Starting phenix.real_space_refine
on Fri Aug 22 23:08:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9umh_64274/08_2025/9umh_64274.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9umh_64274/08_2025/9umh_64274.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9umh_64274/08_2025/9umh_64274.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9umh_64274/08_2025/9umh_64274.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9umh_64274/08_2025/9umh_64274.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9umh_64274/08_2025/9umh_64274.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    2688      2.51       5
     N     735      2.21       5
     O     714      1.98       5
     H    4263      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8421
  Number of models: 1
  Model: ""
    Number of chains: 21
    Chain: "AL"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AM"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AN"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AO"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AP"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AQ"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AR"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AS"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AT"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AU"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AV"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AW"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AX"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AY"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "AZ"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "Aa"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "Ab"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "Ac"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "Ad"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "Ae"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "Af"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 401
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
  Time building chain proxies: 1.42, per 1000 atoms: 0.17
  Number of scatterers: 8421
  At special positions: 0
  Unit cell: (101.01, 58.83, 69.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     O     714      8.00
     N     735      7.00
     C    2688      6.00
     H    4263      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 291.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  924

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 39.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'AL' and resid 14 through 20
      removed outlier: 6.115A  pdb=" N   HISAL  14 " --> pdb=" O   GLNAN  15 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   LEUAN  17 " --> pdb=" O   HISAL  14 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   LYSAL  16 " --> pdb=" O   LEUAN  17 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   PHEAN  19 " --> pdb=" O   LYSAL  16 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VALAL  18 " --> pdb=" O   PHEAN  19 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   LEUAf  17 " --> pdb=" O   HISAd  14 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   LYSAd  16 " --> pdb=" O   LEUAf  17 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   PHEAf  19 " --> pdb=" O   LYSAd  16 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   VALAd  18 " --> pdb=" O   PHEAf  19 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'AL' and resid 30 through 32
      removed outlier: 6.379A  pdb=" N   ILEAL  31 " --> pdb=" O   ILEAN  32 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   ILEAN  31 " --> pdb=" O   ILEAP  32 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ILEAP  31 " --> pdb=" O   ILEAR  32 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   ILEAR  31 " --> pdb=" O   ILEAT  32 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   ILEAT  31 " --> pdb=" O   ILEAV  32 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   ILEAV  31 " --> pdb=" O   ILEAX  32 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   ILEAX  31 " --> pdb=" O   ILEAZ  32 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   ILEAZ  31 " --> pdb=" O   ILEAb  32 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ILEAb  31 " --> pdb=" O   ILEAd  32 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ILEAd  31 " --> pdb=" O   ILEAf  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'AL' and resid 35 through 37
      removed outlier: 6.255A  pdb=" N   VALAL  36 " --> pdb=" O   GLYAN  37 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   VALAN  36 " --> pdb=" O   GLYAP  37 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   VALAP  36 " --> pdb=" O   GLYAR  37 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   VALAR  36 " --> pdb=" O   GLYAT  37 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   VALAT  36 " --> pdb=" O   GLYAV  37 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   VALAV  36 " --> pdb=" O   GLYAX  37 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   VALAX  36 " --> pdb=" O   GLYAZ  37 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'AM' and resid 14 through 20
      removed outlier: 6.117A  pdb=" N   HISAM  14 " --> pdb=" O   GLNAO  15 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   LEUAO  17 " --> pdb=" O   HISAM  14 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LYSAM  16 " --> pdb=" O   LEUAO  17 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   PHEAO  19 " --> pdb=" O   LYSAM  16 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VALAM  18 " --> pdb=" O   PHEAO  19 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   HISAQ  14 " --> pdb=" O   GLNAS  15 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   LEUAS  17 " --> pdb=" O   HISAQ  14 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LYSAQ  16 " --> pdb=" O   LEUAS  17 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   PHEAS  19 " --> pdb=" O   LYSAQ  16 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   VALAQ  18 " --> pdb=" O   PHEAS  19 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'AM' and resid 30 through 37
      removed outlier: 6.330A  pdb=" N   ILEAM  31 " --> pdb=" O   ILEAO  32 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEUAO  34 " --> pdb=" O   ILEAM  31 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   GLYAM  33 " --> pdb=" O   LEUAO  34 " (cutoff:3.500A)
      removed outlier: 10.175A  pdb=" N   VALAO  36 " --> pdb=" O   GLYAM  33 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   METAM  35 " --> pdb=" O   VALAO  36 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   ILEAO  31 " --> pdb=" O   ILEAQ  32 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   ILEAQ  31 " --> pdb=" O   ILEAS  32 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   ILEAS  31 " --> pdb=" O   ILEAU  32 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   ILEAU  31 " --> pdb=" O   ILEAW  32 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ILEAW  31 " --> pdb=" O   ILEAY  32 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ILEAY  31 " --> pdb=" O   ILEAa  32 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   ILEAa  31 " --> pdb=" O   ILEAc  32 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   ILEAc  31 " --> pdb=" O   ILEAe  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'AM' and resid 30 through 37
      removed outlier: 6.330A  pdb=" N   ILEAM  31 " --> pdb=" O   ILEAO  32 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEUAO  34 " --> pdb=" O   ILEAM  31 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   GLYAM  33 " --> pdb=" O   LEUAO  34 " (cutoff:3.500A)
      removed outlier: 10.175A  pdb=" N   VALAO  36 " --> pdb=" O   GLYAM  33 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   METAM  35 " --> pdb=" O   VALAO  36 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   METAQ  35 " --> pdb=" O   ILEAO  32 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   LEUAO  34 " --> pdb=" O   METAQ  35 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   GLYAQ  37 " --> pdb=" O   LEUAO  34 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   VALAO  36 " --> pdb=" O   GLYAQ  37 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   VALAQ  36 " --> pdb=" O   GLYAS  37 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   VALAS  36 " --> pdb=" O   GLYAU  37 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   VALAU  36 " --> pdb=" O   GLYAW  37 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   VALAW  36 " --> pdb=" O   GLYAY  37 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   VALAY  36 " --> pdb=" O   GLYAa  37 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   VALAa  36 " --> pdb=" O   GLYAc  37 " (cutoff:3.500A)

    95 hydrogen bonds defined for protein.
    285 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: 1.33

  Time building geometry restraints manager: 0.58 seconds

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

  Histogram of bond lengths:
        0.85 -     1.04: 4263
        1.04 -     1.23: 291
        1.23 -     1.42: 1473
        1.42 -     1.61: 2415
        1.61 -     1.81: 42
  Bond restraints: 8484
  Sorted by residual:
  bond pdb=" N   ALAAW  30 "
       pdb=" H   ALAAW  30 "
    ideal  model  delta    sigma   weight residual
    0.860  0.915 -0.055 2.00e-02 2.50e+03 7.66e+00
  bond pdb=" N   LYSAS  28 "
       pdb=" H   LYSAS  28 "
    ideal  model  delta    sigma   weight residual
    0.860  0.915 -0.055 2.00e-02 2.50e+03 7.64e+00
  bond pdb=" N   ALAAT  21 "
       pdb=" H   ALAAT  21 "
    ideal  model  delta    sigma   weight residual
    0.860  0.915 -0.055 2.00e-02 2.50e+03 7.63e+00
  bond pdb=" N   LYSAU  16 "
       pdb=" H   LYSAU  16 "
    ideal  model  delta    sigma   weight residual
    0.860  0.915 -0.055 2.00e-02 2.50e+03 7.62e+00
  bond pdb=" N   LYSAZ  28 "
       pdb=" H   LYSAZ  28 "
    ideal  model  delta    sigma   weight residual
    0.860  0.915 -0.055 2.00e-02 2.50e+03 7.62e+00
  ... (remaining 8479 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 12106
        1.48 -     2.95: 1877
        2.95 -     4.43: 436
        4.43 -     5.90: 887
        5.90 -     7.38: 24
  Bond angle restraints: 15330
  Sorted by residual:
  angle pdb=" CA  ASPAQ  23 "
        pdb=" CB  ASPAQ  23 "
        pdb=" CG  ASPAQ  23 "
      ideal   model   delta    sigma   weight residual
     112.60  116.83   -4.23 1.00e+00 1.00e+00 1.79e+01
  angle pdb=" CA  ASPAT  23 "
        pdb=" CB  ASPAT  23 "
        pdb=" CG  ASPAT  23 "
      ideal   model   delta    sigma   weight residual
     112.60  116.81   -4.21 1.00e+00 1.00e+00 1.77e+01
  angle pdb=" CA  ASPAM  23 "
        pdb=" CB  ASPAM  23 "
        pdb=" CG  ASPAM  23 "
      ideal   model   delta    sigma   weight residual
     112.60  116.74   -4.14 1.00e+00 1.00e+00 1.71e+01
  angle pdb=" CA  ASPAa  23 "
        pdb=" CB  ASPAa  23 "
        pdb=" CG  ASPAa  23 "
      ideal   model   delta    sigma   weight residual
     112.60  116.66   -4.06 1.00e+00 1.00e+00 1.65e+01
  angle pdb=" CA  ASPAO  23 "
        pdb=" CB  ASPAO  23 "
        pdb=" CG  ASPAO  23 "
      ideal   model   delta    sigma   weight residual
     112.60  116.65   -4.05 1.00e+00 1.00e+00 1.64e+01
  ... (remaining 15325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.93: 3394
       13.93 -    27.85: 180
       27.85 -    41.78: 73
       41.78 -    55.70: 42
       55.70 -    69.63: 217
  Dihedral angle restraints: 3906
    sinusoidal: 2058
      harmonic: 1848
  Sorted by residual:
  dihedral pdb=" CA  ALAAW  21 "
           pdb=" C   ALAAW  21 "
           pdb=" N   GLUAW  22 "
           pdb=" CA  GLUAW  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.46  -27.54     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  ALAAb  21 "
           pdb=" C   ALAAb  21 "
           pdb=" N   GLUAb  22 "
           pdb=" CA  GLUAb  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.54  -27.46     0      5.00e+00 4.00e-02 3.02e+01
  dihedral pdb=" CA  ALAAa  21 "
           pdb=" C   ALAAa  21 "
           pdb=" N   GLUAa  22 "
           pdb=" CA  GLUAa  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.66  -27.34     0      5.00e+00 4.00e-02 2.99e+01
  ... (remaining 3903 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 108
       0.026 -    0.051: 175
       0.051 -    0.077: 140
       0.077 -    0.103: 153
       0.103 -    0.128: 54
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CB  VALAN  24 "
            pdb=" CA  VALAN  24 "
            pdb=" CG1 VALAN  24 "
            pdb=" CG2 VALAN  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.11e-01
  chirality pdb=" CB  VALAf  39 "
            pdb=" CA  VALAf  39 "
            pdb=" CG1 VALAf  39 "
            pdb=" CG2 VALAf  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality pdb=" CA  ASPAL  23 "
            pdb=" N   ASPAL  23 "
            pdb=" C   ASPAL  23 "
            pdb=" CB  ASPAL  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.69e-01
  ... (remaining 627 not shown)

  Planarity restraints: 1260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHEAV  20 "    0.009 2.00e-02 2.50e+03   6.10e-03 1.12e+00
        pdb=" CG  PHEAV  20 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 PHEAV  20 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHEAV  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHEAV  20 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHEAV  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHEAV  20 "    0.000 2.00e-02 2.50e+03
        pdb=" HD1 PHEAV  20 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD2 PHEAV  20 "    0.002 2.00e-02 2.50e+03
        pdb=" HE1 PHEAV  20 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHEAV  20 "   -0.000 2.00e-02 2.50e+03
        pdb=" HZ  PHEAV  20 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HISAR  13 "   -0.006 2.00e-02 2.50e+03   6.44e-03 1.04e+00
        pdb=" CG  HISAR  13 "    0.018 2.00e-02 2.50e+03
        pdb=" ND1 HISAR  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 HISAR  13 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 HISAR  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE2 HISAR  13 "    0.000 2.00e-02 2.50e+03
        pdb=" HD1 HISAR  13 "   -0.003 2.00e-02 2.50e+03
        pdb=" HD2 HISAR  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 HISAR  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE2 HISAR  13 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HISAZ  13 "   -0.006 2.00e-02 2.50e+03   6.20e-03 9.61e-01
        pdb=" CG  HISAZ  13 "    0.017 2.00e-02 2.50e+03
        pdb=" ND1 HISAZ  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 HISAZ  13 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 HISAZ  13 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HISAZ  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD1 HISAZ  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD2 HISAZ  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 HISAZ  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE2 HISAZ  13 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1257 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 623
        2.21 -     2.81: 16125
        2.81 -     3.40: 20366
        3.40 -     4.00: 31657
        4.00 -     4.60: 45075
  Nonbonded interactions: 113846
  Sorted by model distance:
  nonbonded pdb=" OD1 ASPAZ  23 "
            pdb=" HG  SERAZ  26 "
     model   vdw
     1.610 2.450
  nonbonded pdb=" OD1 ASPAU  23 "
            pdb=" HG  SERAU  26 "
     model   vdw
     1.637 2.450
  nonbonded pdb=" OD1 ASPAP  23 "
            pdb=" HG  SERAP  26 "
     model   vdw
     1.656 2.450
  nonbonded pdb=" O   ASNAc  27 "
            pdb=" H   LYSAe  28 "
     model   vdw
     1.760 2.450
  nonbonded pdb=" O   ASNAa  27 "
            pdb=" H   LYSAc  28 "
     model   vdw
     1.772 2.450
  ... (remaining 113841 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'AL'
  selection = chain 'AM'
  selection = chain 'AN'
  selection = chain 'AO'
  selection = chain 'AP'
  selection = chain 'AQ'
  selection = chain 'AR'
  selection = chain 'AS'
  selection = chain 'AT'
  selection = chain 'AU'
  selection = chain 'AV'
  selection = chain 'AW'
  selection = chain 'AX'
  selection = chain 'AY'
  selection = chain 'AZ'
  selection = chain 'Aa'
  selection = chain 'Ab'
  selection = chain 'Ac'
  selection = chain 'Ad'
  selection = chain 'Ae'
  selection = chain 'Af'
}

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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             5.470
  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:             0.060
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.560
  Find NCS groups from input model:        0.070
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.033   4221  Z= 0.518
  Angle     :  1.169   7.380   5628  Z= 0.729
  Chirality :  0.067   0.128    630
  Planarity :  0.002   0.008    714
  Dihedral  : 11.425  69.626   1428
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 1.08
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 10.10 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.39 (0.29), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.018   0.003   PHEAV  20 
 HIS   0.010   0.002   HISAR  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00849 ( 4221)
  covalent geometry    : angle       1.16911 ( 5628)
  hydrogen bonds       : bond        0.20266 (   95)
  hydrogen bonds       : angle       7.85729 (  285)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: AL   23 ASP cc_start: 0.7895 (p0) cc_final: 0.7045 (p0)
REVERT: AL   28 LYS cc_start: 0.8598 (mttt) cc_final: 0.8283 (mttp)
REVERT: AN   22 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6406 (pt0)
REVERT: AO   23 ASP cc_start: 0.8227 (t0) cc_final: 0.7902 (t0)
REVERT: AP   23 ASP cc_start: 0.7824 (t70) cc_final: 0.7097 (t0)
REVERT: AP   28 LYS cc_start: 0.8255 (mttt) cc_final: 0.7937 (mttp)
REVERT: AR   28 LYS cc_start: 0.8293 (mttt) cc_final: 0.8069 (mttp)
REVERT: AV   22 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6843 (mm-30)
REVERT: AW   28 LYS cc_start: 0.8246 (mttt) cc_final: 0.8021 (mttp)
REVERT: AX   23 ASP cc_start: 0.8099 (t0) cc_final: 0.7887 (t0)
REVERT: AX   28 LYS cc_start: 0.7977 (mttt) cc_final: 0.7770 (mttp)
REVERT: AY   23 ASP cc_start: 0.7666 (m-30) cc_final: 0.7428 (m-30)
REVERT: AY   28 LYS cc_start: 0.8304 (mttt) cc_final: 0.8025 (mttt)
REVERT: AZ   15 GLN cc_start: 0.5815 (mt0) cc_final: 0.5494 (mt0)
REVERT: AZ   23 ASP cc_start: 0.7832 (t70) cc_final: 0.7487 (t0)
REVERT: Aa   23 ASP cc_start: 0.8262 (t0) cc_final: 0.7146 (t0)
REVERT: Ab   23 ASP cc_start: 0.8286 (t0) cc_final: 0.8060 (t0)
REVERT: Ac   23 ASP cc_start: 0.7593 (m-30) cc_final: 0.7346 (m-30)
REVERT: Ac   28 LYS cc_start: 0.8587 (mttt) cc_final: 0.8157 (mttp)
REVERT: Ae   28 LYS cc_start: 0.8668 (mttt) cc_final: 0.8440 (mtmt)
REVERT: Af   28 LYS cc_start: 0.8603 (mttt) cc_final: 0.8345 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1966
  time to fit residues: 31.7407
Evaluate side-chains
  80 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.3980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.4780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.126194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.104295 restraints weight = 17344.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 3.65
r_work: 0.3919 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.4275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4221  Z= 0.166
  Angle     :  0.579   4.195   5628  Z= 0.297
  Chirality :  0.054   0.135    630
  Planarity :  0.002   0.008    714
  Dihedral  :  6.125  25.361    546
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  4.52 %
    Favored  : 94.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.88 (0.31), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.42 (0.23), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.016   0.002   PHEAS  19 
 HIS   0.005   0.001   HISAQ  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4221)
  covalent geometry    : angle       0.57877 ( 5628)
  hydrogen bonds       : bond        0.02762 (   95)
  hydrogen bonds       : angle       4.49243 (  285)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 111
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: AL   23 ASP cc_start: 0.7941 (p0) cc_final: 0.7117 (p0)
REVERT: AL   28 LYS cc_start: 0.8923 (mttt) cc_final: 0.8525 (mttp)
REVERT: AM   22 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6848 (pm20)
REVERT: AM   23 ASP cc_start: 0.8532 (t0) cc_final: 0.8186 (t0)
REVERT: AM   28 LYS cc_start: 0.8768 (mttt) cc_final: 0.8557 (mttt)
REVERT: AN   15 GLN cc_start: 0.5951 (mt0) cc_final: 0.5654 (mt0)
REVERT: AO   23 ASP cc_start: 0.8405 (t0) cc_final: 0.8141 (t0)
REVERT: AP   15 GLN cc_start: 0.5814 (mt0) cc_final: 0.5530 (mt0)
REVERT: AP   23 ASP cc_start: 0.8218 (t0) cc_final: 0.7790 (t0)
REVERT: AP   28 LYS cc_start: 0.8861 (mttt) cc_final: 0.8592 (mttp)
REVERT: AR   28 LYS cc_start: 0.8812 (mttt) cc_final: 0.8580 (mtmt)
REVERT: AS   15 GLN cc_start: 0.6106 (mt0) cc_final: 0.5884 (mt0)
REVERT: AS   22 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7051 (mt-10)
REVERT: AT   23 ASP cc_start: 0.8462 (t0) cc_final: 0.8214 (t0)
REVERT: AU   15 GLN cc_start: 0.5791 (mt0) cc_final: 0.5450 (mt0)
REVERT: AU   22 GLU cc_start: 0.7971 (tp30) cc_final: 0.7667 (tp30)
REVERT: AW   23 ASP cc_start: 0.8407 (t0) cc_final: 0.7756 (t0)
REVERT: AW   28 LYS cc_start: 0.8843 (mttt) cc_final: 0.8480 (mttp)
REVERT: AX   23 ASP cc_start: 0.8135 (t0) cc_final: 0.7918 (t0)
REVERT: AX   28 LYS cc_start: 0.8784 (mttt) cc_final: 0.8522 (mtmt)
REVERT: AY   28 LYS cc_start: 0.8743 (mttt) cc_final: 0.8432 (mttt)
REVERT: Aa   23 ASP cc_start: 0.8225 (t0) cc_final: 0.7533 (t0)
REVERT: Ab   23 ASP cc_start: 0.8351 (t0) cc_final: 0.7813 (t0)
REVERT: Ac   28 LYS cc_start: 0.8886 (mttt) cc_final: 0.8547 (mttp)
REVERT: Ae   28 LYS cc_start: 0.8847 (mttt) cc_final: 0.8632 (mttt)
  outliers start: 3
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1650
  time to fit residues: 23.3804
Evaluate side-chains
  91 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 36 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:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.106017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.083859 restraints weight = 18018.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 3.45
r_work: 0.3634 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.6338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4221  Z= 0.232
  Angle     :  0.589   5.173   5628  Z= 0.307
  Chirality :  0.054   0.128    630
  Planarity :  0.002   0.009    714
  Dihedral  :  6.204  23.656    546
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  :  7.14 %
    Favored  : 90.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.32), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.002   PHEAf  20 
 HIS   0.003   0.001   HISAQ  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 4221)
  covalent geometry    : angle       0.58914 ( 5628)
  hydrogen bonds       : bond        0.03844 (   95)
  hydrogen bonds       : angle       4.92601 (  285)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: AL   23 ASP cc_start: 0.8120 (p0) cc_final: 0.7284 (p0)
REVERT: AL   28 LYS cc_start: 0.8807 (mttt) cc_final: 0.8364 (mttp)
REVERT: AM   19 PHE cc_start: 0.8384 (t80) cc_final: 0.8157 (t80)
REVERT: AN   23 ASP cc_start: 0.8202 (t0) cc_final: 0.7922 (t0)
REVERT: AO   23 ASP cc_start: 0.8074 (t0) cc_final: 0.7719 (t0)
REVERT: AP   15 GLN cc_start: 0.5923 (mt0) cc_final: 0.5646 (mt0)
REVERT: AP   23 ASP cc_start: 0.7959 (t0) cc_final: 0.7338 (t0)
REVERT: AP   28 LYS cc_start: 0.8820 (mttt) cc_final: 0.8504 (mttp)
REVERT: AR   16 LYS cc_start: 0.7826 (mttt) cc_final: 0.7469 (mttm)
REVERT: AR   22 GLU cc_start: 0.7779 (tp30) cc_final: 0.7539 (tp30)
REVERT: AR   28 LYS cc_start: 0.8764 (mttt) cc_final: 0.8508 (mttp)
REVERT: AS   23 ASP cc_start: 0.8048 (m-30) cc_final: 0.7771 (m-30)
REVERT: AU   23 ASP cc_start: 0.8663 (t0) cc_final: 0.8024 (t0)
REVERT: AV   23 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7650 (t0)
REVERT: AW   28 LYS cc_start: 0.8737 (mttt) cc_final: 0.8393 (mttp)
REVERT: AX   28 LYS cc_start: 0.8622 (mttt) cc_final: 0.8369 (mtmt)
REVERT: AX   35 MET cc_start: 0.8743 (ttp) cc_final: 0.8498 (ttm)
REVERT: AZ   23 ASP cc_start: 0.8169 (t0) cc_final: 0.7775 (t0)
REVERT: Aa   23 ASP cc_start: 0.7771 (t0) cc_final: 0.7530 (t0)
REVERT: Ac   28 LYS cc_start: 0.8789 (mttt) cc_final: 0.8076 (mttp)
REVERT: Af   35 MET cc_start: 0.8715 (ttm) cc_final: 0.8496 (ttp)
  outliers start: 11
  outliers final: 7
  residues processed: 87
  average time/residue: 0.1857
  time to fit residues: 20.0232
Evaluate side-chains
  84 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AL residue   24 VAL
Chi-restraints excluded: chain AQ residue   39 VAL
Chi-restraints excluded: chain AV residue   23 ASP
Chi-restraints excluded: chain AV residue   39 VAL
Chi-restraints excluded: chain AW residue   39 VAL
Chi-restraints excluded: chain AX residue   39 VAL
Chi-restraints excluded: chain Ac residue   39 VAL
Chi-restraints excluded: chain Ae residue   23 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.100851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.079526 restraints weight = 19001.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 3.33
r_work: 0.3479 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.7073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   4221  Z= 0.244
  Angle     :  0.548   4.046   5628  Z= 0.284
  Chirality :  0.052   0.131    630
  Planarity :  0.002   0.007    714
  Dihedral  :  6.039  22.924    546
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  9.52 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.34), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.13 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.001   PHEAM  20 
 HIS   0.003   0.001   HISAe  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 4221)
  covalent geometry    : angle       0.54766 ( 5628)
  hydrogen bonds       : bond        0.02992 (   95)
  hydrogen bonds       : angle       5.06514 (  285)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: AL   23 ASP cc_start: 0.8217 (p0) cc_final: 0.7399 (p0)
REVERT: AL   28 LYS cc_start: 0.8717 (mttt) cc_final: 0.8223 (mttp)
REVERT: AM   22 GLU cc_start: 0.7683 (tt0) cc_final: 0.7121 (tp30)
REVERT: AN   23 ASP cc_start: 0.8169 (t0) cc_final: 0.7872 (t0)
REVERT: AO   23 ASP cc_start: 0.8103 (t0) cc_final: 0.7731 (t0)
REVERT: AP   23 ASP cc_start: 0.8106 (t0) cc_final: 0.7218 (t0)
REVERT: AP   28 LYS cc_start: 0.8655 (mttt) cc_final: 0.8331 (mttp)
REVERT: AQ   16 LYS cc_start: 0.8016 (mttt) cc_final: 0.7625 (mttp)
REVERT: AR   28 LYS cc_start: 0.8662 (mttt) cc_final: 0.8428 (mttp)
REVERT: AS   23 ASP cc_start: 0.8294 (m-30) cc_final: 0.7604 (m-30)
REVERT: AU   23 ASP cc_start: 0.8563 (t0) cc_final: 0.8054 (t0)
REVERT: AW   16 LYS cc_start: 0.8040 (mttt) cc_final: 0.7593 (mttp)
REVERT: AW   28 LYS cc_start: 0.8559 (mttt) cc_final: 0.8218 (mttp)
REVERT: AX   35 MET cc_start: 0.8592 (ttp) cc_final: 0.8348 (ttm)
REVERT: AZ   23 ASP cc_start: 0.8191 (t0) cc_final: 0.7627 (t0)
REVERT: Aa   23 ASP cc_start: 0.7937 (t0) cc_final: 0.7597 (t0)
REVERT: Ac   28 LYS cc_start: 0.8575 (mttt) cc_final: 0.8252 (mttp)
  outliers start: 9
  outliers final: 8
  residues processed: 83
  average time/residue: 0.1573
  time to fit residues: 16.2363
Evaluate side-chains
  81 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AL residue   24 VAL
Chi-restraints excluded: chain AO residue   39 VAL
Chi-restraints excluded: chain AQ residue   39 VAL
Chi-restraints excluded: chain AS residue   39 VAL
Chi-restraints excluded: chain AW residue   39 VAL
Chi-restraints excluded: chain AX residue   39 VAL
Chi-restraints excluded: chain Ac residue   39 VAL
Chi-restraints excluded: chain Af residue   23 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.100505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.079432 restraints weight = 18735.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 3.21
r_work: 0.3475 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.7454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.024   4221  Z= 0.258
  Angle     :  0.546   4.396   5628  Z= 0.287
  Chirality :  0.053   0.128    630
  Planarity :  0.002   0.006    714
  Dihedral  :  6.073  23.192    546
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  :  9.76 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.57 (0.35), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.19 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.012   0.001   PHEAf  20 
 HIS   0.002   0.001   HISAe  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 ( 4221)
  covalent geometry    : angle       0.54569 ( 5628)
  hydrogen bonds       : bond        0.03264 (   95)
  hydrogen bonds       : angle       5.15718 (  285)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.198 
Fit side-chains
REVERT: AL   23 ASP cc_start: 0.8389 (p0) cc_final: 0.7549 (p0)
REVERT: AL   28 LYS cc_start: 0.8743 (mttt) cc_final: 0.8389 (mttp)
REVERT: AM   16 LYS cc_start: 0.8021 (mttt) cc_final: 0.7664 (mttm)
REVERT: AN   23 ASP cc_start: 0.8285 (t0) cc_final: 0.7948 (t0)
REVERT: AO   23 ASP cc_start: 0.8290 (t0) cc_final: 0.7982 (t0)
REVERT: AP   23 ASP cc_start: 0.8275 (t0) cc_final: 0.7296 (t0)
REVERT: AP   28 LYS cc_start: 0.8737 (mttt) cc_final: 0.8398 (mttp)
REVERT: AQ   16 LYS cc_start: 0.8187 (mttt) cc_final: 0.7825 (mttp)
REVERT: AR   28 LYS cc_start: 0.8745 (mttt) cc_final: 0.8536 (mttp)
REVERT: AS   23 ASP cc_start: 0.8473 (m-30) cc_final: 0.7791 (m-30)
REVERT: AU   23 ASP cc_start: 0.8831 (t0) cc_final: 0.8034 (t0)
REVERT: AW   16 LYS cc_start: 0.8187 (mttt) cc_final: 0.7733 (mttp)
REVERT: AW   28 LYS cc_start: 0.8685 (mttt) cc_final: 0.8356 (mttp)
REVERT: AX   35 MET cc_start: 0.8684 (ttp) cc_final: 0.8436 (ttm)
REVERT: AZ   23 ASP cc_start: 0.8255 (t0) cc_final: 0.7694 (t0)
REVERT: Aa   23 ASP cc_start: 0.8046 (t0) cc_final: 0.7655 (t0)
REVERT: Ac   28 LYS cc_start: 0.8619 (mttt) cc_final: 0.8298 (mttp)
REVERT: Ad   16 LYS cc_start: 0.8471 (mtpt) cc_final: 0.7966 (mttm)
REVERT: Ad   22 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7367 (mp0)
  outliers start: 13
  outliers final: 10
  residues processed: 82
  average time/residue: 0.1354
  time to fit residues: 14.0623
Evaluate side-chains
  83 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AL residue   24 VAL
Chi-restraints excluded: chain AQ residue   23 ASP
Chi-restraints excluded: chain AQ residue   39 VAL
Chi-restraints excluded: chain AS residue   39 VAL
Chi-restraints excluded: chain AV residue   23 ASP
Chi-restraints excluded: chain AV residue   39 VAL
Chi-restraints excluded: chain AW residue   39 VAL
Chi-restraints excluded: chain AX residue   39 VAL
Chi-restraints excluded: chain AY residue   39 VAL
Chi-restraints excluded: chain Ac residue   39 VAL
Chi-restraints excluded: chain Ad residue   22 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0870
   chunk 1 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.098435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.079504 restraints weight = 20163.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 3.18
r_work: 0.3442 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.7602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   4221  Z= 0.166
  Angle     :  0.463   4.252   5628  Z= 0.248
  Chirality :  0.052   0.129    630
  Planarity :  0.001   0.005    714
  Dihedral  :  5.711  21.751    546
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 10.71 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (0.35), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.007   0.001   PHEAM  20 
 HIS   0.001   0.000   HISAe  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 4221)
  covalent geometry    : angle       0.46307 ( 5628)
  hydrogen bonds       : bond        0.02775 (   95)
  hydrogen bonds       : angle       4.84978 (  285)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.240 
Fit side-chains
REVERT: AL   23 ASP cc_start: 0.8329 (p0) cc_final: 0.7481 (p0)
REVERT: AL   28 LYS cc_start: 0.8693 (mttt) cc_final: 0.8336 (mttp)
REVERT: AM   16 LYS cc_start: 0.7870 (mttt) cc_final: 0.7584 (mttm)
REVERT: AN   23 ASP cc_start: 0.8235 (t0) cc_final: 0.7918 (t0)
REVERT: AO   23 ASP cc_start: 0.8382 (t0) cc_final: 0.8050 (t0)
REVERT: AP   23 ASP cc_start: 0.8242 (t0) cc_final: 0.7320 (t0)
REVERT: AP   28 LYS cc_start: 0.8658 (mttt) cc_final: 0.8334 (mttp)
REVERT: AQ   16 LYS cc_start: 0.8118 (mttt) cc_final: 0.7679 (mttp)
REVERT: AR   28 LYS cc_start: 0.8724 (mttt) cc_final: 0.8515 (mttp)
REVERT: AS   23 ASP cc_start: 0.8350 (m-30) cc_final: 0.7637 (m-30)
REVERT: AU   23 ASP cc_start: 0.8710 (t0) cc_final: 0.8200 (t0)
REVERT: AW   16 LYS cc_start: 0.7980 (mttt) cc_final: 0.7537 (mttp)
REVERT: AW   28 LYS cc_start: 0.8612 (mttt) cc_final: 0.8293 (mttp)
REVERT: AX   16 LYS cc_start: 0.8044 (mttt) cc_final: 0.7707 (mttm)
REVERT: AZ   23 ASP cc_start: 0.8279 (t0) cc_final: 0.7740 (t0)
REVERT: Aa   23 ASP cc_start: 0.8083 (t0) cc_final: 0.7639 (t0)
REVERT: Ac   28 LYS cc_start: 0.8542 (mttt) cc_final: 0.8179 (mttp)
REVERT: Ad   22 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7259 (mp0)
  outliers start: 11
  outliers final: 10
  residues processed: 82
  average time/residue: 0.1669
  time to fit residues: 17.0666
Evaluate side-chains
  84 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AQ residue   23 ASP
Chi-restraints excluded: chain AQ residue   39 VAL
Chi-restraints excluded: chain AS residue   39 VAL
Chi-restraints excluded: chain AV residue   23 ASP
Chi-restraints excluded: chain AV residue   39 VAL
Chi-restraints excluded: chain AW residue   39 VAL
Chi-restraints excluded: chain AX residue   39 VAL
Chi-restraints excluded: chain AY residue   39 VAL
Chi-restraints excluded: chain Ac residue   39 VAL
Chi-restraints excluded: chain Ad residue   22 GLU
Chi-restraints excluded: chain Ae residue   23 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 18 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.098188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.078755 restraints weight = 20105.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 3.20
r_work: 0.3435 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.7836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   4221  Z= 0.206
  Angle     :  0.492   4.358   5628  Z= 0.261
  Chirality :  0.053   0.125    630
  Planarity :  0.001   0.005    714
  Dihedral  :  5.810  22.863    546
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.48 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 10.95 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.36), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.24 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.001   PHEAL  20 
 HIS   0.003   0.000   HISAb  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 4221)
  covalent geometry    : angle       0.49201 ( 5628)
  hydrogen bonds       : bond        0.03075 (   95)
  hydrogen bonds       : angle       4.77494 (  285)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.254 
Fit side-chains
REVERT: AL   23 ASP cc_start: 0.8408 (p0) cc_final: 0.7557 (p0)
REVERT: AL   28 LYS cc_start: 0.8700 (mttt) cc_final: 0.8336 (mttp)
REVERT: AM   16 LYS cc_start: 0.8009 (mttt) cc_final: 0.7743 (mttm)
REVERT: AN   23 ASP cc_start: 0.8277 (t0) cc_final: 0.7917 (t0)
REVERT: AO   23 ASP cc_start: 0.8385 (t0) cc_final: 0.8036 (t0)
REVERT: AP   23 ASP cc_start: 0.8324 (t0) cc_final: 0.7336 (t0)
REVERT: AP   28 LYS cc_start: 0.8634 (mttt) cc_final: 0.8310 (mttp)
REVERT: AQ   16 LYS cc_start: 0.8102 (mttt) cc_final: 0.7674 (mttp)
REVERT: AS   23 ASP cc_start: 0.8362 (m-30) cc_final: 0.7669 (m-30)
REVERT: AU   23 ASP cc_start: 0.8772 (t0) cc_final: 0.8204 (t0)
REVERT: AW   16 LYS cc_start: 0.7996 (mttt) cc_final: 0.7571 (mttp)
REVERT: AW   28 LYS cc_start: 0.8608 (mttt) cc_final: 0.8292 (mttp)
REVERT: AX   16 LYS cc_start: 0.8057 (mttt) cc_final: 0.7728 (mttm)
REVERT: AX   35 MET cc_start: 0.8636 (ttm) cc_final: 0.8417 (ttp)
REVERT: AZ   23 ASP cc_start: 0.8269 (t0) cc_final: 0.7679 (t0)
REVERT: Aa   23 ASP cc_start: 0.8048 (t0) cc_final: 0.7572 (t0)
REVERT: Ac   28 LYS cc_start: 0.8625 (mttt) cc_final: 0.8277 (mttp)
REVERT: Ad   22 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7256 (mp0)
REVERT: Ae   23 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7378 (t0)
  outliers start: 11
  outliers final: 9
  residues processed: 82
  average time/residue: 0.1759
  time to fit residues: 18.1910
Evaluate side-chains
  84 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AQ residue   23 ASP
Chi-restraints excluded: chain AQ residue   39 VAL
Chi-restraints excluded: chain AS residue   39 VAL
Chi-restraints excluded: chain AV residue   23 ASP
Chi-restraints excluded: chain AV residue   39 VAL
Chi-restraints excluded: chain AW residue   39 VAL
Chi-restraints excluded: chain AX residue   39 VAL
Chi-restraints excluded: chain AY residue   39 VAL
Chi-restraints excluded: chain Ac residue   39 VAL
Chi-restraints excluded: chain Ad residue   22 GLU
Chi-restraints excluded: chain Ae residue   23 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0870
   chunk 17 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.097532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.080404 restraints weight = 20428.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.98
r_work: 0.3457 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.8030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.018   4221  Z= 0.195
  Angle     :  0.474   4.242   5628  Z= 0.255
  Chirality :  0.052   0.127    630
  Planarity :  0.001   0.005    714
  Dihedral  :  5.709  21.849    546
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.24 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 10.48 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.66 (0.36), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.26 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.001   PHEAM  20 
 HIS   0.001   0.000   HISAP  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 4221)
  covalent geometry    : angle       0.47377 ( 5628)
  hydrogen bonds       : bond        0.03068 (   95)
  hydrogen bonds       : angle       4.60166 (  285)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: AL   23 ASP cc_start: 0.8371 (p0) cc_final: 0.7532 (p0)
REVERT: AL   28 LYS cc_start: 0.8717 (mttt) cc_final: 0.8353 (mttp)
REVERT: AM   16 LYS cc_start: 0.8106 (mttt) cc_final: 0.7674 (mttm)
REVERT: AN   23 ASP cc_start: 0.8327 (t0) cc_final: 0.8009 (t0)
REVERT: AO   23 ASP cc_start: 0.8437 (t0) cc_final: 0.7990 (t0)
REVERT: AP   23 ASP cc_start: 0.8296 (t0) cc_final: 0.7287 (t0)
REVERT: AP   28 LYS cc_start: 0.8645 (mttt) cc_final: 0.8349 (mttp)
REVERT: AS   23 ASP cc_start: 0.8577 (m-30) cc_final: 0.7830 (m-30)
REVERT: AU   23 ASP cc_start: 0.8696 (t0) cc_final: 0.8182 (t0)
REVERT: AV   16 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7482 (mttp)
REVERT: AW   16 LYS cc_start: 0.8019 (mttt) cc_final: 0.7611 (mttp)
REVERT: AW   28 LYS cc_start: 0.8631 (mttt) cc_final: 0.8320 (mttp)
REVERT: AX   16 LYS cc_start: 0.8134 (mttt) cc_final: 0.7821 (mttm)
REVERT: AZ   23 ASP cc_start: 0.8287 (t0) cc_final: 0.7661 (t0)
REVERT: Aa   23 ASP cc_start: 0.8061 (t0) cc_final: 0.7561 (t0)
REVERT: Ac   28 LYS cc_start: 0.8659 (mttt) cc_final: 0.8310 (mttp)
REVERT: Ad   22 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7309 (mp0)
REVERT: Ae   23 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7443 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 82
  average time/residue: 0.1728
  time to fit residues: 17.7865
Evaluate side-chains
  87 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AO residue   15 GLN
Chi-restraints excluded: chain AQ residue   23 ASP
Chi-restraints excluded: chain AQ residue   39 VAL
Chi-restraints excluded: chain AS residue   39 VAL
Chi-restraints excluded: chain AV residue   23 ASP
Chi-restraints excluded: chain AV residue   39 VAL
Chi-restraints excluded: chain AW residue   39 VAL
Chi-restraints excluded: chain AX residue   39 VAL
Chi-restraints excluded: chain AY residue   39 VAL
Chi-restraints excluded: chain Ac residue   39 VAL
Chi-restraints excluded: chain Ad residue   22 GLU
Chi-restraints excluded: chain Ae residue   23 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    0.0060
   chunk 39 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.100201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.079874 restraints weight = 18665.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 3.03
r_work: 0.3488 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.8164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   4221  Z= 0.213
  Angle     :  0.487   4.387   5628  Z= 0.260
  Chirality :  0.052   0.125    630
  Planarity :  0.001   0.005    714
  Dihedral  :  5.790  22.952    546
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.38 %
    Favored  : 87.62 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 10.48 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.37), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.001   PHEAL  20 
 HIS   0.002   0.000   HISAQ  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 4221)
  covalent geometry    : angle       0.48651 ( 5628)
  hydrogen bonds       : bond        0.03222 (   95)
  hydrogen bonds       : angle       4.53575 (  285)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: AL   23 ASP cc_start: 0.8448 (p0) cc_final: 0.7594 (p0)
REVERT: AL   28 LYS cc_start: 0.8738 (mttt) cc_final: 0.8373 (mttp)
REVERT: AM   16 LYS cc_start: 0.8248 (mttt) cc_final: 0.7818 (mttm)
REVERT: AN   23 ASP cc_start: 0.8366 (t0) cc_final: 0.8041 (t0)
REVERT: AO   23 ASP cc_start: 0.8396 (t0) cc_final: 0.8019 (t0)
REVERT: AP   23 ASP cc_start: 0.8272 (t0) cc_final: 0.7225 (t0)
REVERT: AP   28 LYS cc_start: 0.8676 (mttt) cc_final: 0.8376 (mttp)
REVERT: AS   23 ASP cc_start: 0.8531 (m-30) cc_final: 0.8148 (m-30)
REVERT: AU   23 ASP cc_start: 0.8794 (t0) cc_final: 0.8405 (t0)
REVERT: AW   16 LYS cc_start: 0.8164 (mttt) cc_final: 0.7766 (mttp)
REVERT: AW   28 LYS cc_start: 0.8667 (mttt) cc_final: 0.8357 (mttp)
REVERT: AX   16 LYS cc_start: 0.8182 (mttt) cc_final: 0.7873 (mttm)
REVERT: AZ   23 ASP cc_start: 0.8271 (t0) cc_final: 0.7631 (t0)
REVERT: Aa   23 ASP cc_start: 0.8012 (t0) cc_final: 0.7502 (t0)
REVERT: Ac   28 LYS cc_start: 0.8646 (mttt) cc_final: 0.8301 (mttp)
REVERT: Ad   22 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7393 (mp0)
REVERT: Ae   23 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7450 (t0)
REVERT: Af   16 LYS cc_start: 0.8897 (mttp) cc_final: 0.8644 (mttt)
  outliers start: 12
  outliers final: 10
  residues processed: 84
  average time/residue: 0.1716
  time to fit residues: 18.1639
Evaluate side-chains
  89 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AO residue   15 GLN
Chi-restraints excluded: chain AQ residue   23 ASP
Chi-restraints excluded: chain AQ residue   39 VAL
Chi-restraints excluded: chain AS residue   39 VAL
Chi-restraints excluded: chain AV residue   23 ASP
Chi-restraints excluded: chain AV residue   39 VAL
Chi-restraints excluded: chain AW residue   39 VAL
Chi-restraints excluded: chain AX residue   39 VAL
Chi-restraints excluded: chain AY residue   39 VAL
Chi-restraints excluded: chain Ac residue   39 VAL
Chi-restraints excluded: chain Ad residue   22 GLU
Chi-restraints excluded: chain Ae residue   23 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 41 optimal weight:    0.2980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.100253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.080125 restraints weight = 18406.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 3.08
r_work: 0.3507 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.8248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   4221  Z= 0.191
  Angle     :  0.475   4.308   5628  Z= 0.257
  Chirality :  0.052   0.128    630
  Planarity :  0.001   0.005    714
  Dihedral  :  5.689  21.837    546
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.76 %
    Favored  : 87.24 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 11.19 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.37), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.21 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHEAf  20 
 HIS   0.005   0.000   HISAQ  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 4221)
  covalent geometry    : angle       0.47531 ( 5628)
  hydrogen bonds       : bond        0.03162 (   95)
  hydrogen bonds       : angle       4.45492 (  285)

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.199 
Fit side-chains
REVERT: AL   23 ASP cc_start: 0.8413 (p0) cc_final: 0.7594 (p0)
REVERT: AL   28 LYS cc_start: 0.8748 (mttt) cc_final: 0.8390 (mttp)
REVERT: AM   16 LYS cc_start: 0.8253 (mttt) cc_final: 0.7817 (mttm)
REVERT: AN   23 ASP cc_start: 0.8412 (t0) cc_final: 0.8102 (t0)
REVERT: AO   23 ASP cc_start: 0.8501 (t0) cc_final: 0.8036 (t0)
REVERT: AP   23 ASP cc_start: 0.8342 (t0) cc_final: 0.7349 (t0)
REVERT: AP   28 LYS cc_start: 0.8677 (mttt) cc_final: 0.8387 (mttp)
REVERT: AQ   16 LYS cc_start: 0.8483 (mttt) cc_final: 0.8249 (mttm)
REVERT: AS   23 ASP cc_start: 0.8592 (m-30) cc_final: 0.7863 (m-30)
REVERT: AU   23 ASP cc_start: 0.8686 (t0) cc_final: 0.8191 (t0)
REVERT: AW   16 LYS cc_start: 0.8169 (mttt) cc_final: 0.7760 (mttp)
REVERT: AW   28 LYS cc_start: 0.8651 (mttt) cc_final: 0.8351 (mttp)
REVERT: AX   16 LYS cc_start: 0.8285 (mttt) cc_final: 0.7991 (mttm)
REVERT: AZ   23 ASP cc_start: 0.8246 (t0) cc_final: 0.7625 (t0)
REVERT: Aa   23 ASP cc_start: 0.8037 (t0) cc_final: 0.7548 (t0)
REVERT: Ac   16 LYS cc_start: 0.8115 (mttt) cc_final: 0.7821 (mttp)
REVERT: Ac   28 LYS cc_start: 0.8702 (mttt) cc_final: 0.8360 (mttp)
REVERT: Ad   22 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7326 (mp0)
REVERT: Ae   23 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7485 (t0)
REVERT: Af   14 HIS cc_start: 0.7529 (m-70) cc_final: 0.7260 (t-170)
  outliers start: 11
  outliers final: 9
  residues processed: 86
  average time/residue: 0.1633
  time to fit residues: 17.8472
Evaluate side-chains
  90 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AO residue   15 GLN
Chi-restraints excluded: chain AQ residue   23 ASP
Chi-restraints excluded: chain AQ residue   39 VAL
Chi-restraints excluded: chain AS residue   39 VAL
Chi-restraints excluded: chain AV residue   23 ASP
Chi-restraints excluded: chain AV residue   39 VAL
Chi-restraints excluded: chain AW residue   39 VAL
Chi-restraints excluded: chain AX residue   39 VAL
Chi-restraints excluded: chain AY residue   39 VAL
Chi-restraints excluded: chain Ad residue   22 GLU
Chi-restraints excluded: chain Ae residue   23 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0980
   chunk 17 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0870
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.101219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.081347 restraints weight = 18238.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 3.04
r_work: 0.3536 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.8307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   4221  Z= 0.134
  Angle     :  0.433   4.147   5628  Z= 0.236
  Chirality :  0.053   0.126    630
  Planarity :  0.001   0.005    714
  Dihedral  :  5.459  22.500    546
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.81 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.38 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.37), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.19 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.001   PHEAL  20 
 HIS   0.006   0.000   HISAQ  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4221)
  covalent geometry    : angle       0.43334 ( 5628)
  hydrogen bonds       : bond        0.02716 (   95)
  hydrogen bonds       : angle       4.29270 (  285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2670.80 seconds
wall clock time: 45 minutes 54.84 seconds (2754.84 seconds total)