Starting phenix.real_space_refine
on Tue Feb 11 23:53:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6shs_10204/02_2025/6shs_10204.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6shs_10204/02_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_10204/02_2025/6shs_10204.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6shs_10204/02_2025/6shs_10204.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6shs_10204/02_2025/6shs_10204.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6shs_10204/02_2025/6shs_10204.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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:
    C, B, E, D, G, F, I, H, K, J, L
  Time building chain proxies: 2.12, per 1000 atoms: 0.30
  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: 1.47
  Conformation dependent library (CDL) restraints added in 659.0 milliseconds
  

  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: 0.85
  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: 2.37

  Time building geometry restraints manager: 1.85 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  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:             0.170
  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:             0.130
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     16.260
  Find NCS groups from input model:        0.110
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.880
-------------------------------------------------------------------------------
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= 0.618
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.87 (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
 HIS   0.005   0.003   HIS K  14 
 PHE   0.010   0.003   PHE F   4 
 TYR   0.007   0.002   TYR F  10 
 ARG   0.003   0.001   ARG G   5 

*********************** 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  : 0.556 
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: B   19 PHE cc_start: 0.8540 (t80) cc_final: 0.8324 (t80)
REVERT: C   19 PHE cc_start: 0.8573 (t80) cc_final: 0.8113 (t80)
REVERT: C   32 ILE cc_start: 0.8080 (mt) cc_final: 0.7879 (mp)
REVERT: H   19 PHE cc_start: 0.8907 (t80) cc_final: 0.8675 (t80)
REVERT: J   19 PHE cc_start: 0.8864 (t80) cc_final: 0.8651 (t80)
REVERT: J   32 ILE cc_start: 0.7848 (mt) cc_final: 0.7524 (mp)
REVERT: G    6 HIS cc_start: 0.8247 (t-90) cc_final: 0.7971 (t-170)
REVERT: L    5 ARG cc_start: 0.7687 (mtp180) cc_final: 0.7431 (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: 0.4798
  time to fit residues: 69.2654
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  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
L  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.144152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.126838 restraints weight = 25363.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.130621 restraints weight = 15932.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.133382 restraints weight = 10916.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.4505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6792
moved from start:          0.3988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   3732  Z= 0.291
  Angle     :  0.747   5.186   5004  Z= 0.401
  Chirality :  0.056   0.154    528
  Planarity :  0.005   0.059    660
  Dihedral  :  7.497  29.222    492
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.18 %
    Favored  : 79.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.63 (0.20), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.29 (0.15), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS J   6 
 PHE   0.015   0.003   PHE K  19 
 TYR   0.011   0.001   TYR B  10 
 ARG   0.006   0.001   ARG E   5 

*********************** 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
  81 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.598 
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: B   10 TYR cc_start: 0.6173 (t80) cc_final: 0.5965 (t80)
REVERT: C    4 PHE cc_start: 0.6599 (m-10) cc_final: 0.6341 (m-10)
REVERT: E   35 MET cc_start: 0.4295 (ttt) cc_final: 0.3848 (ttt)
REVERT: F   23 ASP cc_start: 0.6453 (m-30) cc_final: 0.5979 (m-30)
REVERT: F   35 MET cc_start: 0.4780 (ttm) cc_final: 0.4468 (ttm)
REVERT: G   35 MET cc_start: 0.4346 (ttt) cc_final: 0.3194 (mpp)
REVERT: L   20 PHE cc_start: 0.7959 (m-10) cc_final: 0.7130 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.3368
  time to fit residues: 33.9411
Evaluate side-chains
  54 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 38 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
H  27 ASN
I  27 ASN
J  27 ASN
K  27 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.142337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.126295 restraints weight = 24730.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.129852 restraints weight = 14744.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.132371 restraints weight = 9893.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.4551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.4917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3732  Z= 0.168
  Angle     :  0.571   3.748   5004  Z= 0.312
  Chirality :  0.051   0.144    528
  Planarity :  0.002   0.018    660
  Dihedral  :  6.593  24.023    492
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.82 %
    Favored  : 86.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.38 (0.22), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.10 (0.16), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS K  13 
 PHE   0.018   0.002   PHE H  19 
 TYR   0.010   0.001   TYR B  10 
 ARG   0.002   0.000   ARG F   5 

*********************** 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
  76 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 ASP cc_start: 0.7326 (m-30) cc_final: 0.6878 (m-30)
REVERT: H   35 MET cc_start: 0.3614 (ttt) cc_final: 0.3361 (ttt)
REVERT: E   35 MET cc_start: 0.4470 (ttt) cc_final: 0.4135 (ttt)
REVERT: J   20 PHE cc_start: 0.7658 (m-10) cc_final: 0.7331 (m-10)
REVERT: F   35 MET cc_start: 0.4883 (ttm) cc_final: 0.4519 (ttm)
REVERT: K   20 PHE cc_start: 0.7712 (m-10) cc_final: 0.6764 (m-10)
REVERT: K   22 GLU cc_start: 0.7252 (tt0) cc_final: 0.7021 (tt0)
REVERT: G   35 MET cc_start: 0.4700 (ttt) cc_final: 0.3601 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.3418
  time to fit residues: 31.8041
Evaluate side-chains
  54 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 34 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    0.4980
   chunk 2 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
J  27 ASN
K  27 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.140125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.123433 restraints weight = 26367.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.127107 restraints weight = 15876.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.129813 restraints weight = 10741.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.4502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.5477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3732  Z= 0.174
  Angle     :  0.557   4.124   5004  Z= 0.302
  Chirality :  0.052   0.145    528
  Planarity :  0.002   0.013    660
  Dihedral  :  6.357  22.757    492
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.23 %
    Favored  : 83.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.34 (0.22), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.07 (0.17), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  13 
 PHE   0.019   0.002   PHE C   4 
 TYR   0.006   0.001   TYR B  10 
 ARG   0.004   0.001   ARG A   5 

*********************** 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
  70 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 PHE cc_start: 0.6321 (m-10) cc_final: 0.6080 (m-10)
REVERT: A   23 ASP cc_start: 0.7534 (m-30) cc_final: 0.6932 (m-30)
REVERT: B   20 PHE cc_start: 0.8365 (m-10) cc_final: 0.7897 (m-10)
REVERT: H   35 MET cc_start: 0.3524 (ttt) cc_final: 0.3244 (ttt)
REVERT: J   20 PHE cc_start: 0.7800 (m-10) cc_final: 0.7163 (m-10)
REVERT: F   35 MET cc_start: 0.4892 (ttm) cc_final: 0.4543 (ttm)
REVERT: K   22 GLU cc_start: 0.7097 (tt0) cc_final: 0.6767 (tt0)
REVERT: G   35 MET cc_start: 0.4700 (ttt) cc_final: 0.3504 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.2872
  time to fit residues: 25.7700
Evaluate side-chains
  54 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
H  15 GLN
H  27 ASN
I  27 ASN
F  15 GLN
K  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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.128712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.111582 restraints weight = 28181.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.114700 restraints weight = 17944.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.117156 restraints weight = 12624.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.6528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3732  Z= 0.281
  Angle     :  0.649   4.717   5004  Z= 0.351
  Chirality :  0.054   0.157    528
  Planarity :  0.003   0.020    660
  Dihedral  :  6.842  25.154    492
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.71 %
    Favored  : 78.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.83 (0.19), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.44 (0.15), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  13 
 PHE   0.045   0.003   PHE C   4 
 TYR   0.010   0.001   TYR J  10 
 ARG   0.003   0.001   ARG J   5 

*********************** 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
  61 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 ASP cc_start: 0.7734 (m-30) cc_final: 0.7305 (m-30)
REVERT: C   10 TYR cc_start: 0.6941 (t80) cc_final: 0.6673 (t80)
REVERT: H   35 MET cc_start: 0.3625 (ttt) cc_final: 0.3333 (ttt)
REVERT: E   35 MET cc_start: 0.4005 (ttt) cc_final: 0.3699 (ttt)
REVERT: F   35 MET cc_start: 0.5268 (ttm) cc_final: 0.4932 (ttm)
REVERT: K   22 GLU cc_start: 0.7489 (tt0) cc_final: 0.7062 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.2321
  time to fit residues: 19.6410
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  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    3.5990

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.120075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.103402 restraints weight = 29699.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.106293 restraints weight = 19133.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.108586 restraints weight = 13494.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.4246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.7357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   3732  Z= 0.379
  Angle     :  0.715   4.725   5004  Z= 0.392
  Chirality :  0.055   0.144    528
  Planarity :  0.004   0.019    660
  Dihedral  :  7.325  27.576    492
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.22 %
    Favored  : 74.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.92 (0.20), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.50 (0.16), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS K  14 
 PHE   0.032   0.004   PHE D   4 
 TYR   0.012   0.002   TYR J  10 
 ARG   0.006   0.001   ARG D   5 

*********************** 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
  51 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.611 
Fit side-chains
REVERT: B   19 PHE cc_start: 0.8902 (t80) cc_final: 0.8608 (t80)
REVERT: H   15 GLN cc_start: 0.6734 (mt0) cc_final: 0.6097 (tt0)
REVERT: H   35 MET cc_start: 0.4356 (ttt) cc_final: 0.4124 (ttt)
REVERT: I   20 PHE cc_start: 0.7603 (t80) cc_final: 0.7328 (t80)
REVERT: E   35 MET cc_start: 0.4280 (ttt) cc_final: 0.3921 (ttt)
REVERT: K   22 GLU cc_start: 0.7805 (tt0) cc_final: 0.7558 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.2117
  time to fit residues: 14.7879
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  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0050
   chunk 27 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 12 optimal weight:    8.9990
   chunk 39 optimal weight:    0.3980
   chunk 40 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
C  15 GLN
** F  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4518 r_free = 0.4518 target = 0.126058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.110242 restraints weight = 27730.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.113505 restraints weight = 16940.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.116005 restraints weight = 11482.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.7442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3732  Z= 0.146
  Angle     :  0.553   3.776   5004  Z= 0.307
  Chirality :  0.054   0.154    528
  Planarity :  0.002   0.012    660
  Dihedral  :  6.565  24.392    492
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.79 %
    Favored  : 84.21 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.62 (0.21), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.28 (0.16), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I  13 
 PHE   0.023   0.002   PHE J  19 
 TYR   0.005   0.000   TYR K  10 
 ARG   0.002   0.000   ARG D   5 

*********************** 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  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   15 GLN cc_start: 0.7905 (mt0) cc_final: 0.7021 (tp40)
REVERT: E   35 MET cc_start: 0.4227 (ttt) cc_final: 0.3849 (ttt)
REVERT: F   35 MET cc_start: 0.5663 (ttm) cc_final: 0.5390 (ttm)
REVERT: K   22 GLU cc_start: 0.7228 (tt0) cc_final: 0.6965 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2220
  time to fit residues: 18.2740
Evaluate side-chains
  41 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 36 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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**
G  15 GLN
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.125148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.109339 restraints weight = 29077.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.112547 restraints weight = 17797.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.115023 restraints weight = 12093.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.7618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3732  Z= 0.203
  Angle     :  0.561   4.158   5004  Z= 0.312
  Chirality :  0.053   0.142    528
  Planarity :  0.002   0.009    660
  Dihedral  :  6.524  23.937    492
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.96 %
    Favored  : 80.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.69 (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
 HIS   0.011   0.001   HIS G  13 
 PHE   0.015   0.002   PHE L  19 
 TYR   0.007   0.001   TYR J  10 
 ARG   0.001   0.000   ARG A   5 

*********************** 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
  58 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 MET cc_start: 0.4565 (ttt) cc_final: 0.4267 (ttt)
REVERT: D   15 GLN cc_start: 0.7919 (mt0) cc_final: 0.7064 (tp40)
REVERT: E   35 MET cc_start: 0.4307 (ttt) cc_final: 0.4085 (ttt)
REVERT: K   22 GLU cc_start: 0.7345 (tt0) cc_final: 0.7050 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2131
  time to fit residues: 16.9388
Evaluate side-chains
  42 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 45 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
H  15 GLN
** E  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K  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 = 0.4462 r_free = 0.4462 target = 0.124684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.108587 restraints weight = 30345.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.111503 restraints weight = 19385.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.113733 restraints weight = 13595.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6661
moved from start:          0.8027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3732  Z= 0.302
  Angle     :  0.650   4.279   5004  Z= 0.361
  Chirality :  0.055   0.144    528
  Planarity :  0.003   0.017    660
  Dihedral  :  7.052  27.517    492
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.15 %
    Favored  : 77.85 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.82 (0.21), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.43 (0.16), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.002   HIS J  13 
 PHE   0.036   0.004   PHE C  20 
 TYR   0.009   0.001   TYR J  10 
 ARG   0.003   0.000   ARG A   5 

*********************** 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
  49 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   20 PHE cc_start: 0.8815 (m-80) cc_final: 0.8557 (m-80)
REVERT: D   15 GLN cc_start: 0.8471 (mt0) cc_final: 0.7407 (tt0)
REVERT: E   35 MET cc_start: 0.2828 (ttt) cc_final: 0.2300 (ttt)
REVERT: F   35 MET cc_start: 0.4560 (ttm) cc_final: 0.4152 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1844
  time to fit residues: 13.0851
Evaluate side-chains
  36 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.4488 r_free = 0.4488 target = 0.125971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.109723 restraints weight = 30464.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.112753 restraints weight = 19328.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.115034 restraints weight = 13523.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6645
moved from start:          0.8255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3732  Z= 0.230
  Angle     :  0.586   4.072   5004  Z= 0.327
  Chirality :  0.053   0.138    528
  Planarity :  0.002   0.012    660
  Dihedral  :  6.846  26.770    492
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.05 %
    Favored  : 78.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.76 (0.21), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.38 (0.16), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS J  13 
 PHE   0.012   0.002   PHE A  19 
 TYR   0.008   0.001   TYR J  10 
 ARG   0.001   0.000   ARG A   5 

********************** 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
  49 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   20 PHE cc_start: 0.8911 (m-80) cc_final: 0.8661 (m-80)
REVERT: D   15 GLN cc_start: 0.8487 (mt0) cc_final: 0.7439 (tt0)
REVERT: E   35 MET cc_start: 0.2708 (ttt) cc_final: 0.2156 (ttt)
REVERT: F   35 MET cc_start: 0.4512 (ttm) cc_final: 0.4127 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1895
  time to fit residues: 13.3308
Evaluate side-chains
  37 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 44 optimal weight:    0.2980
   chunk 5 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4504 r_free = 0.4504 target = 0.127596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.111722 restraints weight = 29497.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.114832 restraints weight = 18366.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.117167 restraints weight = 12704.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.8249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3732  Z= 0.143
  Angle     :  0.533   3.933   5004  Z= 0.297
  Chirality :  0.053   0.144    528
  Planarity :  0.002   0.009    660
  Dihedral  :  6.372  24.384    492
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.23 %
    Favored  : 83.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.61 (0.22), residues: 456
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.27 (0.17), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS J  13 
 PHE   0.018   0.002   PHE K  20 
 TYR   0.006   0.001   TYR C  10 
 ARG   0.001   0.000   ARG D   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2801.86 seconds
wall clock time: 50 minutes 41.00 seconds (3041.00 seconds total)