Starting phenix.real_space_refine
on Tue Feb 11 11:09:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sel_40421/02_2025/8sel_40421_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sel_40421/02_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_40421/02_2025/8sel_40421.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sel_40421/02_2025/8sel_40421.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sel_40421/02_2025/8sel_40421_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sel_40421/02_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-5592/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: 2.18, 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: 1.15
  Conformation dependent library (CDL) restraints added in 674.4 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: 0.77
  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: 1.39

  Time building geometry restraints manager: 1.35 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: 0.05
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:             1.440
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.700
  Find NCS groups from input model:        0.120
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.360
-------------------------------------------------------------------------------
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  : 0.605 
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: 0.1479
  time to fit residues: 43.2083
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  : 0.641 
-------------------------------------------------------------------------------
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 = 46)----------------|
| r_work = 0.5323 r_free = 0.5323 target = 0.215743 restraints weight = 6913.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5388 r_free = 0.5388 target = 0.221874 restraints weight = 3160.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.5419 r_free = 0.5419 target = 0.225432 restraints weight = 1725.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.5250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6591
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  : 0.647 
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: 0.8301 (OUTLIER) cc_final: 0.5935 (p90)
REVERT: C   13 HIS cc_start: 0.7697 (p90) cc_final: 0.7296 (p90)
REVERT: D   10 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.5916 (p90)
REVERT: E   34 LEU cc_start: 0.7949 (tp) cc_final: 0.7551 (tp)
REVERT: F   10 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.5798 (p90)
REVERT: F   34 LEU cc_start: 0.9486 (tt) cc_final: 0.9283 (tp)
REVERT: H   10 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.5721 (p90)
REVERT: H   16 LYS cc_start: 0.6662 (mmtm) cc_final: 0.6338 (mmtm)
REVERT: I   24 VAL cc_start: 0.8902 (t) cc_final: 0.8692 (t)
REVERT: J   10 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.6333 (p90)
REVERT: L   10 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.6202 (p90)
REVERT: M   34 LEU cc_start: 0.7787 (tp) cc_final: 0.7532 (tp)
REVERT: N   16 LYS cc_start: 0.7085 (tttt) cc_final: 0.6452 (mmtm)
REVERT: Q   26 SER cc_start: 0.8844 (t) cc_final: 0.8519 (m)
REVERT: R    5 ARG cc_start: 0.8065 (mtp180) cc_final: 0.6682 (tpp-160)
REVERT: R    7 ASP cc_start: 0.7815 (t0) cc_final: 0.7525 (t0)
REVERT: R   34 LEU cc_start: 0.9132 (tp) cc_final: 0.8797 (tp)
REVERT: S   26 SER cc_start: 0.8684 (t) cc_final: 0.8273 (m)
REVERT: T    5 ARG cc_start: 0.7924 (mtp180) cc_final: 0.6598 (tpp-160)
REVERT: T    7 ASP cc_start: 0.7684 (t0) cc_final: 0.7408 (t0)
REVERT: T   27 ASN cc_start: 0.7287 (t0) cc_final: 0.5342 (p0)
REVERT: T   34 LEU cc_start: 0.9017 (tp) cc_final: 0.8777 (tp)
  outliers start: 25
  outliers final: 6
  residues processed: 192
  average time/residue: 0.1805
  time to fit residues: 44.5275
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  : 0.578 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.5207 r_free = 0.5207 target = 0.208464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5005 r_free = 0.5005 target = 0.184625 restraints weight = 6538.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5056 r_free = 0.5056 target = 0.189937 restraints weight = 3146.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5088 r_free = 0.5088 target = 0.193560 restraints weight = 1862.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.5136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6719
moved from start:          0.5310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5600  Z= 0.239
  Angle     :  0.792   8.082   7520  Z= 0.431
  Chirality :  0.061   0.184    810
  Planarity :  0.003   0.017    990
  Dihedral  : 11.732  89.768    760
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 15.71 %
    Favored  : 79.11 %
  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: -2.56 (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   0.022   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  : 0.495 
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: 0.7615 (p90) cc_final: 0.7185 (p90)
REVERT: B   10 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.6287 (p90)
REVERT: B   35 MET cc_start: 0.8044 (tpp) cc_final: 0.7787 (tpp)
REVERT: C   13 HIS cc_start: 0.7582 (p90) cc_final: 0.7104 (p90)
REVERT: D   10 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.6197 (p90)
REVERT: E   34 LEU cc_start: 0.8183 (tp) cc_final: 0.7903 (tp)
REVERT: F   10 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.5660 (p90)
REVERT: F   16 LYS cc_start: 0.6849 (mmtm) cc_final: 0.6434 (mmtm)
REVERT: I   35 MET cc_start: 0.7408 (mmm) cc_final: 0.7023 (mmm)
REVERT: K   35 MET cc_start: 0.7458 (mmm) cc_final: 0.7095 (mmm)
REVERT: M   24 VAL cc_start: 0.9001 (t) cc_final: 0.8753 (m)
REVERT: M   34 LEU cc_start: 0.7825 (tp) cc_final: 0.7603 (tp)
REVERT: N   16 LYS cc_start: 0.7293 (tttt) cc_final: 0.6622 (mmtm)
REVERT: O   24 VAL cc_start: 0.8913 (t) cc_final: 0.8674 (m)
REVERT: O   28 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8230 (mmmt)
REVERT: P   35 MET cc_start: 0.7238 (ttm) cc_final: 0.6714 (ttm)
REVERT: Q   26 SER cc_start: 0.8761 (t) cc_final: 0.8493 (m)
REVERT: Q   35 MET cc_start: 0.7498 (mmm) cc_final: 0.7101 (mmm)
REVERT: R    5 ARG cc_start: 0.8105 (mtp180) cc_final: 0.6842 (tpp-160)
REVERT: S   23 ASP cc_start: 0.7741 (p0) cc_final: 0.5970 (m-30)
REVERT: S   26 SER cc_start: 0.8771 (t) cc_final: 0.8335 (m)
REVERT: S   28 LYS cc_start: 0.6254 (mmtt) cc_final: 0.6027 (mmtt)
REVERT: S   35 MET cc_start: 0.7497 (mmm) cc_final: 0.7101 (mmm)
REVERT: T    5 ARG cc_start: 0.8031 (mtp180) cc_final: 0.6784 (tpp-160)
  outliers start: 29
  outliers final: 13
  residues processed: 189
  average time/residue: 0.1812
  time to fit residues: 43.2454
Evaluate side-chains
  179 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 163
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
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:    0.0020
   chunk 58 optimal weight:    0.0570
   chunk 5 optimal weight:    0.0050
   chunk 7 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 36 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5322

-------------------------------------------------------------------------------
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  27 ASN ** 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**
** M  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  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 = 0.5248 r_free = 0.5248 target = 0.253001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.5144 r_free = 0.5144 target = 0.196140 restraints weight = 7215.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.5216 r_free = 0.5216 target = 0.202903 restraints weight = 3421.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.207398 restraints weight = 1985.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.5167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6749
moved from start:          0.5792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5600  Z= 0.230
  Angle     :  0.763   8.690   7520  Z= 0.413
  Chirality :  0.060   0.181    810
  Planarity :  0.003   0.015    990
  Dihedral  : 11.135  89.227    760
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 17.86 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.26), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.20), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  13 
 PHE   0.021   0.003   PHE I  19 
 TYR   0.007   0.001   TYR N  10 
 ARG   0.001   0.000   ARG N   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
  220 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 188
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 HIS cc_start: 0.7644 (p90) cc_final: 0.7108 (p90)
REVERT: B   10 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.6198 (p90)
REVERT: C   13 HIS cc_start: 0.7591 (p90) cc_final: 0.6826 (p90)
REVERT: D   10 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.6270 (p90)
REVERT: E   34 LEU cc_start: 0.8196 (tp) cc_final: 0.7934 (tp)
REVERT: G   13 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.6403 (p90)
REVERT: H   10 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.5979 (p90)
REVERT: H   16 LYS cc_start: 0.6960 (mmtm) cc_final: 0.6487 (mmtm)
REVERT: J   10 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7009 (p90)
REVERT: J   27 ASN cc_start: 0.8352 (t0) cc_final: 0.8069 (t0)
REVERT: L   10 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.6959 (p90)
REVERT: L   27 ASN cc_start: 0.8462 (t0) cc_final: 0.8235 (t0)
REVERT: M   13 HIS cc_start: 0.6722 (OUTLIER) cc_final: 0.6177 (p90)
REVERT: N   16 LYS cc_start: 0.7128 (tttt) cc_final: 0.6549 (mmtm)
REVERT: P   35 MET cc_start: 0.7140 (ttm) cc_final: 0.6877 (ttm)
REVERT: Q   23 ASP cc_start: 0.7304 (p0) cc_final: 0.5550 (m-30)
REVERT: Q   26 SER cc_start: 0.8916 (t) cc_final: 0.8597 (m)
REVERT: Q   35 MET cc_start: 0.7349 (mmm) cc_final: 0.7020 (mmm)
REVERT: S   23 ASP cc_start: 0.7321 (p0) cc_final: 0.5684 (m-30)
REVERT: S   26 SER cc_start: 0.8842 (t) cc_final: 0.8435 (m)
REVERT: S   35 MET cc_start: 0.7505 (mmm) cc_final: 0.7142 (mmm)
  outliers start: 32
  outliers final: 18
  residues processed: 201
  average time/residue: 0.1642
  time to fit residues: 42.5522
Evaluate side-chains
  199 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 174
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
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 D residue   39 VAL
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 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   36 VAL
Chi-restraints excluded: chain J residue   10 TYR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain L residue   10 TYR
Chi-restraints excluded: chain M residue   13 HIS
Chi-restraints excluded: chain N residue   10 TYR
Chi-restraints excluded: chain P residue   10 TYR
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain R residue   10 TYR
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain R residue   36 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 56 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0970
   chunk 25 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 0 optimal weight:    0.6980
   chunk 64 optimal weight:    0.4980
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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**
** C  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**
J  14 HIS
** K  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  15 GLN
** 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 = 0.5247 r_free = 0.5247 target = 0.251217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.5146 r_free = 0.5146 target = 0.195004 restraints weight = 7131.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5218 r_free = 0.5218 target = 0.201772 restraints weight = 3326.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.5263 r_free = 0.5263 target = 0.206321 restraints weight = 1936.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.5163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6258
moved from start:          0.6201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5600  Z= 0.240
  Angle     :  0.749   7.022   7520  Z= 0.410
  Chirality :  0.060   0.173    810
  Planarity :  0.003   0.013    990
  Dihedral  : 11.026  88.935    760
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 18.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.77 %
    Favored  : 86.23 %
  Rotamer:
    Outliers :  7.86 %
    Allowed  : 18.39 %
    Favored  : 73.75 %
  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: -2.97 (0.25), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS N  13 
 PHE   0.028   0.003   PHE S  19 
 TYR   0.006   0.001   TYR L  10 
 ARG   0.001   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
  231 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 187
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 HIS cc_start: 0.7571 (p90) cc_final: 0.7114 (p-80)
REVERT: B   10 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.6105 (p90)
REVERT: C   13 HIS cc_start: 0.7448 (p90) cc_final: 0.6589 (p90)
REVERT: D   10 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.6150 (p90)
REVERT: D   27 ASN cc_start: 0.6516 (t0) cc_final: 0.5692 (t0)
REVERT: D   34 LEU cc_start: 0.8722 (tt) cc_final: 0.8400 (tt)
REVERT: E   34 LEU cc_start: 0.7798 (tp) cc_final: 0.7452 (tp)
REVERT: F   10 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.5378 (p90)
REVERT: F   35 MET cc_start: 0.7592 (mmm) cc_final: 0.6347 (tpt)
REVERT: G   13 HIS cc_start: 0.6644 (OUTLIER) cc_final: 0.5986 (p90)
REVERT: H   10 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.5549 (p90)
REVERT: H   16 LYS cc_start: 0.6191 (mmtm) cc_final: 0.5815 (mmtm)
REVERT: H   34 LEU cc_start: 0.9275 (tt) cc_final: 0.9012 (tp)
REVERT: I   19 PHE cc_start: 0.5508 (OUTLIER) cc_final: 0.4852 (p90)
REVERT: I   35 MET cc_start: 0.7097 (mmm) cc_final: 0.6686 (mmm)
REVERT: J   10 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6404 (p90)
REVERT: J   27 ASN cc_start: 0.7998 (t0) cc_final: 0.7494 (t0)
REVERT: K   19 PHE cc_start: 0.5164 (OUTLIER) cc_final: 0.4581 (p90)
REVERT: K   35 MET cc_start: 0.7205 (mmm) cc_final: 0.6711 (mmm)
REVERT: L   10 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6317 (p90)
REVERT: L   27 ASN cc_start: 0.8016 (t0) cc_final: 0.7658 (t0)
REVERT: M   13 HIS cc_start: 0.6420 (OUTLIER) cc_final: 0.5835 (p90)
REVERT: N   16 LYS cc_start: 0.6964 (tttt) cc_final: 0.6230 (mmtm)
REVERT: P   34 LEU cc_start: 0.9178 (tt) cc_final: 0.8945 (tt)
REVERT: Q   23 ASP cc_start: 0.7462 (p0) cc_final: 0.5648 (m-30)
REVERT: Q   26 SER cc_start: 0.8830 (t) cc_final: 0.8493 (m)
REVERT: Q   35 MET cc_start: 0.7074 (mmm) cc_final: 0.6124 (mpp)
REVERT: R    1 ASP cc_start: 0.4841 (m-30) cc_final: 0.3767 (t70)
REVERT: S   23 ASP cc_start: 0.7573 (p0) cc_final: 0.5843 (m-30)
REVERT: S   26 SER cc_start: 0.8761 (t) cc_final: 0.8475 (m)
REVERT: S   35 MET cc_start: 0.7211 (mmm) cc_final: 0.6770 (mmm)
  outliers start: 44
  outliers final: 25
  residues processed: 206
  average time/residue: 0.1521
  time to fit residues: 41.0008
Evaluate side-chains
  209 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 174
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
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 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 G residue   13 HIS
Chi-restraints excluded: chain G residue   19 PHE
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   17 LEU
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 O residue   35 MET
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   14 HIS
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   14 HIS
Chi-restraints excluded: chain T residue   32 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 7 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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  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  14 HIS
** 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  15 GLN ** 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**
** T  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4966 r_free = 0.4966 target = 0.176913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.158156 restraints weight = 7371.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.162509 restraints weight = 3361.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4849 r_free = 0.4849 target = 0.165304 restraints weight = 1919.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.4858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.6574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.065   5600  Z= 0.555
  Angle     :  1.010  12.118   7520  Z= 0.556
  Chirality :  0.068   0.224    810
  Planarity :  0.004   0.019    990
  Dihedral  : 11.752  87.694    760
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 28.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.09 %
    Favored  : 83.91 %
  Rotamer:
    Outliers :  9.64 %
    Allowed  : 19.82 %
    Favored  : 70.54 %
  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: -3.32 (0.25), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.52 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  13 
 PHE   0.027   0.004   PHE Q  19 
 TYR   0.011   0.002   TYR O  10 
 ARG   0.002   0.001   ARG B   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
  236 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 182
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7839 (mp0) cc_final: 0.6834 (mp0)
REVERT: B    1 ASP cc_start: 0.6568 (m-30) cc_final: 0.6309 (m-30)
REVERT: B    7 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7831 (m-30)
REVERT: B   10 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.6348 (p90)
REVERT: B   11 GLU cc_start: 0.7584 (pm20) cc_final: 0.7315 (pt0)
REVERT: C   11 GLU cc_start: 0.7713 (mp0) cc_final: 0.6715 (mp0)
REVERT: C   19 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6524 (p90)
REVERT: D   10 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.6332 (p90)
REVERT: E   13 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.6203 (p90)
REVERT: E   34 LEU cc_start: 0.8077 (tp) cc_final: 0.7797 (tp)
REVERT: F   10 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.6103 (p90)
REVERT: F   22 GLU cc_start: 0.8107 (tp30) cc_final: 0.7670 (tp30)
REVERT: G   13 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6222 (p90)
REVERT: H   10 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.6122 (p90)
REVERT: H   22 GLU cc_start: 0.8157 (tp30) cc_final: 0.7703 (tp30)
REVERT: I   19 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6142 (p90)
REVERT: I   35 MET cc_start: 0.7758 (mmm) cc_final: 0.7367 (mmm)
REVERT: J   10 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7665 (p90)
REVERT: J   27 ASN cc_start: 0.8856 (t0) cc_final: 0.8071 (t0)
REVERT: J   34 LEU cc_start: 0.9184 (tp) cc_final: 0.8978 (tp)
REVERT: K   35 MET cc_start: 0.7713 (mmm) cc_final: 0.7325 (mmm)
REVERT: L   10 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7722 (p90)
REVERT: L   27 ASN cc_start: 0.8924 (t0) cc_final: 0.8345 (t0)
REVERT: M   13 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6368 (p90)
REVERT: M   35 MET cc_start: 0.8039 (mmm) cc_final: 0.7601 (mmt)
REVERT: N   10 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7210 (p90)
REVERT: N   16 LYS cc_start: 0.7147 (tttt) cc_final: 0.6526 (mmtm)
REVERT: N   22 GLU cc_start: 0.7920 (tp30) cc_final: 0.7608 (tp30)
REVERT: N   35 MET cc_start: 0.7332 (ttm) cc_final: 0.7083 (ttm)
REVERT: O   34 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7399 (tp)
REVERT: P   10 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7254 (p90)
REVERT: P   22 GLU cc_start: 0.7935 (tp30) cc_final: 0.7655 (tp30)
REVERT: Q   19 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6186 (p90)
REVERT: Q   26 SER cc_start: 0.9026 (t) cc_final: 0.8729 (m)
REVERT: Q   35 MET cc_start: 0.7430 (mmm) cc_final: 0.6491 (mpp)
REVERT: R   35 MET cc_start: 0.6236 (OUTLIER) cc_final: 0.5489 (ttm)
REVERT: S   19 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6325 (p90)
REVERT: S   26 SER cc_start: 0.9123 (t) cc_final: 0.8709 (m)
REVERT: S   35 MET cc_start: 0.7400 (mmm) cc_final: 0.6196 (mpp)
REVERT: T   14 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6926 (t-90)
  outliers start: 54
  outliers final: 22
  residues processed: 213
  average time/residue: 0.1414
  time to fit residues: 40.1978
Evaluate side-chains
  212 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 171
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 ASP
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   19 PHE
Chi-restraints excluded: chain D residue    7 ASP
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   36 VAL
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    7 ASP
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 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 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   32 ILE
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   14 HIS
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:    0.3980
   chunk 60 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 45 optimal weight:    9.9990
   chunk 52 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
** B  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  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5067 r_free = 0.5067 target = 0.185427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.165446 restraints weight = 7014.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4914 r_free = 0.4914 target = 0.170061 restraints weight = 3222.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.173016 restraints weight = 1851.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.4967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.6857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   5600  Z= 0.400
  Angle     :  0.917   8.319   7520  Z= 0.498
  Chirality :  0.065   0.221    810
  Planarity :  0.004   0.021    990
  Dihedral  : 11.545  87.661    760
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 25.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.96 %
    Favored  : 83.04 %
  Rotamer:
    Outliers :  8.75 %
    Allowed  : 24.46 %
    Favored  : 66.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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   0.004   0.001   HIS P  13 
 PHE   0.031   0.003   PHE A  19 
 TYR   0.009   0.002   TYR O  10 
 ARG   0.002   0.001   ARG B   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
  235 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 186
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.6400 (p90)
REVERT: B   35 MET cc_start: 0.8273 (tpp) cc_final: 0.7839 (tpp)
REVERT: D    7 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8062 (m-30)
REVERT: D   10 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.6505 (p90)
REVERT: D   16 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7717 (mmtm)
REVERT: E   34 LEU cc_start: 0.8155 (tp) cc_final: 0.7887 (tp)
REVERT: F   10 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.5946 (p90)
REVERT: F   22 GLU cc_start: 0.8099 (tp30) cc_final: 0.7586 (tp30)
REVERT: F   35 MET cc_start: 0.8413 (mmm) cc_final: 0.8196 (mmm)
REVERT: G   13 HIS cc_start: 0.7083 (OUTLIER) cc_final: 0.6227 (p90)
REVERT: G   15 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7208 (tm-30)
REVERT: H    7 ASP cc_start: 0.7780 (t0) cc_final: 0.7419 (m-30)
REVERT: H   10 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.6211 (p90)
REVERT: I   13 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6069 (p90)
REVERT: I   19 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.6137 (p90)
REVERT: I   35 MET cc_start: 0.7661 (mmm) cc_final: 0.7240 (mmm)
REVERT: J   10 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7392 (p90)
REVERT: K   19 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6059 (p90)
REVERT: K   35 MET cc_start: 0.7655 (mmm) cc_final: 0.7247 (mmm)
REVERT: L   10 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7266 (p90)
REVERT: L   34 LEU cc_start: 0.9190 (tp) cc_final: 0.8967 (tp)
REVERT: M   13 HIS cc_start: 0.6973 (OUTLIER) cc_final: 0.6329 (p90)
REVERT: M   34 LEU cc_start: 0.7535 (tt) cc_final: 0.7313 (tt)
REVERT: M   35 MET cc_start: 0.7845 (mmm) cc_final: 0.7516 (mmm)
REVERT: N   10 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7158 (p90)
REVERT: N   16 LYS cc_start: 0.7282 (tttt) cc_final: 0.6659 (mmtm)
REVERT: N   22 GLU cc_start: 0.8044 (tp30) cc_final: 0.7688 (tp30)
REVERT: P   10 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7168 (p90)
REVERT: P   22 GLU cc_start: 0.7969 (tp30) cc_final: 0.7598 (tp30)
REVERT: Q   26 SER cc_start: 0.8641 (t) cc_final: 0.8288 (m)
REVERT: Q   35 MET cc_start: 0.7519 (mmm) cc_final: 0.6864 (mmt)
REVERT: R   35 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5619 (ttm)
REVERT: S   26 SER cc_start: 0.9083 (t) cc_final: 0.8679 (m)
REVERT: T   14 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6851 (t-90)
  outliers start: 49
  outliers final: 25
  residues processed: 210
  average time/residue: 0.1479
  time to fit residues: 41.2882
Evaluate side-chains
  219 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 178
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
Chi-restraints excluded: chain B residue    7 ASP
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 D residue    7 ASP
Chi-restraints excluded: chain D residue   10 TYR
Chi-restraints excluded: chain D residue   11 GLU
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 G residue   13 HIS
Chi-restraints excluded: chain G residue   19 PHE
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   10 TYR
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain K residue   17 LEU
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 R residue   10 TYR
Chi-restraints excluded: chain R residue   14 HIS
Chi-restraints excluded: chain R residue   32 ILE
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   14 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0980
   chunk 39 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  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**
** L  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  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**
** T  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5228 r_free = 0.5228 target = 0.197185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5014 r_free = 0.5014 target = 0.175923 restraints weight = 7009.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5072 r_free = 0.5072 target = 0.180988 restraints weight = 3245.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5101 r_free = 0.5101 target = 0.184249 restraints weight = 1873.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.5126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.7088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5600  Z= 0.298
  Angle     :  0.864   9.023   7520  Z= 0.458
  Chirality :  0.062   0.230    810
  Planarity :  0.003   0.017    990
  Dihedral  : 11.304  86.918    760
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 23.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.81 %
    Favored  : 83.19 %
  Rotamer:
    Outliers :  8.39 %
    Allowed  : 24.64 %
    Favored  : 66.96 %
  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   0.032   0.003   PHE A  19 
 TYR   0.006   0.001   TYR J  10 
 ARG   0.002   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
  217 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 170
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7708 (mp0) cc_final: 0.6701 (mp0)
REVERT: C   11 GLU cc_start: 0.7558 (mp0) cc_final: 0.6589 (mp0)
REVERT: C   19 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6488 (p90)
REVERT: D   10 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.6373 (p90)
REVERT: D   12 VAL cc_start: 0.7712 (OUTLIER) cc_final: 0.7508 (p)
REVERT: D   16 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7876 (mmtm)
REVERT: E   15 GLN cc_start: 0.7270 (tm-30) cc_final: 0.6731 (tm-30)
REVERT: E   34 LEU cc_start: 0.8204 (tp) cc_final: 0.7955 (tp)
REVERT: F   10 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.6100 (p90)
REVERT: F   16 LYS cc_start: 0.6889 (mmtm) cc_final: 0.6553 (mmtm)
REVERT: F   35 MET cc_start: 0.8166 (mmm) cc_final: 0.6727 (tpt)
REVERT: G   13 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.6185 (p90)
REVERT: H   10 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.6464 (p90)
REVERT: H   22 GLU cc_start: 0.8099 (tp30) cc_final: 0.7515 (tp30)
REVERT: I   13 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6063 (p90)
REVERT: I   19 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.5959 (p90)
REVERT: I   35 MET cc_start: 0.7650 (mmm) cc_final: 0.7194 (mmm)
REVERT: J   10 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7341 (p90)
REVERT: J   26 SER cc_start: 0.8347 (m) cc_final: 0.8086 (t)
REVERT: J   34 LEU cc_start: 0.9178 (tp) cc_final: 0.8919 (tp)
REVERT: K   19 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.5590 (p90)
REVERT: K   35 MET cc_start: 0.7797 (mmm) cc_final: 0.7463 (mmm)
REVERT: L   10 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7157 (p90)
REVERT: M   13 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.6301 (p90)
REVERT: M   34 LEU cc_start: 0.7272 (tt) cc_final: 0.6996 (tt)
REVERT: M   35 MET cc_start: 0.7815 (mmm) cc_final: 0.7478 (mmm)
REVERT: N   16 LYS cc_start: 0.7281 (tttt) cc_final: 0.6580 (mmtm)
REVERT: N   22 GLU cc_start: 0.7809 (tp30) cc_final: 0.7454 (tp30)
REVERT: O   35 MET cc_start: 0.8323 (mmm) cc_final: 0.7950 (mmm)
REVERT: P   22 GLU cc_start: 0.7893 (tp30) cc_final: 0.7531 (tp30)
REVERT: Q   35 MET cc_start: 0.7535 (mmm) cc_final: 0.6933 (mmt)
REVERT: S   26 SER cc_start: 0.8953 (t) cc_final: 0.8527 (m)
REVERT: S   35 MET cc_start: 0.7551 (mmm) cc_final: 0.6816 (mmt)
  outliers start: 47
  outliers final: 26
  residues processed: 193
  average time/residue: 0.1416
  time to fit residues: 36.5479
Evaluate side-chains
  203 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 165
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASN
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 D residue   10 TYR
Chi-restraints excluded: chain D residue   11 GLU
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 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 J residue   10 TYR
Chi-restraints excluded: chain K residue   13 HIS
Chi-restraints excluded: chain K residue   19 PHE
Chi-restraints excluded: chain L residue    7 ASP
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    7 ASP
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0970
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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**
** 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**
** 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**
** 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 = 0.5117 r_free = 0.5117 target = 0.187821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.168030 restraints weight = 7096.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4959 r_free = 0.4959 target = 0.172477 restraints weight = 3213.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4994 r_free = 0.4994 target = 0.175474 restraints weight = 1836.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.5022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.7212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   5600  Z= 0.395
  Angle     :  0.921   8.337   7520  Z= 0.493
  Chirality :  0.064   0.197    810
  Planarity :  0.004   0.019    990
  Dihedral  : 11.395  89.663    760
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 26.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.81 %
    Favored  : 83.19 %
  Rotamer:
    Outliers :  7.50 %
    Allowed  : 24.64 %
    Favored  : 67.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.25), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS P  13 
 PHE   0.039   0.003   PHE A  19 
 TYR   0.008   0.001   TYR M  10 
 ARG   0.002   0.001   ARG P   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
  208 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 166
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7682 (mp0) cc_final: 0.6681 (mp0)
REVERT: B   10 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.6265 (p90)
REVERT: C   11 GLU cc_start: 0.7544 (mp0) cc_final: 0.6561 (mp0)
REVERT: C   19 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6460 (p90)
REVERT: D   10 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.6401 (p90)
REVERT: D   12 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7492 (p)
REVERT: D   16 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8065 (mmtm)
REVERT: E   13 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.5770 (p90)
REVERT: E   15 GLN cc_start: 0.7377 (tm-30) cc_final: 0.6831 (tm-30)
REVERT: F   10 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.5821 (p90)
REVERT: F   22 GLU cc_start: 0.7936 (tp30) cc_final: 0.7519 (tp30)
REVERT: F   34 LEU cc_start: 0.9675 (tt) cc_final: 0.9322 (tp)
REVERT: G   13 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.5828 (p90)
REVERT: H   10 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.6415 (p90)
REVERT: H   22 GLU cc_start: 0.7982 (tp30) cc_final: 0.7556 (tp30)
REVERT: I   13 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6114 (p90)
REVERT: I   19 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6254 (p90)
REVERT: I   35 MET cc_start: 0.7632 (mmm) cc_final: 0.7221 (mmm)
REVERT: J   10 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7710 (p90)
REVERT: J   26 SER cc_start: 0.8547 (m) cc_final: 0.8277 (t)
REVERT: K   13 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.6406 (p90)
REVERT: K   19 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6113 (p90)
REVERT: K   35 MET cc_start: 0.7769 (mmm) cc_final: 0.7433 (mmm)
REVERT: L   10 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7454 (p90)
REVERT: M   13 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.6305 (p90)
REVERT: M   35 MET cc_start: 0.7865 (mmm) cc_final: 0.7543 (mmm)
REVERT: N   16 LYS cc_start: 0.7248 (tttt) cc_final: 0.6638 (mmtm)
REVERT: N   22 GLU cc_start: 0.7761 (tp30) cc_final: 0.7432 (tp30)
REVERT: O   35 MET cc_start: 0.8177 (mmm) cc_final: 0.7832 (mmm)
REVERT: P   22 GLU cc_start: 0.7836 (tp30) cc_final: 0.7472 (tp30)
REVERT: Q   35 MET cc_start: 0.7490 (mmm) cc_final: 0.6792 (mmt)
REVERT: S   35 MET cc_start: 0.7592 (mmm) cc_final: 0.6728 (mmt)
  outliers start: 42
  outliers final: 26
  residues processed: 186
  average time/residue: 0.1526
  time to fit residues: 37.7317
Evaluate side-chains
  202 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 161
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
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   39 VAL
Chi-restraints excluded: chain C residue   19 PHE
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain D residue   10 TYR
Chi-restraints excluded: chain D residue   11 GLU
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 E residue   36 VAL
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 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 J residue   10 TYR
Chi-restraints excluded: chain K residue   13 HIS
Chi-restraints excluded: chain K residue   19 PHE
Chi-restraints excluded: chain L residue    7 ASP
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   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   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:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  27 ASN
D  14 HIS
** 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**
** L  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  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**
** 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 = 0.5289 r_free = 0.5289 target = 0.198504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5101 r_free = 0.5101 target = 0.179498 restraints weight = 7283.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5151 r_free = 0.5151 target = 0.183990 restraints weight = 3371.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5178 r_free = 0.5178 target = 0.186952 restraints weight = 1926.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.5199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.7349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5600  Z= 0.322
  Angle     :  0.866   8.452   7520  Z= 0.462
  Chirality :  0.061   0.179    810
  Planarity :  0.003   0.018    990
  Dihedral  : 11.283  89.164    760
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 23.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.23 %
    Favored  : 83.77 %
  Rotamer:
    Outliers :  6.96 %
    Allowed  : 25.71 %
    Favored  : 67.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.36 (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   0.004   0.001   HIS P  13 
 PHE   0.041   0.003   PHE A  19 
 TYR   0.006   0.001   TYR J  10 
 ARG   0.002   0.001   ARG P   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
  196 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 157
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7610 (mp0) cc_final: 0.6628 (mp0)
REVERT: B   10 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.6459 (p90)
REVERT: C   11 GLU cc_start: 0.7469 (mp0) cc_final: 0.6537 (mp0)
REVERT: C   19 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6586 (p90)
REVERT: D   10 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.6283 (p90)
REVERT: D   12 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7348 (p)
REVERT: D   16 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8101 (mmtm)
REVERT: E   13 HIS cc_start: 0.6956 (OUTLIER) cc_final: 0.5958 (p90)
REVERT: E   15 GLN cc_start: 0.7644 (tm-30) cc_final: 0.7166 (tm-30)
REVERT: F   10 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.5980 (p90)
REVERT: F   16 LYS cc_start: 0.7077 (mmtm) cc_final: 0.6771 (mmtm)
REVERT: F   22 GLU cc_start: 0.8135 (tp30) cc_final: 0.7713 (tp30)
REVERT: F   35 MET cc_start: 0.8184 (mmm) cc_final: 0.6552 (tpt)
REVERT: G   13 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.5906 (p90)
REVERT: H   10 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.6668 (p90)
REVERT: H   22 GLU cc_start: 0.8112 (tp30) cc_final: 0.7669 (tp30)
REVERT: I   13 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6226 (p90)
REVERT: I   19 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.6071 (p90)
REVERT: I   35 MET cc_start: 0.7591 (mmm) cc_final: 0.7330 (mmm)
REVERT: J   10 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7616 (p90)
REVERT: K   13 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6365 (p90)
REVERT: K   19 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.5893 (p90)
REVERT: K   35 MET cc_start: 0.7760 (mmm) cc_final: 0.7520 (mmm)
REVERT: L   10 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7259 (p90)
REVERT: M   13 HIS cc_start: 0.6908 (OUTLIER) cc_final: 0.6293 (p90)
REVERT: N   16 LYS cc_start: 0.7376 (tttt) cc_final: 0.6797 (mmtm)
REVERT: N   22 GLU cc_start: 0.7939 (tp30) cc_final: 0.7664 (tp30)
REVERT: O   35 MET cc_start: 0.8207 (mmm) cc_final: 0.7913 (mmm)
REVERT: P   22 GLU cc_start: 0.7913 (tp30) cc_final: 0.7579 (tp30)
REVERT: Q   35 MET cc_start: 0.7439 (mmm) cc_final: 0.6870 (mmt)
REVERT: S   35 MET cc_start: 0.7619 (mmm) cc_final: 0.7045 (mmt)
  outliers start: 39
  outliers final: 22
  residues processed: 176
  average time/residue: 0.1418
  time to fit residues: 33.3922
Evaluate side-chains
  192 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 155
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
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   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   11 GLU
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 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 J residue   10 TYR
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 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 S residue   19 PHE
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:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 52 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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**
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**
** F  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  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5334 r_free = 0.5334 target = 0.258974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.5384 r_free = 0.5384 target = 0.204182 restraints weight = 7667.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5454 r_free = 0.5454 target = 0.209214 restraints weight = 3504.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.5494 r_free = 0.5494 target = 0.212426 restraints weight = 1941.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.5254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.7390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073   5600  Z= 0.495
  Angle     :  1.000   8.621   7520  Z= 0.537
  Chirality :  0.068   0.234    810
  Planarity :  0.004   0.019    990
  Dihedral  : 11.621  88.840    760
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 29.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.25 %
    Favored  : 82.75 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 26.25 %
    Favored  : 66.61 %
  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: -3.56 (0.24), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS N   6 
 PHE   0.044   0.004   PHE A  19 
 TYR   0.010   0.002   TYR M  10 
 ARG   0.003   0.001   ARG B   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1945.64 seconds
wall clock time: 35 minutes 41.61 seconds (2141.61 seconds total)