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3732  Z= 0.121
  Angle     :  0.541   3.657   5004  Z= 0.301
  Chirality :  0.053   0.157    528
  Planarity :  0.002   0.012    660
  Dihedral  :  6.283  24.069    492
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.11 %
    Favored  : 82.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  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: -5.68 (0.21), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.33 (0.16), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D   5 
 TYR   0.006   0.001   TYR B  10 
 PHE   0.015   0.002   PHE D   4 
 HIS   0.009   0.001   HIS J  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 3732)
  covalent geometry    : angle       0.54067 ( 5004)
  hydrogen bonds       : bond        0.02987 (   54)
  hydrogen bonds       : angle       5.15339 (  162)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   35 MET cc_start: 0.4134 (ttt) cc_final: 0.3793 (ttt)
REVERT: F   35 MET cc_start: 0.5566 (ttm) cc_final: 0.5320 (ttm)
REVERT: K   22 GLU cc_start: 0.7349 (tt0) cc_final: 0.6425 (tt0)
REVERT: L   20 PHE cc_start: 0.7597 (m-80) cc_final: 0.7395 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0987
  time to fit residues: 8.1399
Evaluate side-chains
  46 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 42 optimal weight:    0.0970
   chunk 3 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
D  15 GLN
F  15 GLN
** G  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.121688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.106132 restraints weight = 29790.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.108930 restraints weight = 19646.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.111024 restraints weight = 14028.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.112736 restraints weight = 10606.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.113902 restraints weight = 8323.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.7610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3732  Z= 0.159
  Angle     :  0.583   4.437   5004  Z= 0.323
  Chirality :  0.053   0.138    528
  Planarity :  0.002   0.012    660
  Dihedral  :  6.502  24.961    492
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.83 %
    Favored  : 79.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  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: -5.71 (0.21), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.35 (0.16), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C   5 
 TYR   0.007   0.001   TYR J  10 
 PHE   0.014   0.002   PHE A  20 
 HIS   0.014   0.001   HIS G  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3732)
  covalent geometry    : angle       0.58310 ( 5004)
  hydrogen bonds       : bond        0.03387 (   54)
  hydrogen bonds       : angle       5.28169 (  162)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8083 (m-10) cc_final: 0.7521 (m-10)
REVERT: H   35 MET cc_start: 0.4536 (ttt) cc_final: 0.4332 (ttt)
REVERT: E   20 PHE cc_start: 0.7300 (m-10) cc_final: 0.7024 (m-10)
REVERT: E   35 MET cc_start: 0.4324 (ttt) cc_final: 0.3845 (ttt)
REVERT: F   35 MET cc_start: 0.6218 (ttm) cc_final: 0.6005 (ttm)
REVERT: K   22 GLU cc_start: 0.7189 (tt0) cc_final: 0.6906 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0898
  time to fit residues: 6.4679
Evaluate side-chains
  39 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 40 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.121730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.105638 restraints weight = 30044.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.108616 restraints weight = 19230.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.110946 restraints weight = 13395.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.112641 restraints weight = 9958.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.113961 restraints weight = 7767.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.7866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3732  Z= 0.165
  Angle     :  0.580   3.970   5004  Z= 0.323
  Chirality :  0.053   0.139    528
  Planarity :  0.002   0.016    660
  Dihedral  :  6.542  25.353    492
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.61 %
    Favored  : 79.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  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: -5.77 (0.20), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.40 (0.16), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D   5 
 TYR   0.008   0.001   TYR J  10 
 PHE   0.027   0.002   PHE D   4 
 HIS   0.007   0.001   HIS G  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3732)
  covalent geometry    : angle       0.57952 ( 5004)
  hydrogen bonds       : bond        0.03469 (   54)
  hydrogen bonds       : angle       5.34076 (  162)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8106 (m-10) cc_final: 0.7766 (m-10)
REVERT: H   35 MET cc_start: 0.4414 (ttt) cc_final: 0.4199 (ttt)
REVERT: D   15 GLN cc_start: 0.7836 (mt0) cc_final: 0.7162 (tp40)
REVERT: E   35 MET cc_start: 0.3862 (ttt) cc_final: 0.3506 (ttt)
REVERT: K   22 GLU cc_start: 0.7016 (tt0) cc_final: 0.6764 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1051
  time to fit residues: 7.1610
Evaluate side-chains
  40 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.123685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.107785 restraints weight = 29412.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.110795 restraints weight = 18260.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.113182 restraints weight = 12626.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.114973 restraints weight = 9283.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.116363 restraints weight = 7134.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.7989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3732  Z= 0.097
  Angle     :  0.526   4.009   5004  Z= 0.292
  Chirality :  0.052   0.144    528
  Planarity :  0.002   0.011    660
  Dihedral  :  6.204  24.057    492
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.98 %
    Favored  : 82.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  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: -5.64 (0.21), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.29 (0.16), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K   5 
 TYR   0.005   0.001   TYR K  10 
 PHE   0.023   0.002   PHE D   4 
 HIS   0.005   0.001   HIS E  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 3732)
  covalent geometry    : angle       0.52582 ( 5004)
  hydrogen bonds       : bond        0.02937 (   54)
  hydrogen bonds       : angle       5.11741 (  162)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   15 GLN cc_start: 0.7822 (mt0) cc_final: 0.7092 (tt0)
REVERT: K   22 GLU cc_start: 0.6780 (tt0) cc_final: 0.6575 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0732
  time to fit residues: 5.4660
Evaluate side-chains
  40 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 12 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 16 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** G  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.125507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.109556 restraints weight = 29002.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.112718 restraints weight = 17994.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.115181 restraints weight = 12285.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.116978 restraints weight = 8954.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.118322 restraints weight = 6835.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.4383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.8005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3732  Z= 0.088
  Angle     :  0.510   4.159   5004  Z= 0.285
  Chirality :  0.053   0.144    528
  Planarity :  0.002   0.012    660
  Dihedral  :  5.936  22.760    492
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.23 %
    Favored  : 83.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -5.58 (0.22), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.25 (0.17), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C   5 
 TYR   0.005   0.001   TYR K  10 
 PHE   0.021   0.002   PHE D   4 
 HIS   0.010   0.001   HIS E  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 3732)
  covalent geometry    : angle       0.51023 ( 5004)
  hydrogen bonds       : bond        0.02749 (   54)
  hydrogen bonds       : angle       4.99452 (  162)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1652.75 seconds
wall clock time: 29 minutes 6.47 seconds (1746.47 seconds total)