Starting phenix.real_space_refine
on Thu Mar  6 07:43:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sel_40421/03_2025/8sel_40421_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sel_40421/03_2025/8sel_40421.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sel_40421/03_2025/8sel_40421.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sel_40421/03_2025/8sel_40421.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sel_40421/03_2025/8sel_40421_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sel_40421/03_2025/8sel_40421_neut.cif"
  }
  resolution = 3.8
  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=   0.010 sd=   0.297
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3510      2.51       5
     N     940      2.21       5
     O    1030      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5500
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 244
          Classifications: {'peptide': 33}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 32}
    Chain: "B"
      Number of atoms: 306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 306
          Classifications: {'peptide': 40}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 39}
  Restraints were copied for chains:
    D, F, H, J, L, N, P, R, T, C, E, G, I, K, M, O, Q, S
  Time building chain proxies: 2.21, per 1000 atoms: 0.40
  Number of scatterers: 5500
  At special positions: 0
  Unit cell: (152.83, 60.078, 41.106, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1030      8.00
     N     940      7.00
     C    3510      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.33
  Conformation dependent library (CDL) restraints added in 672.1 milliseconds
  

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1220

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 47.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13
      removed outlier: 6.365A  pdb=" N   TYR A  10 " --> pdb=" O   GLU E  11 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   HIS E  13 " --> pdb=" O   TYR A  10 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL A  12 " --> pdb=" O   HIS E  13 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   TYR E  10 " --> pdb=" O   GLU I  11 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   HIS I  13 " --> pdb=" O   TYR E  10 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL E  12 " --> pdb=" O   HIS I  13 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   TYR I  10 " --> pdb=" O   GLU M  11 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   HIS M  13 " --> pdb=" O   TYR I  10 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL I  12 " --> pdb=" O   HIS M  13 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   TYR M  10 " --> pdb=" O   GLU Q  11 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   HIS Q  13 " --> pdb=" O   TYR M  10 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   VAL M  12 " --> pdb=" O   HIS Q  13 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 21
    Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 26
      removed outlier: 7.972A  pdb=" N   VAL A  24 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   VAL E  24 " --> pdb=" O   GLY I  25 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   VAL I  24 " --> pdb=" O   GLY M  25 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   VAL M  24 " --> pdb=" O   GLY Q  25 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 36
      removed outlier: 6.930A  pdb=" N   ILE E  31 " --> pdb=" O   ALA A  30 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ILE A  32 " --> pdb=" O   ILE E  31 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLY E  33 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ILE I  31 " --> pdb=" O   ALA E  30 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ILE E  32 " --> pdb=" O   ILE I  31 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY I  33 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ILE M  31 " --> pdb=" O   ALA I  30 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ILE I  32 " --> pdb=" O   ILE M  31 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY M  33 " --> pdb=" O   ILE I  32 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ILE Q  31 " --> pdb=" O   ALA M  30 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ILE M  32 " --> pdb=" O   ILE Q  31 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY Q  33 " --> pdb=" O   ILE M  32 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12
    Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 21
    Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 36
      removed outlier: 6.896A  pdb=" N   ALA B  30 " --> pdb=" O   GLY F  29 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ILE F  31 " --> pdb=" O   ALA B  30 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE B  32 " --> pdb=" O   ILE F  31 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   GLY F  33 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ALA F  30 " --> pdb=" O   GLY J  29 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ILE J  31 " --> pdb=" O   ALA F  30 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE F  32 " --> pdb=" O   ILE J  31 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLY J  33 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ALA J  30 " --> pdb=" O   GLY N  29 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ILE N  31 " --> pdb=" O   ALA J  30 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE J  32 " --> pdb=" O   ILE N  31 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   GLY N  33 " --> pdb=" O   ILE J  32 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ALA N  30 " --> pdb=" O   GLY R  29 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ILE R  31 " --> pdb=" O   ALA N  30 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE N  32 " --> pdb=" O   ILE R  31 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   GLY R  33 " --> pdb=" O   ILE N  32 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 9 through 13
      removed outlier: 6.353A  pdb=" N   TYR C  10 " --> pdb=" O   GLU G  11 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   HIS G  13 " --> pdb=" O   TYR C  10 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   VAL C  12 " --> pdb=" O   HIS G  13 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   TYR G  10 " --> pdb=" O   GLU K  11 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   HIS K  13 " --> pdb=" O   TYR G  10 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   VAL G  12 " --> pdb=" O   HIS K  13 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   TYR K  10 " --> pdb=" O   GLU O  11 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   HIS O  13 " --> pdb=" O   TYR K  10 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   VAL K  12 " --> pdb=" O   HIS O  13 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   TYR O  10 " --> pdb=" O   GLU S  11 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   HIS S  13 " --> pdb=" O   TYR O  10 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   VAL O  12 " --> pdb=" O   HIS S  13 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 21
    Processing sheet with id=AB2, first strand: chain 'C' and resid 24 through 26
      removed outlier: 7.962A  pdb=" N   VAL C  24 " --> pdb=" O   GLY G  25 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   VAL G  24 " --> pdb=" O   GLY K  25 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   VAL K  24 " --> pdb=" O   GLY O  25 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   VAL O  24 " --> pdb=" O   GLY S  25 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 30 through 36
      removed outlier: 6.914A  pdb=" N   ILE G  31 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   ILE C  32 " --> pdb=" O   ILE G  31 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLY G  33 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ILE K  31 " --> pdb=" O   ALA G  30 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ILE G  32 " --> pdb=" O   ILE K  31 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLY K  33 " --> pdb=" O   ILE G  32 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ILE O  31 " --> pdb=" O   ALA K  30 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ILE K  32 " --> pdb=" O   ILE O  31 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLY O  33 " --> pdb=" O   ILE K  32 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   ILE S  31 " --> pdb=" O   ALA O  30 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ILE O  32 " --> pdb=" O   ILE S  31 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   GLY S  33 " --> pdb=" O   ILE O  32 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6
    Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12
    Processing sheet with id=AB6, first strand: chain 'D' and resid 15 through 21
    Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 36
      removed outlier: 6.884A  pdb=" N   ALA D  30 " --> pdb=" O   GLY H  29 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE H  31 " --> pdb=" O   ALA D  30 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ILE D  32 " --> pdb=" O   ILE H  31 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLY H  33 " --> pdb=" O   ILE D  32 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ALA H  30 " --> pdb=" O   GLY L  29 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ILE L  31 " --> pdb=" O   ALA H  30 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ILE H  32 " --> pdb=" O   ILE L  31 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLY L  33 " --> pdb=" O   ILE H  32 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ALA L  30 " --> pdb=" O   GLY P  29 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ILE P  31 " --> pdb=" O   ALA L  30 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ILE L  32 " --> pdb=" O   ILE P  31 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLY P  33 " --> pdb=" O   ILE L  32 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ALA P  30 " --> pdb=" O   GLY T  29 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE T  31 " --> pdb=" O   ALA P  30 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ILE P  32 " --> pdb=" O   ILE T  31 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLY T  33 " --> pdb=" O   ILE P  32 " (cutoff:3.500A)

    176 hydrogen bonds defined for protein.
    528 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: 1.46

  Time building geometry restraints manager: 1.58 seconds

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

  Histogram of bond lengths:
        1.20 -     1.31: 1228
        1.31 -     1.43: 1272
        1.43 -     1.54: 2932
        1.54 -     1.66: 128
        1.66 -     1.78: 40
  Bond restraints: 5600
  Sorted by residual:
  bond pdb=" CG  GLN N  15 "
       pdb=" CD  GLN N  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.357  0.159 2.50e-02 1.60e+03 4.07e+01
  bond pdb=" CG  GLN R  15 "
       pdb=" CD  GLN R  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.357  0.159 2.50e-02 1.60e+03 4.07e+01
  bond pdb=" CG  GLN F  15 "
       pdb=" CD  GLN F  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.357  0.159 2.50e-02 1.60e+03 4.06e+01
  bond pdb=" CG  GLN B  15 "
       pdb=" CD  GLN B  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.357  0.159 2.50e-02 1.60e+03 4.04e+01
  bond pdb=" CG  GLN D  15 "
       pdb=" CD  GLN D  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.357  0.159 2.50e-02 1.60e+03 4.04e+01
  ... (remaining 5595 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 6237
        2.59 -     5.19: 975
        5.19 -     7.78: 218
        7.78 -    10.37: 70
       10.37 -    12.96: 20
  Bond angle restraints: 7520
  Sorted by residual:
  angle pdb=" N   HIS E  13 "
        pdb=" CA  HIS E  13 "
        pdb=" C   HIS E  13 "
      ideal   model   delta    sigma   weight residual
     108.79  120.11  -11.32 1.53e+00 4.27e-01 5.47e+01
  angle pdb=" N   HIS O  13 "
        pdb=" CA  HIS O  13 "
        pdb=" C   HIS O  13 "
      ideal   model   delta    sigma   weight residual
     108.79  120.10  -11.31 1.53e+00 4.27e-01 5.47e+01
  angle pdb=" N   HIS S  13 "
        pdb=" CA  HIS S  13 "
        pdb=" C   HIS S  13 "
      ideal   model   delta    sigma   weight residual
     108.79  120.09  -11.30 1.53e+00 4.27e-01 5.46e+01
  angle pdb=" N   HIS M  13 "
        pdb=" CA  HIS M  13 "
        pdb=" C   HIS M  13 "
      ideal   model   delta    sigma   weight residual
     108.79  120.09  -11.30 1.53e+00 4.27e-01 5.45e+01
  angle pdb=" N   HIS Q  13 "
        pdb=" CA  HIS Q  13 "
        pdb=" C   HIS Q  13 "
      ideal   model   delta    sigma   weight residual
     108.79  120.09  -11.30 1.53e+00 4.27e-01 5.45e+01
  ... (remaining 7515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 2970
       17.47 -    34.93: 110
       34.93 -    52.40: 30
       52.40 -    69.87: 0
       69.87 -    87.33: 20
  Dihedral angle restraints: 3130
    sinusoidal: 1180
      harmonic: 1950
  Sorted by residual:
  dihedral pdb=" N   HIS F  13 "
           pdb=" C   HIS F  13 "
           pdb=" CA  HIS F  13 "
           pdb=" CB  HIS F  13 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.46   -7.66     0      2.50e+00 1.60e-01 9.38e+00
  dihedral pdb=" N   HIS H  13 "
           pdb=" C   HIS H  13 "
           pdb=" CA  HIS H  13 "
           pdb=" CB  HIS H  13 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.41   -7.61     0      2.50e+00 1.60e-01 9.26e+00
  dihedral pdb=" N   HIS B  13 "
           pdb=" C   HIS B  13 "
           pdb=" CA  HIS B  13 "
           pdb=" CB  HIS B  13 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.41   -7.61     0      2.50e+00 1.60e-01 9.26e+00
  ... (remaining 3127 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.102: 518
       0.102 -    0.203: 232
       0.203 -    0.305: 26
       0.305 -    0.406: 24
       0.406 -    0.508: 10
  Chirality restraints: 810
  Sorted by residual:
  chirality pdb=" CA  HIS F  13 "
            pdb=" N   HIS F  13 "
            pdb=" C   HIS F  13 "
            pdb=" CB  HIS F  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.45e+00
  chirality pdb=" CA  HIS B  13 "
            pdb=" N   HIS B  13 "
            pdb=" C   HIS B  13 "
            pdb=" CB  HIS B  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.40e+00
  chirality pdb=" CA  HIS J  13 "
            pdb=" N   HIS J  13 "
            pdb=" C   HIS J  13 "
            pdb=" CB  HIS J  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.36e+00
  ... (remaining 807 not shown)

  Planarity restraints: 990
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL O  40 "   -0.025 2.00e-02 2.50e+03   4.99e-02 2.49e+01
        pdb=" C   VAL O  40 "    0.086 2.00e-02 2.50e+03
        pdb=" O   VAL O  40 "   -0.031 2.00e-02 2.50e+03
        pdb=" OXT VAL O  40 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL K  40 "   -0.025 2.00e-02 2.50e+03   4.98e-02 2.48e+01
        pdb=" C   VAL K  40 "    0.086 2.00e-02 2.50e+03
        pdb=" O   VAL K  40 "   -0.031 2.00e-02 2.50e+03
        pdb=" OXT VAL K  40 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL M  40 "   -0.025 2.00e-02 2.50e+03   4.98e-02 2.48e+01
        pdb=" C   VAL M  40 "    0.086 2.00e-02 2.50e+03
        pdb=" O   VAL M  40 "   -0.031 2.00e-02 2.50e+03
        pdb=" OXT VAL M  40 "   -0.031 2.00e-02 2.50e+03
  ... (remaining 987 not shown)

  Histogram of nonbonded interaction distances:
        2.47 -     2.96: 3029
        2.96 -     3.44: 5294
        3.44 -     3.93: 8855
        3.93 -     4.41: 11486
        4.41 -     4.90: 20185
  Nonbonded interactions: 48849
  Sorted by model distance:
  nonbonded pdb=" O   HIS N  13 "
            pdb=" N   GLN N  15 "
     model   vdw
     2.474 3.120
  nonbonded pdb=" O   HIS D  13 "
            pdb=" N   GLN D  15 "
     model   vdw
     2.475 3.120
  nonbonded pdb=" O   HIS T  13 "
            pdb=" N   GLN T  15 "
     model   vdw
     2.475 3.120
  nonbonded pdb=" O   HIS L  13 "
            pdb=" N   GLN L  15 "
     model   vdw
     2.475 3.120
  nonbonded pdb=" O   HIS B  13 "
            pdb=" N   GLN B  15 "
     model   vdw
     2.475 3.120
  ... (remaining 48844 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
  selection = chain 'L'
  selection = chain 'N'
  selection = chain 'P'
  selection = chain 'R'
  selection = chain 'T'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'K'
  selection = chain 'M'
  selection = chain 'O'
  selection = chain 'Q'
  selection = chain 'S'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  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:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     15.730
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  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:   20.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
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      :  0.026   0.159   5600  Z= 1.721
  Angle     :  2.245  12.963   7520  Z= 1.380
  Chirality :  0.132   0.508    810
  Planarity :  0.010   0.050    990
  Dihedral  : 12.887  87.332   1910
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  2.90 %
    Allowed  :  4.35 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.27), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.20 (0.21), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J  13 
 PHE   0.017   0.006   PHE R  19 
 TYR   0.029   0.010   TYR R  10 
 ARG   0.001   0.000   ARG T   5 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 VAL cc_start: 0.8272 (t) cc_final: 0.8001 (m)
REVERT: D   24 VAL cc_start: 0.8182 (t) cc_final: 0.7958 (m)
REVERT: M   34 LEU cc_start: 0.8312 (tp) cc_final: 0.8064 (tp)
REVERT: N   16 LYS cc_start: 0.7781 (tttt) cc_final: 0.7459 (mmtm)
REVERT: Q   26 SER cc_start: 0.8867 (t) cc_final: 0.8562 (m)
REVERT: S   26 SER cc_start: 0.8852 (t) cc_final: 0.8416 (m)
REVERT: S   27 ASN cc_start: 0.7148 (t0) cc_final: 0.6548 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1438
  time to fit residues: 42.3976
Evaluate side-chains
  158 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  14 HIS
D  14 HIS
F  14 HIS
H  14 HIS
J  14 HIS
L  14 HIS
N  14 HIS
P  14 HIS
Q  15 GLN
R  14 HIS
** R  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  15 GLN
T  14 HIS
** T  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5325 r_free = 0.5325 target = 0.264119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5324 r_free = 0.5324 target = 0.215894 restraints weight = 6913.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.5388 r_free = 0.5388 target = 0.221881 restraints weight = 3147.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.5419 r_free = 0.5419 target = 0.225480 restraints weight = 1724.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.5247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6593
moved from start:          0.4495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5600  Z= 0.310
  Angle     :  0.900   7.845   7520  Z= 0.491
  Chirality :  0.063   0.221    810
  Planarity :  0.003   0.017    990
  Dihedral  : 12.932  86.739    760
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  1.45 %
    Allowed  : 10.14 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 14.29 %
    Favored  : 81.25 %
  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: -2.25 (0.26), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.20), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS R  14 
 PHE   0.017   0.003   PHE O  19 
 TYR   0.011   0.002   TYR J  10 
 ARG   0.001   0.000   ARG L   5 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 190
  time to evaluate  : 0.622 
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: A   13 HIS cc_start: 0.7655 (p90) cc_final: 0.7291 (p90)
REVERT: B   10 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.5936 (p90)
REVERT: C   13 HIS cc_start: 0.7697 (p90) cc_final: 0.7296 (p90)
REVERT: D   10 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.5918 (p90)
REVERT: E   34 LEU cc_start: 0.7953 (tp) cc_final: 0.7554 (tp)
REVERT: F   10 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.5797 (p90)
REVERT: F   34 LEU cc_start: 0.9485 (tt) cc_final: 0.9282 (tp)
REVERT: H   10 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.5724 (p90)
REVERT: H   16 LYS cc_start: 0.6663 (mmtm) cc_final: 0.6339 (mmtm)
REVERT: I   24 VAL cc_start: 0.8908 (t) cc_final: 0.8697 (t)
REVERT: J   10 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.6332 (p90)
REVERT: L   10 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.6206 (p90)
REVERT: M   34 LEU cc_start: 0.7791 (tp) cc_final: 0.7536 (tp)
REVERT: N   16 LYS cc_start: 0.7086 (tttt) cc_final: 0.6453 (mmtm)
REVERT: Q   26 SER cc_start: 0.8847 (t) cc_final: 0.8524 (m)
REVERT: R    5 ARG cc_start: 0.8056 (mtp180) cc_final: 0.6672 (tpp-160)
REVERT: R    7 ASP cc_start: 0.7807 (t0) cc_final: 0.7516 (t0)
REVERT: R   34 LEU cc_start: 0.9131 (tp) cc_final: 0.8796 (tp)
REVERT: S   26 SER cc_start: 0.8686 (t) cc_final: 0.8274 (m)
REVERT: T    5 ARG cc_start: 0.7940 (mtp180) cc_final: 0.6610 (tpp-160)
REVERT: T    7 ASP cc_start: 0.7697 (t0) cc_final: 0.7421 (t0)
REVERT: T   27 ASN cc_start: 0.7289 (t0) cc_final: 0.5339 (p0)
REVERT: T   34 LEU cc_start: 0.9017 (tp) cc_final: 0.8778 (tp)
  outliers start: 25
  outliers final: 6
  residues processed: 192
  average time/residue: 0.1723
  time to fit residues: 42.5677
Evaluate side-chains
  171 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 TYR
Chi-restraints excluded: chain D residue   10 TYR
Chi-restraints excluded: chain F residue   10 TYR
Chi-restraints excluded: chain H residue   10 TYR
Chi-restraints excluded: chain I residue   17 LEU
Chi-restraints excluded: chain J residue   10 TYR
Chi-restraints excluded: chain K residue   17 LEU
Chi-restraints excluded: chain L residue   10 TYR
Chi-restraints excluded: chain P residue   36 VAL
Chi-restraints excluded: chain R residue   10 TYR
Chi-restraints excluded: chain S residue   17 LEU
Chi-restraints excluded: chain T residue   10 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 9 optimal weight:    0.0870
   chunk 33 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 35 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 24 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 GLN ** 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 = 0.5194 r_free = 0.5194 target = 0.207744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4989 r_free = 0.4989 target = 0.184091 restraints weight = 6577.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5040 r_free = 0.5040 target = 0.189418 restraints weight = 3178.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.5076 r_free = 0.5076 target = 0.193054 restraints weight = 1875.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.5121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6726
moved from start:          0.5307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5600  Z= 0.246
  Angle     :  0.796   8.077   7520  Z= 0.434
  Chirality :  0.061   0.185    810
  Planarity :  0.003   0.016    990
  Dihedral  : 11.742  89.838    760
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 17.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 15.54 %
    Favored  : 79.29 %
  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: -2.55 (0.26), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.20), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS R  13 
 PHE   0.023   0.003   PHE Q  19 
 TYR   0.011   0.001   TYR J  10 
 ARG   0.001   0.000   ARG P   5 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 173
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 HIS cc_start: 0.7624 (p90) cc_final: 0.7164 (p90)
REVERT: B   10 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.6184 (p90)
REVERT: B   35 MET cc_start: 0.8066 (tpp) cc_final: 0.7818 (tpp)
REVERT: C   13 HIS cc_start: 0.7591 (p90) cc_final: 0.7085 (p90)
REVERT: D   10 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.6066 (p90)
REVERT: E   34 LEU cc_start: 0.8182 (tp) cc_final: 0.7888 (tp)
REVERT: F   10 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.5676 (p90)
REVERT: F   16 LYS cc_start: 0.6801 (mmtm) cc_final: 0.6392 (mmtm)
REVERT: I   35 MET cc_start: 0.7402 (mmm) cc_final: 0.7018 (mmm)
REVERT: K   35 MET cc_start: 0.7443 (mmm) cc_final: 0.7083 (mmm)
REVERT: M   28 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8319 (mmtt)
REVERT: M   34 LEU cc_start: 0.7804 (tp) cc_final: 0.7581 (tp)
REVERT: N   16 LYS cc_start: 0.7230 (tttt) cc_final: 0.6590 (mmtm)
REVERT: O   24 VAL cc_start: 0.8939 (t) cc_final: 0.8687 (m)
REVERT: O   28 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8221 (mmmt)
REVERT: P   35 MET cc_start: 0.7270 (ttm) cc_final: 0.6740 (ttm)
REVERT: Q   26 SER cc_start: 0.8767 (t) cc_final: 0.8509 (m)
REVERT: Q   35 MET cc_start: 0.7509 (mmm) cc_final: 0.7094 (mmm)
REVERT: R    5 ARG cc_start: 0.8082 (mtp180) cc_final: 0.6822 (tpp-160)
REVERT: S   23 ASP cc_start: 0.7776 (p0) cc_final: 0.5992 (m-30)
REVERT: S   26 SER cc_start: 0.8775 (t) cc_final: 0.8333 (m)
REVERT: S   35 MET cc_start: 0.7496 (mmm) cc_final: 0.7078 (mmm)
REVERT: T    5 ARG cc_start: 0.8054 (mtp180) cc_final: 0.6821 (tpp-160)
REVERT: T   16 LYS cc_start: 0.5087 (tppt) cc_final: 0.4487 (mmtm)
  outliers start: 29
  outliers final: 13
  residues processed: 189
  average time/residue: 0.1787
  time to fit residues: 42.8836
Evaluate side-chains
  181 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 TYR
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   10 TYR
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain F residue   10 TYR
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue   36 VAL
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain K residue   36 VAL
Chi-restraints excluded: chain N residue   10 TYR
Chi-restraints excluded: chain P residue   10 TYR
Chi-restraints excluded: chain R residue   10 TYR
Chi-restraints excluded: chain T residue   10 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  15 GLN ** 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 = 0.4998 r_free = 0.4998 target = 0.183304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.163655 restraints weight = 7319.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4840 r_free = 0.4840 target = 0.168050 restraints weight = 3433.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.171074 restraints weight = 1994.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.4893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.5928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   5600  Z= 0.422
  Angle     :  0.917  10.193   7520  Z= 0.506
  Chirality :  0.066   0.220    810
  Planarity :  0.004   0.018    990
  Dihedral  : 11.569  87.092    760
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 22.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  8.39 %
    Allowed  : 16.61 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.89 (0.26), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.20), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  13 
 PHE   0.022   0.004   PHE I  19 
 TYR   0.008   0.002   TYR N  10 
 ARG   0.001   0.000   ARG L   5 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 196
  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: symmetry clash
REVERT: A   13 HIS cc_start: 0.7661 (p90) cc_final: 0.6895 (p90)
REVERT: A   22 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8409 (tp30)
REVERT: B   10 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.6327 (p90)
REVERT: C   11 GLU cc_start: 0.7787 (mp0) cc_final: 0.6786 (mp0)
REVERT: C   22 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8371 (tp30)
REVERT: C   24 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8961 (m)
REVERT: D   10 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.6424 (p90)
REVERT: D   35 MET cc_start: 0.8291 (tpp) cc_final: 0.7761 (tpp)
REVERT: E   34 LEU cc_start: 0.8069 (tp) cc_final: 0.7701 (tp)
REVERT: F   10 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.5866 (p90)
REVERT: F   22 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7612 (tp30)
REVERT: G   13 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.6305 (p90)
REVERT: G   22 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8027 (tp30)
REVERT: H   10 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.6011 (p90)
REVERT: H   22 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7629 (tp30)
REVERT: I   19 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.5781 (p90)
REVERT: I   35 MET cc_start: 0.7473 (mmm) cc_final: 0.7227 (mmm)
REVERT: J   10 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7269 (p90)
REVERT: J   22 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7827 (tp30)
REVERT: J   27 ASN cc_start: 0.8684 (t0) cc_final: 0.8191 (t0)
REVERT: K   19 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.5792 (p90)
REVERT: K   35 MET cc_start: 0.7516 (mmm) cc_final: 0.7267 (mmm)
REVERT: L   10 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7438 (p90)
REVERT: L   27 ASN cc_start: 0.8761 (t0) cc_final: 0.8189 (t0)
REVERT: M   13 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.6320 (p90)
REVERT: N   10 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7196 (p90)
REVERT: N   16 LYS cc_start: 0.7341 (tttt) cc_final: 0.6524 (mmtm)
REVERT: N   22 GLU cc_start: 0.7818 (tp30) cc_final: 0.7563 (tp30)
REVERT: P   10 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7265 (p90)
REVERT: P   22 GLU cc_start: 0.7826 (tp30) cc_final: 0.7410 (tp30)
REVERT: Q   19 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6214 (p90)
REVERT: Q   26 SER cc_start: 0.8829 (t) cc_final: 0.8539 (m)
REVERT: Q   35 MET cc_start: 0.7464 (mmm) cc_final: 0.7005 (mpp)
REVERT: R    5 ARG cc_start: 0.8348 (mtp180) cc_final: 0.6733 (tpp-160)
REVERT: S   19 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6334 (p90)
REVERT: S   26 SER cc_start: 0.9046 (t) cc_final: 0.8706 (m)
REVERT: S   35 MET cc_start: 0.7368 (mmm) cc_final: 0.7114 (mmm)
REVERT: T    5 ARG cc_start: 0.8318 (mtp180) cc_final: 0.6692 (tpp-160)
REVERT: T   16 LYS cc_start: 0.4130 (tppt) cc_final: 0.3762 (tppt)
  outliers start: 47
  outliers final: 25
  residues processed: 223
  average time/residue: 0.1526
  time to fit residues: 44.6720
Evaluate side-chains
  226 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 186
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain B residue   10 TYR
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain D residue   10 TYR
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   19 PHE
Chi-restraints excluded: chain F residue   10 TYR
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   19 PHE
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain H residue   10 TYR
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue   19 PHE
Chi-restraints excluded: chain I residue   36 VAL
Chi-restraints excluded: chain J residue   10 TYR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain K residue   19 PHE
Chi-restraints excluded: chain L residue   10 TYR
Chi-restraints excluded: chain M residue   13 HIS
Chi-restraints excluded: chain M residue   19 PHE
Chi-restraints excluded: chain N residue   10 TYR
Chi-restraints excluded: chain O residue   19 PHE
Chi-restraints excluded: chain P residue   10 TYR
Chi-restraints excluded: chain Q residue   19 PHE
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain Q residue   40 VAL
Chi-restraints excluded: chain R residue   10 TYR
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain S residue   19 PHE
Chi-restraints excluded: chain S residue   32 ILE
Chi-restraints excluded: chain S residue   40 VAL
Chi-restraints excluded: chain T residue   10 TYR
Chi-restraints excluded: chain T residue   32 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0770
   chunk 65 optimal weight:    0.0970
   chunk 25 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 0 optimal weight:    0.6980
   chunk 64 optimal weight:    0.3980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 GLN ** 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 = 0.5274 r_free = 0.5274 target = 0.246375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5196 r_free = 0.5196 target = 0.195979 restraints weight = 7128.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.5267 r_free = 0.5267 target = 0.202524 restraints weight = 3292.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.5304 r_free = 0.5304 target = 0.206638 restraints weight = 1882.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.5188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6363
moved from start:          0.6423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5600  Z= 0.223
  Angle     :  0.756   8.605   7520  Z= 0.407
  Chirality :  0.059   0.183    810
  Planarity :  0.003   0.013    990
  Dihedral  : 11.403  88.473    760
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.20 %
    Favored  : 85.80 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 22.14 %
    Favored  : 70.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.26), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.20), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS P  13 
 PHE   0.021   0.003   PHE I  19 
 TYR   0.006   0.001   TYR P  10 
 ARG   0.000   0.000   ARG N   5 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 190
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 HIS cc_start: 0.7590 (p90) cc_final: 0.7036 (p-80)
REVERT: B    5 ARG cc_start: 0.8336 (mtp180) cc_final: 0.8060 (mtp-110)
REVERT: C   11 GLU cc_start: 0.7525 (mp0) cc_final: 0.6493 (mp0)
REVERT: C   13 HIS cc_start: 0.7513 (p90) cc_final: 0.6713 (p-80)
REVERT: D    5 ARG cc_start: 0.8345 (mtp180) cc_final: 0.8076 (mtp-110)
REVERT: D   16 LYS cc_start: 0.7333 (mmtm) cc_final: 0.7020 (mmtm)
REVERT: F   10 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.5458 (p90)
REVERT: F   35 MET cc_start: 0.7620 (tpt) cc_final: 0.7415 (tpt)
REVERT: G   13 HIS cc_start: 0.6660 (OUTLIER) cc_final: 0.5953 (p90)
REVERT: H    7 ASP cc_start: 0.7202 (t0) cc_final: 0.6910 (m-30)
REVERT: H   10 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.5863 (p90)
REVERT: I   19 PHE cc_start: 0.5444 (OUTLIER) cc_final: 0.5032 (p90)
REVERT: J   10 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.6248 (p90)
REVERT: J   22 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7214 (tp30)
REVERT: K   19 PHE cc_start: 0.5391 (OUTLIER) cc_final: 0.4966 (p90)
REVERT: L   10 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6286 (p90)
REVERT: L   35 MET cc_start: 0.7482 (ttm) cc_final: 0.6881 (tpt)
REVERT: M   13 HIS cc_start: 0.6488 (OUTLIER) cc_final: 0.5852 (p90)
REVERT: N   16 LYS cc_start: 0.6822 (tttt) cc_final: 0.6045 (mmtm)
REVERT: P   10 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.6739 (p90)
REVERT: Q   26 SER cc_start: 0.8743 (t) cc_final: 0.8400 (m)
REVERT: R    1 ASP cc_start: 0.4727 (m-30) cc_final: 0.3652 (t70)
REVERT: S   23 ASP cc_start: 0.6987 (p0) cc_final: 0.5232 (m-30)
REVERT: S   26 SER cc_start: 0.8937 (t) cc_final: 0.8552 (m)
REVERT: S   35 MET cc_start: 0.7141 (mmm) cc_final: 0.6533 (mmm)
REVERT: T    1 ASP cc_start: 0.4846 (m-30) cc_final: 0.3681 (t70)
REVERT: T   35 MET cc_start: 0.4862 (OUTLIER) cc_final: 0.4585 (ttm)
  outliers start: 40
  outliers final: 23
  residues processed: 211
  average time/residue: 0.1629
  time to fit residues: 44.7563
Evaluate side-chains
  207 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 174
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   19 PHE
Chi-restraints excluded: chain F residue   10 TYR
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   19 PHE
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain H residue   10 TYR
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain I residue   19 PHE
Chi-restraints excluded: chain J residue   10 TYR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   32 ILE
Chi-restraints excluded: chain K residue   19 PHE
Chi-restraints excluded: chain L residue   10 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain M residue   13 HIS
Chi-restraints excluded: chain M residue   19 PHE
Chi-restraints excluded: chain N residue   10 TYR
Chi-restraints excluded: chain O residue   19 PHE
Chi-restraints excluded: chain P residue   10 TYR
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain Q residue   40 VAL
Chi-restraints excluded: chain R residue   10 TYR
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain S residue   32 ILE
Chi-restraints excluded: chain S residue   40 VAL
Chi-restraints excluded: chain T residue   10 TYR
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain T residue   35 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 7 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 28 optimal weight:    0.4980
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 GLN ** 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 = 0.5024 r_free = 0.5024 target = 0.181345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.161924 restraints weight = 7249.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.166356 restraints weight = 3306.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4909 r_free = 0.4909 target = 0.169264 restraints weight = 1904.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.4931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.6628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054   5600  Z= 0.470
  Angle     :  0.943   8.044   7520  Z= 0.516
  Chirality :  0.065   0.268    810
  Planarity :  0.004   0.016    990
  Dihedral  : 12.010  89.585    760
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 27.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.80 %
    Favored  : 84.20 %
  Rotamer:
    Outliers :  9.64 %
    Allowed  : 21.79 %
    Favored  : 68.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.25), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  13 
 PHE   0.022   0.004   PHE K  19 
 TYR   0.011   0.002   TYR O  10 
 ARG   0.001   0.000   ARG P   5 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 178
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.6477 (p90)
REVERT: C   11 GLU cc_start: 0.7674 (mp0) cc_final: 0.6689 (mp0)
REVERT: C   19 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.6434 (p90)
REVERT: D   10 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.6465 (p90)
REVERT: E   13 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.5899 (p90)
REVERT: F    7 ASP cc_start: 0.7672 (t0) cc_final: 0.7435 (m-30)
REVERT: F   10 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.6044 (p90)
REVERT: F   22 GLU cc_start: 0.7968 (tp30) cc_final: 0.7522 (tp30)
REVERT: G   13 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.5906 (p90)
REVERT: H    7 ASP cc_start: 0.7752 (t0) cc_final: 0.7547 (m-30)
REVERT: H   10 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.6407 (p90)
REVERT: H   22 GLU cc_start: 0.8069 (tp30) cc_final: 0.7645 (tp30)
REVERT: H   34 LEU cc_start: 0.9675 (tt) cc_final: 0.9442 (tp)
REVERT: I   13 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.6303 (p90)
REVERT: I   19 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.6145 (p90)
REVERT: I   35 MET cc_start: 0.7527 (mmm) cc_final: 0.7047 (mmm)
REVERT: J    5 ARG cc_start: 0.8631 (mtp85) cc_final: 0.8057 (mtp85)
REVERT: J    7 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7735 (m-30)
REVERT: J   10 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7746 (p90)
REVERT: J   22 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7776 (tp30)
REVERT: J   34 LEU cc_start: 0.9203 (tp) cc_final: 0.8903 (tp)
REVERT: K   13 HIS cc_start: 0.7130 (OUTLIER) cc_final: 0.6523 (p90)
REVERT: K   19 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.6070 (p90)
REVERT: K   35 MET cc_start: 0.7623 (mmm) cc_final: 0.7000 (mmm)
REVERT: L   10 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7772 (p90)
REVERT: L   34 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9033 (tp)
REVERT: M   13 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.6350 (p90)
REVERT: N   16 LYS cc_start: 0.7283 (tttt) cc_final: 0.6607 (mmtm)
REVERT: P   10 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7227 (p90)
REVERT: P   22 GLU cc_start: 0.8033 (tp30) cc_final: 0.7645 (tp30)
REVERT: Q   19 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6829 (p90)
REVERT: Q   26 SER cc_start: 0.8839 (t) cc_final: 0.8491 (m)
REVERT: S   19 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6720 (p90)
REVERT: S   26 SER cc_start: 0.9042 (t) cc_final: 0.8557 (m)
REVERT: S   28 LYS cc_start: 0.5422 (mmtt) cc_final: 0.5199 (mmtm)
  outliers start: 54
  outliers final: 27
  residues processed: 206
  average time/residue: 0.1608
  time to fit residues: 42.8410
Evaluate side-chains
  212 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 166
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 TYR
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain C residue   19 PHE
Chi-restraints excluded: chain D residue   10 TYR
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   13 HIS
Chi-restraints excluded: chain E residue   19 PHE
Chi-restraints excluded: chain F residue   10 TYR
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   19 PHE
Chi-restraints excluded: chain G residue   36 VAL
Chi-restraints excluded: chain H residue   10 TYR
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain I residue   19 PHE
Chi-restraints excluded: chain I residue   24 VAL
Chi-restraints excluded: chain I residue   36 VAL
Chi-restraints excluded: chain J residue    7 ASP
Chi-restraints excluded: chain J residue   10 TYR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   32 ILE
Chi-restraints excluded: chain K residue   13 HIS
Chi-restraints excluded: chain K residue   19 PHE
Chi-restraints excluded: chain L residue   10 TYR
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain M residue   13 HIS
Chi-restraints excluded: chain M residue   19 PHE
Chi-restraints excluded: chain M residue   24 VAL
Chi-restraints excluded: chain N residue   10 TYR
Chi-restraints excluded: chain O residue   19 PHE
Chi-restraints excluded: chain P residue   10 TYR
Chi-restraints excluded: chain Q residue   19 PHE
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain Q residue   40 VAL
Chi-restraints excluded: chain R residue   10 TYR
Chi-restraints excluded: chain R residue   14 HIS
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain S residue   19 PHE
Chi-restraints excluded: chain S residue   32 ILE
Chi-restraints excluded: chain T residue   10 TYR
Chi-restraints excluded: chain T residue   32 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 60 optimal weight:    0.0470
   chunk 29 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 45 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    0.9080

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
C  27 ASN
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  14 HIS
** L  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5160 r_free = 0.5160 target = 0.193426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4952 r_free = 0.4952 target = 0.172488 restraints weight = 7114.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.5009 r_free = 0.5009 target = 0.177420 restraints weight = 3317.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.5039 r_free = 0.5039 target = 0.180687 restraints weight = 1916.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.5064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.6916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   5600  Z= 0.319
  Angle     :  0.849   8.566   7520  Z= 0.454
  Chirality :  0.061   0.167    810
  Planarity :  0.003   0.016    990
  Dihedral  : 11.811  89.096    760
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 23.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.23 %
    Favored  : 83.77 %
  Rotamer:
    Outliers : 10.36 %
    Allowed  : 22.50 %
    Favored  : 67.14 %
  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: -3.21 (0.25), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  13 
 PHE   0.027   0.003   PHE A  19 
 TYR   0.007   0.001   TYR M  10 
 ARG   0.002   0.000   ARG L   5 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 178
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.6422 (p90)
REVERT: C   11 GLU cc_start: 0.7514 (mp0) cc_final: 0.6576 (mp0)
REVERT: C   19 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6447 (p90)
REVERT: D   10 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.6498 (p90)
REVERT: D   16 LYS cc_start: 0.7649 (mmtm) cc_final: 0.7330 (mmtm)
REVERT: E   13 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.6088 (p90)
REVERT: F    7 ASP cc_start: 0.7828 (t0) cc_final: 0.7612 (m-30)
REVERT: F   10 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.5915 (p90)
REVERT: F   22 GLU cc_start: 0.8017 (tp30) cc_final: 0.7528 (tp30)
REVERT: F   32 ILE cc_start: 0.8638 (mt) cc_final: 0.8335 (mm)
REVERT: G   13 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6185 (p90)
REVERT: H   10 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.6339 (p90)
REVERT: H   22 GLU cc_start: 0.8122 (tp30) cc_final: 0.7618 (tp30)
REVERT: H   34 LEU cc_start: 0.9608 (tt) cc_final: 0.9408 (tp)
REVERT: I   19 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.5843 (p90)
REVERT: I   35 MET cc_start: 0.7634 (mmm) cc_final: 0.7216 (mmm)
REVERT: J   10 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7469 (p90)
REVERT: K   19 PHE cc_start: 0.6266 (OUTLIER) cc_final: 0.5581 (p90)
REVERT: K   34 LEU cc_start: 0.8226 (tp) cc_final: 0.7827 (tp)
REVERT: K   35 MET cc_start: 0.7540 (mmm) cc_final: 0.7044 (mmm)
REVERT: L   10 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7027 (p90)
REVERT: L   34 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9092 (tp)
REVERT: M   13 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.6191 (p90)
REVERT: M   35 MET cc_start: 0.7939 (mmm) cc_final: 0.7021 (mmm)
REVERT: N   16 LYS cc_start: 0.7178 (tttt) cc_final: 0.6444 (mmtm)
REVERT: P   10 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.6960 (p90)
REVERT: P   22 GLU cc_start: 0.8096 (tp30) cc_final: 0.7704 (tp30)
REVERT: Q   26 SER cc_start: 0.8812 (t) cc_final: 0.8422 (m)
REVERT: Q   35 MET cc_start: 0.7511 (mmm) cc_final: 0.6653 (mmm)
REVERT: S   26 SER cc_start: 0.8952 (t) cc_final: 0.8509 (m)
REVERT: S   35 MET cc_start: 0.7448 (mmm) cc_final: 0.6857 (mmm)
REVERT: T   14 HIS cc_start: 0.7168 (OUTLIER) cc_final: 0.6892 (t-90)
REVERT: T   35 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.4958 (ttm)
  outliers start: 58
  outliers final: 33
  residues processed: 205
  average time/residue: 0.1486
  time to fit residues: 40.4295
Evaluate side-chains
  219 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 170
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   10 TYR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   19 PHE
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain D residue   10 TYR
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   13 HIS
Chi-restraints excluded: chain E residue   19 PHE
Chi-restraints excluded: chain F residue   10 TYR
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   19 PHE
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain H residue   10 TYR
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain I residue   19 PHE
Chi-restraints excluded: chain I residue   24 VAL
Chi-restraints excluded: chain I residue   36 VAL
Chi-restraints excluded: chain J residue   10 TYR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   32 ILE
Chi-restraints excluded: chain K residue   19 PHE
Chi-restraints excluded: chain K residue   24 VAL
Chi-restraints excluded: chain K residue   36 VAL
Chi-restraints excluded: chain L residue   10 TYR
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain M residue   13 HIS
Chi-restraints excluded: chain M residue   19 PHE
Chi-restraints excluded: chain M residue   24 VAL
Chi-restraints excluded: chain N residue   10 TYR
Chi-restraints excluded: chain O residue   19 PHE
Chi-restraints excluded: chain P residue   10 TYR
Chi-restraints excluded: chain Q residue   19 PHE
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain R residue   10 TYR
Chi-restraints excluded: chain R residue   14 HIS
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain S residue   19 PHE
Chi-restraints excluded: chain S residue   32 ILE
Chi-restraints excluded: chain T residue   10 TYR
Chi-restraints excluded: chain T residue   14 HIS
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain T residue   35 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 69 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 48 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
C  27 ASN
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 GLN ** 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 = 0.5150 r_free = 0.5150 target = 0.191603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4947 r_free = 0.4947 target = 0.171494 restraints weight = 7149.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5001 r_free = 0.5001 target = 0.176205 restraints weight = 3262.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.5035 r_free = 0.5035 target = 0.179348 restraints weight = 1866.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.5052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.7081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5600  Z= 0.327
  Angle     :  0.856   8.349   7520  Z= 0.459
  Chirality :  0.062   0.180    810
  Planarity :  0.003   0.016    990
  Dihedral  : 11.031  89.428    760
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 24.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.94 %
    Favored  : 84.06 %
  Rotamer:
    Outliers :  9.11 %
    Allowed  : 24.82 %
    Favored  : 66.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.25), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  13 
 PHE   0.031   0.003   PHE A  19 
 TYR   0.007   0.001   TYR O  10 
 ARG   0.003   0.001   ARG P   5 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 167
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.6442 (p90)
REVERT: C   11 GLU cc_start: 0.7533 (mp0) cc_final: 0.6510 (mp0)
REVERT: C   19 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.6459 (p90)
REVERT: D   10 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.6518 (p90)
REVERT: D   35 MET cc_start: 0.7978 (tpp) cc_final: 0.7667 (tpp)
REVERT: E   13 HIS cc_start: 0.6785 (OUTLIER) cc_final: 0.5765 (p90)
REVERT: F    7 ASP cc_start: 0.7819 (t0) cc_final: 0.7598 (m-30)
REVERT: F   10 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.6131 (p90)
REVERT: F   22 GLU cc_start: 0.8073 (tp30) cc_final: 0.7562 (tp30)
REVERT: G   13 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.5929 (p90)
REVERT: H   10 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.6289 (p90)
REVERT: H   22 GLU cc_start: 0.7998 (tp30) cc_final: 0.7496 (tp30)
REVERT: I   13 HIS cc_start: 0.7059 (OUTLIER) cc_final: 0.6203 (p90)
REVERT: I   19 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.5982 (p90)
REVERT: I   35 MET cc_start: 0.7588 (mmm) cc_final: 0.7080 (mmm)
REVERT: J   10 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7524 (p90)
REVERT: J   35 MET cc_start: 0.7631 (ttm) cc_final: 0.7266 (tpt)
REVERT: K   13 HIS cc_start: 0.7041 (OUTLIER) cc_final: 0.6385 (p90)
REVERT: K   19 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.5957 (p90)
REVERT: K   35 MET cc_start: 0.7542 (mmm) cc_final: 0.7002 (mmm)
REVERT: L   10 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7083 (p90)
REVERT: M   13 HIS cc_start: 0.6937 (OUTLIER) cc_final: 0.6341 (p90)
REVERT: M   35 MET cc_start: 0.7943 (mmm) cc_final: 0.7490 (mmm)
REVERT: N   16 LYS cc_start: 0.7280 (tttt) cc_final: 0.6523 (mmtm)
REVERT: P   22 GLU cc_start: 0.7908 (tp30) cc_final: 0.7529 (tp30)
REVERT: Q   26 SER cc_start: 0.8810 (t) cc_final: 0.8415 (m)
REVERT: Q   35 MET cc_start: 0.7513 (mmm) cc_final: 0.6862 (mmt)
REVERT: R   35 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.5479 (ttm)
REVERT: S   26 SER cc_start: 0.8636 (t) cc_final: 0.8258 (m)
REVERT: S   35 MET cc_start: 0.7477 (mmm) cc_final: 0.6792 (mmt)
REVERT: T   35 MET cc_start: 0.5983 (OUTLIER) cc_final: 0.5296 (ttm)
  outliers start: 51
  outliers final: 29
  residues processed: 191
  average time/residue: 0.1479
  time to fit residues: 37.4939
Evaluate side-chains
  209 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 164
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain B residue   10 TYR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   19 PHE
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain D residue   10 TYR
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   13 HIS
Chi-restraints excluded: chain E residue   19 PHE
Chi-restraints excluded: chain F residue   10 TYR
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   19 PHE
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain H residue   10 TYR
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain I residue   19 PHE
Chi-restraints excluded: chain I residue   24 VAL
Chi-restraints excluded: chain J residue   10 TYR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain K residue   13 HIS
Chi-restraints excluded: chain K residue   19 PHE
Chi-restraints excluded: chain L residue   10 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain M residue   13 HIS
Chi-restraints excluded: chain M residue   19 PHE
Chi-restraints excluded: chain M residue   24 VAL
Chi-restraints excluded: chain N residue   10 TYR
Chi-restraints excluded: chain O residue   19 PHE
Chi-restraints excluded: chain P residue   10 TYR
Chi-restraints excluded: chain Q residue   19 PHE
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain R residue   10 TYR
Chi-restraints excluded: chain R residue   14 HIS
Chi-restraints excluded: chain R residue   35 MET
Chi-restraints excluded: chain S residue   19 PHE
Chi-restraints excluded: chain S residue   32 ILE
Chi-restraints excluded: chain T residue   10 TYR
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain T residue   35 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 34 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
C  27 ASN
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 GLN ** 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 = 0.5281 r_free = 0.5281 target = 0.198379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5079 r_free = 0.5079 target = 0.179467 restraints weight = 7181.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5131 r_free = 0.5131 target = 0.183853 restraints weight = 3350.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.5163 r_free = 0.5163 target = 0.186888 restraints weight = 1951.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.5180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.7282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5600  Z= 0.307
  Angle     :  0.858  10.506   7520  Z= 0.451
  Chirality :  0.062   0.208    810
  Planarity :  0.003   0.016    990
  Dihedral  : 10.774  89.421    760
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 23.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.51 %
    Favored  : 84.49 %
  Rotamer:
    Outliers :  9.46 %
    Allowed  : 26.07 %
    Favored  : 64.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.33 (0.25), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J  13 
 PHE   0.037   0.003   PHE A  19 
 TYR   0.006   0.001   TYR H  10 
 ARG   0.002   0.001   ARG N   5 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 161
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7647 (mp0) cc_final: 0.7263 (mp0)
REVERT: B   10 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.6506 (p90)
REVERT: B   12 VAL cc_start: 0.7827 (OUTLIER) cc_final: 0.7595 (p)
REVERT: C   11 GLU cc_start: 0.7486 (mp0) cc_final: 0.6502 (mp0)
REVERT: C   19 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6567 (p90)
REVERT: D   10 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.6460 (p90)
REVERT: D   12 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7321 (p)
REVERT: D   16 LYS cc_start: 0.7725 (mmtm) cc_final: 0.7478 (mmtm)
REVERT: E   13 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.5798 (p90)
REVERT: F    7 ASP cc_start: 0.7866 (t0) cc_final: 0.7645 (m-30)
REVERT: F   10 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.6257 (p90)
REVERT: F   22 GLU cc_start: 0.8173 (tp30) cc_final: 0.7722 (tp30)
REVERT: G   13 HIS cc_start: 0.6881 (OUTLIER) cc_final: 0.6075 (p90)
REVERT: H   10 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.6370 (p90)
REVERT: H   22 GLU cc_start: 0.8117 (tp30) cc_final: 0.7635 (tp30)
REVERT: H   35 MET cc_start: 0.7913 (tpp) cc_final: 0.7585 (tpt)
REVERT: I   13 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6258 (p90)
REVERT: I   19 PHE cc_start: 0.6469 (OUTLIER) cc_final: 0.5935 (p90)
REVERT: I   35 MET cc_start: 0.7595 (mmm) cc_final: 0.7171 (mmm)
REVERT: J   10 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7501 (p90)
REVERT: K   19 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.5817 (p90)
REVERT: K   35 MET cc_start: 0.7814 (mmm) cc_final: 0.7292 (mmm)
REVERT: L   10 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7242 (p90)
REVERT: L   34 LEU cc_start: 0.9169 (tp) cc_final: 0.8922 (tp)
REVERT: M   13 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6344 (p90)
REVERT: M   35 MET cc_start: 0.7924 (mmm) cc_final: 0.7205 (mmm)
REVERT: N   16 LYS cc_start: 0.7350 (tttt) cc_final: 0.6665 (mmtm)
REVERT: N   34 LEU cc_start: 0.9538 (tt) cc_final: 0.9303 (tt)
REVERT: O   35 MET cc_start: 0.8026 (mmm) cc_final: 0.7035 (mmm)
REVERT: P   22 GLU cc_start: 0.7935 (tp30) cc_final: 0.7526 (tp30)
REVERT: Q   26 SER cc_start: 0.8795 (t) cc_final: 0.8360 (m)
REVERT: Q   35 MET cc_start: 0.7483 (mmm) cc_final: 0.6863 (mmt)
REVERT: S   35 MET cc_start: 0.7591 (mmm) cc_final: 0.6434 (mmt)
  outliers start: 53
  outliers final: 32
  residues processed: 185
  average time/residue: 0.1495
  time to fit residues: 36.6714
Evaluate side-chains
  202 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 155
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   10 TYR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain C residue   19 PHE
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain D residue   10 TYR
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   13 HIS
Chi-restraints excluded: chain E residue   19 PHE
Chi-restraints excluded: chain F residue   10 TYR
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   19 PHE
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain H residue    1 ASP
Chi-restraints excluded: chain H residue   10 TYR
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain I residue   19 PHE
Chi-restraints excluded: chain I residue   24 VAL
Chi-restraints excluded: chain J residue   10 TYR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain K residue   13 HIS
Chi-restraints excluded: chain K residue   19 PHE
Chi-restraints excluded: chain L residue   10 TYR
Chi-restraints excluded: chain M residue   13 HIS
Chi-restraints excluded: chain M residue   19 PHE
Chi-restraints excluded: chain N residue    7 ASP
Chi-restraints excluded: chain N residue   10 TYR
Chi-restraints excluded: chain O residue   19 PHE
Chi-restraints excluded: chain O residue   34 LEU
Chi-restraints excluded: chain P residue   10 TYR
Chi-restraints excluded: chain Q residue   19 PHE
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain R residue   10 TYR
Chi-restraints excluded: chain R residue   14 HIS
Chi-restraints excluded: chain S residue   19 PHE
Chi-restraints excluded: chain S residue   32 ILE
Chi-restraints excluded: chain T residue   10 TYR
Chi-restraints excluded: chain T residue   14 HIS
Chi-restraints excluded: chain T residue   35 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 54 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
C  27 ASN
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 GLN ** 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 = 0.5281 r_free = 0.5281 target = 0.198409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5086 r_free = 0.5086 target = 0.179560 restraints weight = 7240.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.5136 r_free = 0.5136 target = 0.183950 restraints weight = 3402.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5165 r_free = 0.5165 target = 0.186879 restraints weight = 1975.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.5182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.7372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   5600  Z= 0.327
  Angle     :  0.864   8.719   7520  Z= 0.459
  Chirality :  0.062   0.205    810
  Planarity :  0.003   0.018    990
  Dihedral  : 10.670  89.001    760
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 23.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.36 %
    Favored  : 84.64 %
  Rotamer:
    Outliers :  8.75 %
    Allowed  : 27.68 %
    Favored  : 63.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.34 (0.25), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  13 
 PHE   0.041   0.003   PHE A  19 
 TYR   0.007   0.001   TYR H  10 
 ARG   0.002   0.001   ARG N   5 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 158
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7644 (mp0) cc_final: 0.7411 (mp0)
REVERT: B   10 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.6470 (p90)
REVERT: B   12 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7704 (p)
REVERT: C   11 GLU cc_start: 0.7563 (mp0) cc_final: 0.6673 (mp0)
REVERT: C   19 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6479 (p90)
REVERT: D   10 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.6602 (p90)
REVERT: E   13 HIS cc_start: 0.6793 (OUTLIER) cc_final: 0.5799 (p90)
REVERT: F    7 ASP cc_start: 0.7886 (t0) cc_final: 0.7659 (m-30)
REVERT: F   10 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.6520 (p90)
REVERT: F   22 GLU cc_start: 0.8164 (tp30) cc_final: 0.7703 (tp30)
REVERT: G   13 HIS cc_start: 0.6840 (OUTLIER) cc_final: 0.5740 (p90)
REVERT: H   10 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.6321 (p90)
REVERT: H   22 GLU cc_start: 0.8075 (tp30) cc_final: 0.7578 (tp30)
REVERT: I   13 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.6295 (p90)
REVERT: I   19 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.5987 (p90)
REVERT: I   35 MET cc_start: 0.7738 (mmm) cc_final: 0.7263 (mmm)
REVERT: J   10 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7546 (p90)
REVERT: K   13 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6368 (p90)
REVERT: K   19 PHE cc_start: 0.6542 (OUTLIER) cc_final: 0.5936 (p90)
REVERT: K   35 MET cc_start: 0.7804 (mmm) cc_final: 0.7285 (mmm)
REVERT: L   10 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7278 (p90)
REVERT: L   34 LEU cc_start: 0.9024 (tp) cc_final: 0.8747 (tp)
REVERT: M   13 HIS cc_start: 0.6934 (OUTLIER) cc_final: 0.6347 (p90)
REVERT: M   17 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6757 (tp)
REVERT: M   28 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8444 (mtpp)
REVERT: M   35 MET cc_start: 0.7835 (mmm) cc_final: 0.7126 (mmm)
REVERT: N   16 LYS cc_start: 0.7325 (tttt) cc_final: 0.6729 (mmtm)
REVERT: N   34 LEU cc_start: 0.9414 (tt) cc_final: 0.9069 (tt)
REVERT: O   35 MET cc_start: 0.7994 (mmm) cc_final: 0.7025 (mmm)
REVERT: P   22 GLU cc_start: 0.7945 (tp30) cc_final: 0.7568 (tp30)
REVERT: Q   26 SER cc_start: 0.8846 (t) cc_final: 0.8398 (m)
REVERT: Q   32 ILE cc_start: 0.2554 (OUTLIER) cc_final: 0.2191 (tp)
REVERT: Q   35 MET cc_start: 0.7484 (mmm) cc_final: 0.6752 (mmt)
REVERT: R   35 MET cc_start: 0.6161 (OUTLIER) cc_final: 0.5526 (ttm)
REVERT: S   35 MET cc_start: 0.7576 (mmm) cc_final: 0.6441 (mmt)
  outliers start: 49
  outliers final: 31
  residues processed: 183
  average time/residue: 0.1466
  time to fit residues: 35.9501
Evaluate side-chains
  204 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 155
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   10 TYR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain C residue   19 PHE
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain D residue   10 TYR
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   13 HIS
Chi-restraints excluded: chain E residue   19 PHE
Chi-restraints excluded: chain F residue   10 TYR
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   31 ILE
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   19 PHE
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain H residue    1 ASP
Chi-restraints excluded: chain H residue   10 TYR
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain I residue   19 PHE
Chi-restraints excluded: chain I residue   24 VAL
Chi-restraints excluded: chain J residue   10 TYR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain K residue   13 HIS
Chi-restraints excluded: chain K residue   19 PHE
Chi-restraints excluded: chain L residue   10 TYR
Chi-restraints excluded: chain M residue   13 HIS
Chi-restraints excluded: chain M residue   17 LEU
Chi-restraints excluded: chain M residue   19 PHE
Chi-restraints excluded: chain N residue    7 ASP
Chi-restraints excluded: chain N residue   10 TYR
Chi-restraints excluded: chain O residue   19 PHE
Chi-restraints excluded: chain O residue   34 LEU
Chi-restraints excluded: chain P residue   10 TYR
Chi-restraints excluded: chain Q residue   19 PHE
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain R residue   10 TYR
Chi-restraints excluded: chain R residue   14 HIS
Chi-restraints excluded: chain R residue   35 MET
Chi-restraints excluded: chain S residue   19 PHE
Chi-restraints excluded: chain S residue   32 ILE
Chi-restraints excluded: chain T residue   10 TYR
Chi-restraints excluded: chain T residue   35 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 6 optimal weight:    0.0010
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0570
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 3 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.0106

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
C  27 ASN
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 GLN ** 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 = 0.5275 r_free = 0.5275 target = 0.196471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5089 r_free = 0.5089 target = 0.178171 restraints weight = 7272.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.5138 r_free = 0.5138 target = 0.182437 restraints weight = 3391.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.5166 r_free = 0.5166 target = 0.185283 restraints weight = 1947.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.5186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.7498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   5600  Z= 0.344
  Angle     :  0.879   8.414   7520  Z= 0.468
  Chirality :  0.063   0.240    810
  Planarity :  0.003   0.017    990
  Dihedral  : 10.734  89.738    760
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 24.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.94 %
    Favored  : 84.06 %
  Rotamer:
    Outliers :  8.75 %
    Allowed  : 27.68 %
    Favored  : 63.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.35 (0.25), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.55 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS P  13 
 PHE   0.040   0.003   PHE A  19 
 TYR   0.007   0.001   TYR M  10 
 ARG   0.002   0.001   ARG N   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1985.42 seconds
wall clock time: 35 minutes 23.28 seconds (2123.28 seconds total)